LMU BioDB 2019 - User contributions [en]

Sulfiknights Deliverables

2019-12-13T23:13:14Z

Jnimmers: /* Joey Nimmers-Minor's Final Reflection */ Final reflection finish

{{Sulfiknights}}

==Checklist:==
#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) '''COMPLETE'''
#Group Report (.doc, .docx or .pdf file) '''COMPLETE'''
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to Dr. Dahlquist)'''COMPLETE'''
#Group PowerPoint presentation (given on Tuesday, December 10, .ppt, .pptx or .pdf file) '''COMPLETE'''
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx) '''COMPLETE'''
#PowerPoint of ANOVA table, screenshots of stem results (.pptx), screenshot of black and white GRNsight input network and colored GRNsight output networks '''COMPLETE'''
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file) '''COMPLETE'''
#YEASTRACT "rank by TF" results (.xlsx) '''COMPLETE'''
#GRNmap input workbook (with network adjacency matrix, .xlsx) '''COMPLETE'''
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''COMPLETE'''
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''COMPLETE'''
#ReadMe for the database that describes the design of the database, references the sources of the data, and has a database schema diagram (.doc, .docx, .pdf) '''COMPLETE'''
#Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, .txt) '''COMPLETE'''
#Electronic notebook corresponding to these the microarray results files (Week 12/13 and Week 15) to support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results. '''COMPLETE'''

==Group Report==

==Individual Statements of Work, Assessments, Reflections==
===Joey Nimmers-Minor's Final Reflection===
====Individual Assessment and Reflection====
=====Statement of Work=====

*Describe exactly what you did on the project.
**For this project, I worked in my role as Quality Assurance. I worked along with the rest of my team to understand the data provided by the original journal paper, working alongside Naomi and Delisa to convert and format the data sets to create a uniform set of databases with the other groups. I created and was assisted in the creation and editing of the Access database, as well as the original query done on that database (not to be confused with the finalized schema carried out by Delisa). I assisted my fellow QA with any work she requiremed my help on as well as created/assisted in the creation of the final presentation, namely the materials and methods portion of it.
*Provide references or links to artifacts of your work
**[[Media:SK_Expression-and-Degradation-rate-database_2019.zip | Expression and Degradation Sheet of Thorsen & Dahlquist Data]]
**[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]
=== Assessment of Project ===

# Give an objective assessment of the success of your project workflow and teamwork.
#*I feel that our workflow always lead to productive sessions in the lab in preparation for our project. I truly enjoyed working together with this team of people, out communication and overall chemistry as a team led to great productivity and made the difficulty of this project much more bearable.
# What worked and what didn't work?
#*In the beginning, we had a hard time splitting up assignments optimally, so we would have 2 people working on the same assignment at the same time when it would be a better usage of our limited time to have people working on separate tasks in tandem. As we realized this problem, however, we immediately worked to fix it and the standard of work that we began to produce in a short amount of time improved greatly because we didn't feel rushed and we were able to reach out to each other for assistance/review which allowed for a fresh pair of eyes to look at the assignment being done and judge it correctly and without bias.
# What would you do differently if you could do it all over again?
#*Simply put, I would make sure that we fixed out mistakes slightly earlier and used more of our time over Thanksgiving break to work so we had more time to practice and relax once the project deadline began to come closer.

* Evaluate your team’s portion of the Final Project and Group Report in the following areas:
# Content: What is the quality of the work?
#* The quality of work that came out of my team was tremendously high! I appreciate all that they did to make sure we never settled for less and we always found ways to improve on our work as we went into the finals leg of the project.
# Organization: Comment on the organization of the project and of your group's wiki pages.
#*I thought it was pretty good! I feel that in the beginning, we were only slightly unorganized in the very beginning of the project, but once we got over the hump, we worked very efficiently and maintained organization of our project and presentation throughout the rest of the allotted time.
# Completeness: Did your team achieve all of the project objectives? Why or why not?
#*Yes, the team reached all of the projects objectives thanks to our communication, teamwork, work-ethic, and cohesiveness as a unit. With everyone doing their own work simultaneously and a purpose, I feel that we produced a quality product that completed all of the objectives in what seemed like a very short span of time.
=== Reflection on the Process ===

*What did you learn?
# With your head (biological or computer science principles)
#*I learned so much about how to operate seemingly complex database systems in order to present data in a new and informed way. Computer science seemed so complex when I came into this semester, but I feel that I've created a good starting point for myself if I decide to move further down the road of computer science.
# With your heart (personal qualities and teamwork qualities that make things work or not work)?
#*I learned that a key component of efficiency in a group project setting is chemistry. I was lucky to be put with a group of genuinely kind and fun people, and I feel that knowing that they were partially depending on me made me want to work much harder to produce a good product.
#With your hands (technical skills)?
#*I learned how specific and knit-picky the coding aspect of computer science is. From a simple task such as wiki syntax, I found out how much detail must go into anything that has to do with computer science. This is a lesson that will help me later if I decide to work more with computer science in the future. Detail and observation is key.
#What lesson will you take away from this project that you will still use a year from now?
#*I learned the importance of time management in a class with stringent deadlines and requirements. I get away with procrastinating often as a student and a worker, but this class and it's unusual schedule of assignment times and dates forced me to learn new methods of time managements that made my approcah to other classes different and I can see myself using this method of time management for a very long time outside of this classroom.
[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 15:13, 13 December 2019 (PST)

===Marcus Avila's Final Reflection===
==== Individual Assessment and Reflection ====
===== Statement of Work =====

* Describe exactly what you did on the project.
** For the project I worked with Ivy to decide how to organize the Thorsen data to run an ANOVA. After doing the ANOVA and running STEM, I then downloaded the [[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip| Gene Lists]] for Profiles 40 & 48 and combined them to input into "Rank by TF" on YEASTRACT. Next, I selected the 15 most significant transcription factors to include on the network. After inputting the 15 transcription factors into the Generate Regulation Matrix I downloaded and transposed the [[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 network excel sheet]]. I then used GRNsight to create the weighted and unweighted network maps.
** I then created the production rate sheet, degradation rate sheet, expression data sheet, network sheet, network weights sheet, optimization parameters, and the threshold b sheet using the [https://github.com/kdahlquist/DahlquistLab/raw/master/data/Spring2019/15-genes_28-edges_sample_Sigmoid_estimation_2019.xlsx sample workbook] provided. Finally, I input the GRNmap input workbook from the [[Media:GRNmap4048 input worksheet.xlsx|GRNmap Input Worksheet Profiles 40 and 48]] into MATLAB for analysis.

===== Assessment of Project =====

# Give an objective assessment of the success of your project workflow and teamwork.
#* The team did a good job making sure things were done in a timely manner and we also had very few problems meeting up outside of class time to work on the project which made the workflow much more efficient.
# What worked and what didn't work?
#* Communication via text messages and scheduling meet up times worked very well. It seemed like the work load distribution was not completely equal, but this is not something we could change as a group.
# What would you do differently if you could do it all over again?
#* I would ensure that each job had defined tasks or were assigned to help other members in their tasks.
# Evaluate your team’s portion of the Final Project and Group Report in the following areas:
#* Content: What is the quality of the work?
#** The quality of the work was good, but might have some issues because some steps were unclear and did not always parallel the steps done in the example data analysis assignment.
#* Organization: Comment on the organization of the project and of your group's wiki pages.
#** Our wiki page was very organized because each section included a header and files were broken up into categories/steps.
#* Completeness: Did your team achieve all of the project objectives? Why or why not?
#** Yes, the Microsoft Access database was successfully made after analyzing the publish microarray data.

===== Reflection on the Process =====

* What did you learn?
# With your head (biological or computer science principles)
#* I learned about how microarray experiments can be used to study gene expression changes in response to stress.
# With your heart (personal qualities and teamwork qualities that make things work or not work)?
#* I learned that meeting up is much more effective than working individually or texting when analyzing and interpreting data, as well as when working on editing presentations.
# With your hands (technical skills)?
#* I learned how to input microarray data into MS Access, how to use GRNsight, YEASTRACT, and MATLAB.
* What lesson will you take away from this project that you will still use a year from now?
# I will take away the lesson that my attitude plays a major role in whether each person is equally invested in a group assignment or not.

===DeLisa Madere's Final Reflection===
====Statement of Work====
#'''Role as Designer'''
#*My role in this project was a Designer. As a designer, I collaborated with the other coders to come up with a metadata sheet incorporating information regarding the citations of the paper as well as the sample-to-data sheet including the different treatments, yeast strains, timepoints, concentrations, and replicates. After creating the metadata sheet, I worked with the QAs to create the database compiling the datasets from our microarray data for the Data Analysts to analyze further. Once all the data was analyzed, I then worked with the QAs and the other coders to create a database compiling our data, the degradation rates, production rates, metadata table, as well as the other datasets from the other groups (FunGals, Skinny Genes, Dahlquist Lab) to visualize the relationships in a database schema. Each dataset was standardized under common headers such as author_publicationyear_log2_expression, and each dataset had common headers as well representing each replicate such as yeaststrain_treatment_concentration_LogFC_time-replicate. The final database is linked together through a standardized ID that each of the datasets contained.
#'''Links to Artifacts'''
#*[[Sulfiknights]]
#*[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]
#*[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip ‎|BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip‎]]
#*[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]

====Assessment of Project====
#'''Objective Assessment'''
#*Overall, our team did a great job with staying on task. With the responsibilities that we were given for this project, our team carried them out in a timely manner, and we all worked together to get it done. We consistently met up to talk about our project and asked each other for help along the way, creating a strong group dynamic.
#'''What worked and didn't work?'''
#*What worked really well was that we each focused on our specific responsibilities and asked each other if we needed assistance. From focusing on our own tasks, we were able to understand our roles more. The only difficulty with this project was the workload that we each had outside of this, so maintaining a balance between our Database coursework and our other coursework.
#'''What would you do differently?'''
#*Since my responsibility came a little later on in the milestones, I would have liked to understand more what the other members of my group were doing, specifically the data analysts. I would have had a better understanding early on what actions were being carried out in the project. I would like to also have taken more initiative in helping the other members.
#'''Team Evaluation'''
#*'''Content'''
#::-I think the quality of work was good. I feel very proud of our team in the way that we presented our data to the class and was happy with the outcome.
#*'''Organization'''
#::-The organization of our project was good. Since the project itself was very step-by-step, that helped us with coming up with a timeline of each of our milestones. Regarding the wiki page, our deliverables page is very well organized with each assignment that needs to be on it and whether or not the task is complete. There is always room for improvement with organization in general, so there could have been a better flow with navigating certain links, but overall our organization turned out good.
#*'''Completedness'''
#::-Our team completed all of the project objectives. There was not one moment where we forgot to do something or neglected to include something. We were able to complete everything and in a timely manner.

====Reflection on the Process====
#'''What did you learn?'''
#*'''With your Head'''
#::-From this project as well as this whole semester, I have learned how to analyze data in a microarray with understanding gene expression as well as why databases are important in these specific experiments. I have also learned more about what Microsoft Access is (I have always had it on my computer just sitting there) and how it is important in storing data and creating databases.
#*'''With your Heart'''
#::-From my team, I was able to learn that it is okay to ask for help. I constantly asked my team to explain certain things to me especially since I had to miss half of class the first day, we were assigned these tasks. I have also learned that being understanding of each other really helps when working in a team. Our team was very understanding of other coursework that needed to be done and was able to work around all of our schedules.
#*'''With your Hands'''
#::-I have learned more about technology in general and how computer technology can be incorporated into Biology. I was always interested in seeing how these two relate and through this have learned the importance of having comprehensible reproducible data.
#'''What lessons did you take away from this project that you will still use a year from now?'''
#*From this project, I have learned that it is important to always be consistent and comprehensible when producing different experiments for others to understand and take away. It is important to lay out everything and to not neglect to include different methods or vital information when explaining data.

===Naomi Tesfaiohannes's Final Reflection===

'''Statement of Work'''

Describe exactly what you did on the project.

For this project I served as the project manager and the quality assurance guild. As project manager I communicated with Dr. Dahlquist of the steps that were made and need to continue to be made for the project. I also checked in with my team members of their progress with their roles. As QA I worked along with Joey on the datasheets to hand off to the Data Analysts. I also contributed to presenting and putting together the final presentation.

'''Provide references or links to artifacts of your work, such as:'''

[[Sulfiknights]]

[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]

'''Give an objective assessment of the success of your project workflow and teamwork.'''

What worked and what didn't work?

What worked was meeting outside of class and keeping in touch with progress by using the group chat
What didn't work was sometimes not being able to answer each other's questions. Leaving us all confused.

What would you do differently if you could do it all over again?

Ask more questions about analyzing new data instead of trying to figure it out on my own.

'''Evaluate your team’s portion of the Final Project and Group Report in the following areas:'''

Content: What is the quality of the work?

Our work is a reflection of the collaborative effort from all of the team members in trying to understand the new data we reanalyzed.

Organization: Comment on the organization of the project and of your group's wiki pages.

Our group stayed organized by splitting up what sections we would work on. That way we could come together at the end of the slides to review what still needs to be understood.

Completeness: Did your team achieve all of the project objectives? Why or why not?

Yes, but at our own pace. The objectives were completed by going through the deliverables for each members.

Reflection on the Process

What did you learn?

With your head (biological or computer science principles)

Connecting the affects of arsenic to budding yeast

With your heart (personal qualities and teamwork qualities that make things work or not work)?

Teamwork and collaborating with others by contributing my own section of work with theirs to form an overall analysis of the data.

With your hands (technical skills)?

Formatting the database column titles

What lesson will you take away from this project that you will still use a year from now?

It's important to ask questions when struggling with something new, for example a database format you are not familiar with. It's not a bad thing to ask questions, and it doesn't mean you are unaware of what is happening. Questions help with understanding making it easier for the student to present on the material.

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:02, 9 December 2019 (PST)

===Ivy Macaraeg's Final Reflection===
==== Statement of Work ====

* Describe exactly what you did on the project.
:-For this project, I worked with Marcus to organize and analyze the data. We worked together during and outside of class time to figure out what we needed to do so that the other members of our team could complete their jobs. I also worked with the other groups to better understand my role and the project in general. I helped do the ANOVA, STEM, GO, GRNsight, and GRNmap analyses. I also helped put together the final project and the final report.
* Provide references or links to artifacts of my work:
:-[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]
:-[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]
:-[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]
:-[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]]
:-[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]
:-[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]]
:-[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]
:-[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]
:-[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]
:-[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]
:-[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]
:-[[Sulfiknights DA Week 12/13]]
:-[[Sulfiknights DA Week 14]]

==== Assessment of Project ====

* Give an objective assessment of the success of your project workflow and teamwork.
:-At first, I think we were a little uneasy and going about our tasks was a little rough because we didn't really know what we were doing. As time moved on, and we remembered the methods of previous weeks, it got easier to complete our tasks. I thought the team work was good. Even though it felt like there was a lot more work for the Data Analysts, everyone was able to do what they needed to and we always offered to help each other out if we needed help.
* What worked and what didn't work?
:-I think what worked the best was how willing everyone was to work together and offer help. Communication between all of us was good, and we helped each other understand what needed to be done.
* What would you do differently if you could do it all over again?
:-If I could do it all over again, I would not be data analyst, not because I did not enjoy the work, but because I would like to see what the coders/designers did and how the schema worked.
* Evaluate your team’s portion of the Final Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*#:-I think I did well in terms of doing what needed to be done. I think I was pretty thorough, but I probably could have been a little bit neater in terms of getting my files together in an organized spot and formatting everything correctly.
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*#:- I got confused from time to time about what needed to be where. I felt like there were a lot of wiki pages to be managed (Group, individual, deliverables), and I wasn't sure about what exactly had to go on what page. Each page had a lot of components to it and I felt as though it got a little messy.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?
*#:-Yes, we did achieve all of the project objectives because we were able to work efficiently together.

==== Reflection on the Process ====

* What did you learn?
** With your head (biological or computer science principles)
**:-I learned how database worked because I had no idea how the technology was organized. I wasn't even familiar with how wiki worked. Biologically related, the biggest takeaway was how microarray data was relevant to biology. I did not know that that method existed.
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
**:- I learned that communication is absolutely key. I feel very lucky that I had a team that was dedicated to understanding what we had to do and was able to effectively do their jobs and help me too. I learned that I don't neccesary like the "number crunching" but it makes me pay attention to the directions more.
** With your hands (technical skills)?
**:- I became really familiar with Excel and statistical analysis, more so than I have done before. I also learned how wiki work, and even though it was hard at first, I got the hang of it by the end of the semester. Both of these things were pretty overwhelming at first but I think I just needed more time and practice.
* What lesson will you take away from this project that you will still use a year from now?
**:- Even though this was a very dense project, I think the biggest thing for me was how well my team worked together. I've been in other group projects before, but I think this one worked really well, and I want to learn from it and keep practicing these skills as I go on to work with other people in the future.

[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 15:04, 13 December 2019 (PST)

==Group Powerpoint Presentation==

[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]

==Excel Spreadsheet with ANOVA Results/STEM Formatting==
[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]

==PowerPoint of ANOVA Table...==
[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]

[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]]

[[Image:Profil923_GRNsight_matrix.PNG|500px]]
[[Image:Colored_GRNsight_923.PNG|500px]]

[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]

[[Image:Profile4048_GRNsight_matrix.PNG|500px]]
[[Image:Colored GRNsight 4048.PNG|500px]]

==Gene List and GO List files==
[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]]

[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]

==YEASTRACT "Rank by TF" Results==
[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]

[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]

==GRNmap input workbook==
[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]

[[Media:GRNmap4048 input worksheet.xlsx|GRNmap Input Worksheet: Profiles 40 and 48]]

==GRNmap output workbook and output plots==
[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]

[[Media:GRNmap4048_output.zip|GRNmap Output Files: Profiles 40 and 48]]

==MS Access database==
[[Media: SK_Expression-and-Degradation-rate-database_2019.zip | MS Access Database of Thorsen & Dahlquist data]]

==ReadMe==
[[Media:DM_Metadata_Sheet.xlsx|Metadata Sheet]]

[[Media:DM_ReadMe_Database_Design.docx|Design of Database]]

==Query design for populating a GRNmap input workbook from the database==
'''Profiles 9 and 23:'''

[[Image:Productionrates_923_querydesign.PNG|500px]]
[[Image:Degradationrates_923_querydesign.PNG|500px]]
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG|1000px]]

'''Profiles 40 and 48:'''

[[Image:ProductionRates 4048 QueryDesign.PNG|500px]]
[[Image:DegradationRates 4048 QueryDesign.PNG|500px]]
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG|1000px]]

==Electronic notebook corresponding to the microarray results files==
'''Electronic notebook for Data Analysts:'''

[[Sulfiknights DA Week 12/13]]

[[Sulfiknights DA Week 14]]

'''Electronic notebook for Quality Assurance'''

[[Ntesfaio Week 12/13]]

[[Ntesfaio Week 15]]

'''Electronic notebook for Designer'''

[[Dmadere Week 12|Dmadere Week 12/13]]

[[Dmadere Week 15]]

==Merge completed databases into a single database==
[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip ‎|BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip ‎]]

[[Image:Access_Database_Schema_Screenshot.PNG|1000px|Access_Database_Schema_Screenshot.PNG]]

Sulfiknights Deliverables

2019-12-13T22:37:37Z

Jnimmers: /* Individual Statements of Work, Assessments, Reflections */ Added statement of work

{{Sulfiknights}}

==Checklist:==
#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) '''INCOMPLETE'''
#Group Report (.doc, .docx or .pdf file) '''INCOMPLETE'''
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to Dr. Dahlquist)'''INCOMPLETE'''
#Group PowerPoint presentation (given on Tuesday, December 10, .ppt, .pptx or .pdf file) '''COMPLETE'''
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx) '''COMPLETE'''
#PowerPoint of ANOVA table, screenshots of stem results (.pptx), screenshot of black and white GRNsight input network and colored GRNsight output networks '''COMPLETE'''
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file) '''COMPLETE'''
#YEASTRACT "rank by TF" results (.xlsx) '''COMPLETE'''
#GRNmap input workbook (with network adjacency matrix, .xlsx) '''COMPLETE'''
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''COMPLETE'''
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''COMPLETE'''
#ReadMe for the database that describes the design of the database, references the sources of the data, and has a database schema diagram (.doc, .docx, .pdf) '''COMPLETE'''
#Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, .txt) '''COMPLETE'''
#Electronic notebook corresponding to these the microarray results files (Week 12/13 and Week 15) to support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results. '''INCOMPLETE'''

==Group Report==
==Individual Statements of Work, Assessments, Reflections==
===Joey Nimmers-Minor's Final Reflection===
====Individual Assessment and Reflection====
=====Statement of Work=====

*Describe exactly what you did on the project.
**For this project, I worked in my role as Quality Assurance. I worked along with the rest of my team to understand the data provided by the original journal paper, working alongside Naomi and Delisa to convert and format the data sets to create a uniform set of databases with the other groups. I created and was assisted in the creation and editing of the Access database, as well as the original query done on that database (not to be confused with the finalized schema carried out by Delisa). I assisted my fellow QA with any work she requiremed my help on as well as created/assisted in the creation of the final presentation, namely the materials and methods portion of it.
*Provide references or links to artifacts of your work
**[[Media:SK_Expression-and-Degradation-rate-database_2019.zip | Expression and Degradation Sheet of Thorsen & Dahlquist Data]]
**[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]

===== Assessment of Project =====

===== Reflection on the Process =====

===Marcus Avila's Final Reflection===
==== Individual Assessment and Reflection ====
===== Statement of Work =====

* Describe exactly what you did on the project.
** For the project I worked with Ivy to decide how to organize the Thorsen data to run an ANOVA. After doing the ANOVA and running STEM, I then downloaded the [[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip| Gene Lists]] for Profiles 40 & 48 and combined them to input into "Rank by TF" on YEASTRACT. Next, I selected the 15 most significant transcription factors to include on the network. After inputting the 15 transcription factors into the Generate Regulation Matrix I downloaded and transposed the [[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 network excel sheet]]. I then used GRNsight to create the weighted and unweighted network maps.
** I then created the production rate sheet, degradation rate sheet, expression data sheet, network sheet, network weights sheet, optimization parameters, and the threshold b sheet using the [https://github.com/kdahlquist/DahlquistLab/raw/master/data/Spring2019/15-genes_28-edges_sample_Sigmoid_estimation_2019.xlsx sample workbook] provided. Finally, I input the GRNmap input workbook from the [[Media:GRNmap4048 input worksheet.xlsx|GRNmap Input Worksheet Profiles 40 and 48]] into MATLAB for analysis.

===== Assessment of Project =====

# Give an objective assessment of the success of your project workflow and teamwork.
#* The team did a good job making sure things were done in a timely manner and we also had very few problems meeting up outside of class time to work on the project which made the workflow much more efficient.
# What worked and what didn't work?
#* Communication via text messages and scheduling meet up times worked very well. It seemed like the work load distribution was not completely equal, but this is not something we could change as a group.
# What would you do differently if you could do it all over again?
#* I would ensure that each job had defined tasks or were assigned to help other members in their tasks.
# Evaluate your team’s portion of the Final Project and Group Report in the following areas:
#* Content: What is the quality of the work?
#** The quality of the work was good, but might have some issues because some steps were unclear and did not always parallel the steps done in the example data analysis assignment.
#* Organization: Comment on the organization of the project and of your group's wiki pages.
#** Our wiki page was very organized because each section included a header and files were broken up into categories/steps.
#* Completeness: Did your team achieve all of the project objectives? Why or why not?
#** Yes, the Microsoft Access database was successfully made after analyzing the publish microarray data.

===== Reflection on the Process =====

* What did you learn?
# With your head (biological or computer science principles)
#* I learned about how microarray experiments can be used to study gene expression changes in response to stress.
# With your heart (personal qualities and teamwork qualities that make things work or not work)?
#* I learned that meeting up is much more effective than working individually or texting when analyzing and interpreting data, as well as when working on editing presentations.
# With your hands (technical skills)?
#* I learned how to input microarray data into MS Access, how to use GRNsight, YEASTRACT, and MATLAB.
* What lesson will you take away from this project that you will still use a year from now?
# I will take away the lesson that my attitude plays a major role in whether each person is equally invested in a group assignment or not.

===DeLisa Madere's Final Reflection===
====Statement of Work====
#'''Role as Designer'''
#*My role in this project was a Designer. As a designer, I collaborated with the other coders to come up with a metadata sheet incorporating information regarding the citations of the paper as well as the sample-to-data sheet including the different treatments, yeast strains, timepoints, concentrations, and replicates. After creating the metadata sheet, I worked with the QAs to create the database compiling the datasets from our microarray data for the Data Analysts to analyze further. Once all the data was analyzed, I then worked with the QAs and the other coders to create a database compiling our data, the degradation rates, production rates, metadata table, as well as the other datasets from the other groups (FunGals, Skinny Genes, Dahlquist Lab) to visualize the relationships in a database schema. Each dataset was standardized under common headers such as author_publicationyear_log2_expression, and each dataset had common headers as well representing each replicate such as yeaststrain_treatment_concentration_LogFC_time-replicate. The final database is linked together through a standardized ID that each of the datasets contained.
#'''Links to Artifacts'''
#*[[Sulfiknights]]
#*[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]
#*[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip ‎|BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip‎]]
#*[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]

====Assessment of Project====
#'''Objective Assessment'''
#*Overall, our team did a great job with staying on task. With the responsibilities that we were given for this project, our team carried them out in a timely manner, and we all worked together to get it done. We consistently met up to talk about our project and asked each other for help along the way, creating a strong group dynamic.
#'''What worked and didn't work?'''
#*What worked really well was that we each focused on our specific responsibilities and asked each other if we needed assistance. From focusing on our own tasks, we were able to understand our roles more. The only difficulty with this project was the workload that we each had outside of this, so maintaining a balance between our Database coursework and our other coursework.
#'''What would you do differently?'''
#*Since my responsibility came a little later on in the milestones, I would have liked to understand more what the other members of my group were doing, specifically the data analysts. I would have had a better understanding early on what actions were being carried out in the project. I would like to also have taken more initiative in helping the other members.
#'''Team Evaluation'''
#*'''Content'''
#::-I think the quality of work was good. I feel very proud of our team in the way that we presented our data to the class and was happy with the outcome.
#*'''Organization'''
#::-The organization of our project was good. Since the project itself was very step-by-step, that helped us with coming up with a timeline of each of our milestones. Regarding the wiki page, our deliverables page is very well organized with each assignment that needs to be on it and whether or not the task is complete. There is always room for improvement with organization in general, so there could have been a better flow with navigating certain links, but overall our organization turned out good.
#*'''Completedness'''
#::-Our team completed all of the project objectives. There was not one moment where we forgot to do something or neglected to include something. We were able to complete everything and in a timely manner.

====Reflection on the Process====
#'''What did you learn?'''
#*'''With your Head'''
#::-From this project as well as this whole semester, I have learned how to analyze data in a microarray with understanding gene expression as well as why databases are important in these specific experiments. I have also learned more about what Microsoft Access is (I have always had it on my computer just sitting there) and how it is important in storing data and creating databases.
#*'''With your Heart'''
#::-From my team, I was able to learn that it is okay to ask for help. I constantly asked my team to explain certain things to me especially since I had to miss half of class the first day, we were assigned these tasks. I have also learned that being understanding of each other really helps when working in a team. Our team was very understanding of other coursework that needed to be done and was able to work around all of our schedules.
#*'''With your Hands'''
#::-I have learned more about technology in general and how computer technology can be incorporated into Biology. I was always interested in seeing how these two relate and through this have learned the importance of having comprehensible reproducible data.
#'''What lessons did you take away from this project that you will still use a year from now?'''
#*From this project, I have learned that it is important to always be consistent and comprehensible when producing different experiments for others to understand and take away. It is important to lay out everything and to not neglect to include different methods or vital information when explaining data.

===Naomi Tesfaiohannes's Final Reflection===

'''Statement of Work'''

Describe exactly what you did on the project.

For this project I served as the project manager and the quality assurance guild. As project manager I communicated with Dr. Dahlquist of the steps that were made and need to continue to be made for the project. I also checked in with my team members of their progress with their roles. As QA I worked along with Joey on the datasheets to hand off to the Data Analysts. I also contributed to presenting and putting together the final presentation.

'''Provide references or links to artifacts of your work, such as:'''

[[Sulfiknights]]

[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]

'''Give an objective assessment of the success of your project workflow and teamwork.'''

What worked and what didn't work?

What worked was meeting outside of class and keeping in touch with progress by using the group chat
What didn't work was sometimes not being able to answer each other's questions. Leaving us all confused.

What would you do differently if you could do it all over again?

Ask more questions about analyzing new data instead of trying to figure it out on my own.

'''Evaluate your team’s portion of the Final Project and Group Report in the following areas:'''

Content: What is the quality of the work?

Our work is a reflection of the collaborative effort from all of the team members in trying to understand the new data we reanalyzed.

Organization: Comment on the organization of the project and of your group's wiki pages.

Our group stayed organized by splitting up what sections we would work on. That way we could come together at the end of the slides to review what still needs to be understood.

Completeness: Did your team achieve all of the project objectives? Why or why not?

Yes, but at our own pace. The objectives were completed by going through the deliverables for each members.

Reflection on the Process

What did you learn?

With your head (biological or computer science principles)

Connecting the affects of arsenic to budding yeast

With your heart (personal qualities and teamwork qualities that make things work or not work)?

Teamwork and collaborating with others by contributing my own section of work with theirs to form an overall analysis of the data.

With your hands (technical skills)?

Formatting the database column titles

What lesson will you take away from this project that you will still use a year from now?

It's important to ask questions when struggling with something new, for example a database format you are not familiar with. It's not a bad thing to ask questions, and it doesn't mean you are unaware of what is happening. Questions help with understanding making it easier for the student to present on the material.

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:02, 9 December 2019 (PST)

===Ivy Macaraeg's Final Reflection===
==== Statement of Work ====

* Describe exactly what you did on the project.
:-For this project, I worked with Marcus to organize and analyze the data. We worked together during and outside of class time to figure out what we needed to do so that the other members of our team could complete their jobs. I also worked with the other groups to better understand my role and the project in general. I helped do the ANOVA, STEM, GO, GRNsight, and GRNmap analyses. I also helped put together the final project and the final report.
* Provide references or links to artifacts of my work:
:-[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]
:-[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]
:-[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]
:-[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]], [[Media:Profil923_GRNsight_matrix.PNG]]
:-[[Media:Colored_GRNsight_923.PNG]]
:-[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]
:-[[Media:Profile4048_GRNsight_matrix.PNG]], [[Media:Colored GRNsight 4048.PNG]]
:-[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]]
:-[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]
:-[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]
:-[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]
:-[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]
:-[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]
:-[[Sulfiknights DA Week 12/13]]
:-[[Sulfiknights DA Week 14]]

==== Assessment of Project ====

* Give an objective assessment of the success of your project workflow and teamwork.
:-At first, I think we were a little uneasy and going about our tasks was a little rough because we didn't really know what we were doing. As time moved on, and we remembered the methods of previous weeks, it got easier to complete our tasks. I thought the team work was good. Even though it felt like there was a lot more work for the Data Analysts, everyone was able to do what they needed to and we always offered to help each other out if we needed help.
* What worked and what didn't work?
:-I think what worked the best was how willing everyone was to work together and offer help. Communication between all of us was good, and we helped each other understand what needed to be done.
* What would you do differently if you could do it all over again?
:-If I could do it all over again, I would not be data analyst, not because I did not enjoy the work, but because I would like to see what the coders/designers did and how the schema worked.
* Evaluate your team’s portion of the Final Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*#:-I think I did well in terms of doing what needed to be done. I think I was pretty thorough, but I probably could have been a little bit neater in terms of getting my files together in an organized spot and formatting everything correctly.
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*#:- I got confused from time to time about what needed to be where. I felt like there were a lot of wiki pages to be managed (Group, individual, deliverables), and I wasn't sure about what exactly had to go on what page. Each page had a lot of components to it and I felt as though it got a little messy.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?
*#:-Yes, we did achieve all of the project objectives because we were able to work efficiently together.

==== Reflection on the Process ====

* What did you learn?
** With your head (biological or computer science principles)
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
** With your hands (technical skills)?
* What lesson will you take away from this project that you will still use a year from now?

==Group Powerpoint Presentation==

[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]

==Excel Spreadsheet with ANOVA Results/STEM Formatting==
[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]

==PowerPoint of ANOVA Table...==
[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]

[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]]

[[Image:Profil923_GRNsight_matrix.PNG|500px]]
[[Image:Colored_GRNsight_923.PNG|500px]]

[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]

[[Image:Profile4048_GRNsight_matrix.PNG|500px]]
[[Image:Colored GRNsight 4048.PNG|500px]]

==Gene List and GO List files==
[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]]

[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]

==YEASTRACT "Rank by TF" Results==
[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]

[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]

==GRNmap input workbook==
[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]

[[Media:GRNmap4048 input worksheet.xlsx|GRNmap Input Worksheet: Profiles 40 and 48]]

==GRNmap output workbook and output plots==
[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]

[[Media:GRNmap4048_output.zip|GRNmap Output Files: Profiles 40 and 48]]

==MS Access database==
[[Media: SK_Expression-and-Degradation-rate-database_2019.zip | MS Access Database of Thorsen & Dahlquist data]]

==ReadMe==

==Query design for populating a GRNmap input workbook from the database==
'''Profiles 9 and 23:'''

[[Image:Productionrates_923_querydesign.PNG|500px]]
[[Image:Degradationrates_923_querydesign.PNG|500px]]
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG|1000px]]

'''Profiles 40 and 48:'''

[[Image:ProductionRates 4048 QueryDesign.PNG|500px]]
[[Image:DegradationRates 4048 QueryDesign.PNG|500px]]
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG|1000px]]

==Electronic notebook corresponding to the microarray results files==
'''Electronic notebook for Data Analysts:'''

[[Sulfiknights DA Week 12/13]]

[[Sulfiknights DA Week 14]]

'''Electronic notebook for Quality Assurance'''

[[Ntesfaio Week 12/13]]

[[Ntesfaio Week 15]]

'''Electronic notebook for Designer'''

[[Dmadere Week 12|Dmadere Week 12/13]]

[[Dmadere Week 15]]

==Merge completed databases into a single database==
[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip ‎|BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip ‎]]

[[Media:DM_Metadata_Sheet.xlsx|Metadata Sheet]]

[[Image:Access_Database_Schema_Screenshot.PNG|1000px|Access_Database_Schema_Screenshot.PNG]]

Sulfiknights Deliverables

2019-12-03T23:41:14Z

Jnimmers: /* MS Access database */ Update access database

Sulfiknights

2019-12-03T23:40:58Z

Jnimmers: /* Data/Files */ Update database link

{{Sulfiknights}}

==Week 12/13 Milestones==

===Project Manager===

Create a schedule by Tuesday, November 26 that has goals for each member of the Sulfiknights team. Though this may not be completely followed day-by-day it is still helpful to have a outline of checkpoints that should be met for completing this assignment.

Check in with the members of the team to assist in making sure the assignment is complete.

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 20:44, 21 November 2019 (PST)

===Quality Assurance===

As on Thursday, November 21st the Quality Assurance guilds were an intermediate for our designer (DeLisa) and our Data Analysts (Marcus and Ivy).

Our goal before Tuesday, November 26 is to assist the Data Analysts in running an ANOVA and running stem. As for Quality Assurance we have completed Milestone 4 and are moving onto Milestone 5 as of Thursday, November 21st.

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:40, 23 November 2019 (PST)

===Data Analysis===

===Coder/Designer===

==Team Journal Assignments==
===Week 12/13===
====Naomi Tesfaiohannes====

Each team member should reflect on the team's progress:

What worked?

Working together in class and taking advantage of asking questions while going through the assignment

What didn't work?

Not working on a shared document or excel workbook because progress could be made on one and not seen by the other partner. Also the metasheet was difficult to put together because of the inconsistent datapoints between the groups.

What will I do next to fix what didn't work?

Continue communicating with my team on how we want to progress through with the assignment

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 21:20, 25 November 2019 (PST)

====Ivy Macaraeg====
#What worked?
#*We figured out what we needed to be working on, and that helped get us going even more than before.
#What didn't work?
#*We had some trouble organizing the data in a way that would be clear but compatible with future programs.
#What will I do next to fix what didn't work?
#*I think sticking to the directions and making sure that we are thorough will help us.
====John Nimmers-Minor====
Each team member should reflect on the team's progress:

What worked?

A. Splitting up the work and knowing exactly what each role was in charge of helped tremendously this week.

What didn't work?

A. Having two people work on the exact same task didn't help because one of those two individuals could have potentially been working on a separate piece of the project.

What will I do next to fix what didn't work?

A. Communication throughout the project group will make sure that two people are not doing the same thing at the same time unnecessarily. This will allow us to complete more tasks in a shorter amount of time.

====DeLisa Madere====
#What worked?
#*It really helped that our team all were focused on the individual tasks at hand and we were able to finish the tasks efficiently.
#What didn't work?
#*For me, it was a little difficult to understand what was happening with my other group members' tasks since I had my own individual task.
#What will I do next to fix what didn't work?
#*To fix this, I will try harder to understand the purpose behind each step in order to completely give all my input if needed, or help is needed.
#[[User:Dmadere|Dmadere]] ([[User talk:Dmadere|talk]]) 22:38, 25 November 2019 (PST)

====Marcus Avila====
#What worked?
#*We did a good job dividing the work and ensuring that everything was done.
#What didn't work?
#*We struggled with communication because it seemed each person had a lot going on as the break was approaching.
#What will I do next time to fix what didn't work?
#* Next time I will try to do a better job with communicating with my team members.
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 23:59, 25 November 2019 (PST)

===Week 11===
====Naomi Tesfaiohannes====
Each team member should reflect on the team's progress:

*What worked?
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure.

*What didn't work?
My time management due to other coursework

*What will I do next to fix what didn't work?
Have a better control of what work I put in each day for this assignment

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)
====Joey Nimmers-Minor====
*What worked?
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.
*What didn't work?
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week
*What will I do next to fix what didn't work?
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.

[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)
====Marcus Avila====
# What worked?
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.
# What didn't work?
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.
# What will I do next to fix what didn't work?
#* Next time I will allocate more time to the assignment.
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)
====DeLisa Madere====

'''What Worked?'''
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.

'''What didn't work?'''
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.

'''What will I do next to fix what didn't work?'''
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.
====Ivy Macaraeg====
*What worked?
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out.
*What didn't work?
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it.
*What will I do next to fix what didn't work?
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)

==Annotated Bibliography Sources==
===DeLisa Madere===

1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938

2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x
===Naomi Tesfaiohannes===

1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013

2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003
===Ivy Macaraeg===

1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712

2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5
===Marcus Avila===

1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98

2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0
===John Nimmers-Minor===

1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005

2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x

==Data/Files==
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]
*Other files can be found on our [[Sulfiknights Deliverables|deliverables page]]

[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]

[[Media:SK_Expression-and-Degradation-rate-database_2019.zip | Expression and Degradation Sheet of Thorsen & Dahlquist Data]]

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006

[[Category:Group Projects]]
[[Category:Sulfiknights]]

File:SK Expression-and-Degradation-rate-database 2019.zip

2019-12-03T23:40:28Z

Jnimmers:

File:Expression-and-Degradation-rate-database 2019.zip

2019-12-03T23:37:55Z

Jnimmers: Jnimmers uploaded a new version of File:Expression-and-Degradation-rate-database 2019.zip

File:DM Metadata Sheet.xlsx

2019-12-03T23:35:42Z

Jnimmers: Jnimmers uploaded a new version of File:DM Metadata Sheet.xlsx

== Summary ==
uploaded metadata sheet

Sulfiknights Deliverables

2019-12-03T23:02:58Z

Jnimmers: /* MS Access database */ Upload MS Access deliverable

Sulfiknights

2019-12-03T23:02:10Z

Jnimmers: /* Data/Files */ upload access data

{{Sulfiknights}}

==Week 12/13 Milestones==

===Project Manager===

Create a schedule by Tuesday, November 26 that has goals for each member of the Sulfiknights team. Though this may not be completely followed day-by-day it is still helpful to have a outline of checkpoints that should be met for completing this assignment.

Check in with the members of the team to assist in making sure the assignment is complete.

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 20:44, 21 November 2019 (PST)

===Quality Assurance===

As on Thursday, November 21st the Quality Assurance guilds were an intermediate for our designer (DeLisa) and our Data Analysts (Marcus and Ivy).

Our goal before Tuesday, November 26 is to assist the Data Analysts in running an ANOVA and running stem. As for Quality Assurance we have completed Milestone 4 and are moving onto Milestone 5 as of Thursday, November 21st.

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:40, 23 November 2019 (PST)

===Data Analysis===

===Coder/Designer===

==Team Journal Assignments==
===Week 12/13===
====Naomi Tesfaiohannes====

Each team member should reflect on the team's progress:

What worked?

Working together in class and taking advantage of asking questions while going through the assignment

What didn't work?

Not working on a shared document or excel workbook because progress could be made on one and not seen by the other partner. Also the metasheet was difficult to put together because of the inconsistent datapoints between the groups.

What will I do next to fix what didn't work?

Continue communicating with my team on how we want to progress through with the assignment

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 21:20, 25 November 2019 (PST)

====Ivy Macaraeg====
#What worked?
#*We figured out what we needed to be working on, and that helped get us going even more than before.
#What didn't work?
#*We had some trouble organizing the data in a way that would be clear but compatible with future programs.
#What will I do next to fix what didn't work?
#*I think sticking to the directions and making sure that we are thorough will help us.
====John Nimmers-Minor====
Each team member should reflect on the team's progress:

What worked?

A. Splitting up the work and knowing exactly what each role was in charge of helped tremendously this week.

What didn't work?

A. Having two people work on the exact same task didn't help because one of those two individuals could have potentially been working on a separate piece of the project.

What will I do next to fix what didn't work?

A. Communication throughout the project group will make sure that two people are not doing the same thing at the same time unnecessarily. This will allow us to complete more tasks in a shorter amount of time.

====DeLisa Madere====
#What worked?
#*It really helped that our team all were focused on the individual tasks at hand and we were able to finish the tasks efficiently.
#What didn't work?
#*For me, it was a little difficult to understand what was happening with my other group members' tasks since I had my own individual task.
#What will I do next to fix what didn't work?
#*To fix this, I will try harder to understand the purpose behind each step in order to completely give all my input if needed, or help is needed.
#[[User:Dmadere|Dmadere]] ([[User talk:Dmadere|talk]]) 22:38, 25 November 2019 (PST)

====Marcus Avila====
#What worked?
#*We did a good job dividing the work and ensuring that everything was done.
#What didn't work?
#*We struggled with communication because it seemed each person had a lot going on as the break was approaching.
#What will I do next time to fix what didn't work?
#* Next time I will try to do a better job with communicating with my team members.
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 23:59, 25 November 2019 (PST)

===Week 11===
====Naomi Tesfaiohannes====
Each team member should reflect on the team's progress:

*What worked?
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure.

*What didn't work?
My time management due to other coursework

*What will I do next to fix what didn't work?
Have a better control of what work I put in each day for this assignment

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)
====Joey Nimmers-Minor====
*What worked?
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.
*What didn't work?
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week
*What will I do next to fix what didn't work?
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.

[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)
====Marcus Avila====
# What worked?
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.
# What didn't work?
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.
# What will I do next to fix what didn't work?
#* Next time I will allocate more time to the assignment.
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)
====DeLisa Madere====

'''What Worked?'''
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.

'''What didn't work?'''
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.

'''What will I do next to fix what didn't work?'''
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.
====Ivy Macaraeg====
*What worked?
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out.
*What didn't work?
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it.
*What will I do next to fix what didn't work?
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)

==Annotated Bibliography Sources==
===DeLisa Madere===

1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938

2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x
===Naomi Tesfaiohannes===

1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013

2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003
===Ivy Macaraeg===

1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712

2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5
===Marcus Avila===

1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98

2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0
===John Nimmers-Minor===

1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005

2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x

==Data/Files==
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]
*Other files can be found on our [[Sulfiknights Deliverables|deliverables page]]

[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]

[[Media:Expression-and-Degradation-rate-database_12_3.zip | Expression and Degradation Sheet of Thorsen & Dahlquist Data]]

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006

[[Category:Group Projects]]
[[Category:Sulfiknights]]

File:Expression-and-Degradation-rate-database 12 3.zip

2019-12-03T23:01:42Z

Jnimmers:

File:Expression-and-Degradation-rate-database 2019.zip

2019-12-03T22:59:57Z

Jnimmers: Jnimmers uploaded a new version of File:Expression-and-Degradation-rate-database 2019.zip

File:Thorsendata sulfiknights.xlsx

2019-11-27T00:01:14Z

Jnimmers: Jnimmers uploaded a new version of File:Thorsendata sulfiknights.xlsx

Sulfiknights

2019-11-27T00:00:16Z

Jnimmers: /* Data/Files */ Upload access fatabase

{{Sulfiknights}}

==Week 12/13 Milestones==

===Project Manager===

Create a schedule by Tuesday, November 26 that has goals for each member of the Sulfiknights team. Though this may not be completely followed day-by-day it is still helpful to have a outline of checkpoints that should be met for completing this assignment.

Check in with the members of the team to assist in making sure the assignment is complete.

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 20:44, 21 November 2019 (PST)

===Quality Assurance===

As on Thursday, November 21st the Quality Assurance guilds were an intermediate for our designer (DeLisa) and our Data Analysts (Marcus and Ivy).

Our goal before Tuesday, November 26 is to assist the Data Analysts in running an ANOVA and running stem. As for Quality Assurance we have completed Milestone 4 and are moving onto Milestone 5 as of Thursday, November 21st.

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:40, 23 November 2019 (PST)

===Data Analysis===

===Coder/Designer===

==Team Journal Assignments==
===Week 12/13===
====Naomi Tesfaiohannes====

Each team member should reflect on the team's progress:

What worked?

Working together in class and taking advantage of asking questions while going through the assignment

What didn't work?

Not working on a shared document or excel workbook because progress could be made on one and not seen by the other partner. Also the metasheet was difficult to put together because of the inconsistent datapoints between the groups.

What will I do next to fix what didn't work?

Continue communicating with my team on how we want to progress through with the assignment

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 21:20, 25 November 2019 (PST)

====Ivy Macaraeg====
#What worked?
#*We figured out what we needed to be working on, and that helped get us going even more than before.
#What didn't work?
#*We had some trouble organizing the data in a way that would be clear but compatible with future programs.
#What will I do next to fix what didn't work?
#*I think sticking to the directions and making sure that we are thorough will help us.
====John Nimmers-Minor====
Each team member should reflect on the team's progress:

What worked?

A. Splitting up the work and knowing exactly what each role was in charge of helped tremendously this week.

What didn't work?

A. Having two people work on the exact same task didn't help because one of those two individuals could have potentially been working on a separate piece of the project.

What will I do next to fix what didn't work?

A. Communication throughout the project group will make sure that two people are not doing the same thing at the same time unnecessarily. This will allow us to complete more tasks in a shorter amount of time.

====DeLisa Madere====
#What worked?
#*It really helped that our team all were focused on the individual tasks at hand and we were able to finish the tasks efficiently.
#What didn't work?
#*For me, it was a little difficult to understand what was happening with my other group members' tasks since I had my own individual task.
#What will I do next to fix what didn't work?
#*To fix this, I will try harder to understand the purpose behind each step in order to completely give all my input if needed, or help is needed.
#[[User:Dmadere|Dmadere]] ([[User talk:Dmadere|talk]]) 22:38, 25 November 2019 (PST)

====Marcus Avila====
#What worked?
#*We did a good job dividing the work and ensuring that everything was done.
#What didn't work?
#*We struggled with communication because it seemed each person had a lot going on as the break was approaching.
#What will I do next time to fix what didn't work?
#* Next time I will try to do a better job with communicating with my team members.
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 23:59, 25 November 2019 (PST)

===Week 11===
====Naomi Tesfaiohannes====
Each team member should reflect on the team's progress:

*What worked?
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure.

*What didn't work?
My time management due to other coursework

*What will I do next to fix what didn't work?
Have a better control of what work I put in each day for this assignment

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)
====Joey Nimmers-Minor====
*What worked?
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.
*What didn't work?
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week
*What will I do next to fix what didn't work?
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.

[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)
====Marcus Avila====
# What worked?
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.
# What didn't work?
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.
# What will I do next to fix what didn't work?
#* Next time I will allocate more time to the assignment.
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)
====DeLisa Madere====

'''What Worked?'''
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.

'''What didn't work?'''
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.

'''What will I do next to fix what didn't work?'''
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.
====Ivy Macaraeg====
*What worked?
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out.
*What didn't work?
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it.
*What will I do next to fix what didn't work?
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)

==Annotated Bibliography Sources==
===DeLisa Madere===

1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938

2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x
===Naomi Tesfaiohannes===

1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013

2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003
===Ivy Macaraeg===

1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712

2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5
===Marcus Avila===

1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98

2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0
===John Nimmers-Minor===

1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005

2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x

==Data/Files==
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]
*Other files can be found on our [[Sulfiknights Deliverables|deliverables page]]

[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]
[[Media:Expression-and-Degradation-rate-database_2019.zip | Expression and Degradation Sheet of Thorsen & Dahlquist Data]]

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006

[[Category:Group Projects]]
[[Category:Sulfiknights]]

File:Expression-and-Degradation-rate-database 2019.zip

2019-11-26T23:59:08Z

Jnimmers:

Jnimmers Week 12/13

2019-11-26T04:16:55Z

Jnimmers: Invoke template

{{jnimmers}}
==Electronic Lab Notebook==
===Purpose===
This week, [[User:Ntesfaio | Naomi Tesfaiohannes]] and I assisted the Data Analysis team in the creation of the spreadsheet that will be used in the analysis and coding of our groups data work. The purpose of this was to prepare the Excel document for further analysis, understanding and to further the group's project to be worked on by the coding team.

===Methods===
*Create a shared excel sheet online.
*Convert the gene names provided by the paper and convert them to their ORF names through the [http://www.yeastract.com/formorftogene.php "ORF List <-> Gene List"] tool at YEASTRACT.
*Make sure that the Standard ID and Systematic names were both available in the data table
*Next week, the Quality Assurance team will work with the Coder/Designers in order to verify the ANOVA tests and sanity checks done by the Data Analysts
===Data & Files===
[[Media:Thorsendata_sulfiknights.xlsx|Excel Spreadsheet with ANOVA Results]]
===Conclusion===
A number of deliverables were created and started by our group including the Excel spreadsheet and the ANOVA test/sanity check. Next class the ANOVA test will be rechecked for any errors and the process towards creating the GRNMap will begin.
===Acknowledgements===
*I would like to thank [[User:Kdahlquist|Dr. Kam D. Dahlquist]] for her continued support and instruction for this assignment. She assisted my team with the understanding of our paper's data and allowed for us to move forward with our analysis.
*I would like to thank my partners [[Sulfiknights | The Sufiknights]] for working together with me on this assignment as we prepare our deliveribles and our final project presentation.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 19:18, 25 November 2019 (PST)
===References===
*LMU BioDB 2019. (2019). Week 8. Retrieved November 25, 2019, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8 https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8].
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006

[[Category:Journal Entry]]

Template:Jnimmers

2019-11-26T04:16:25Z

Jnimmers: Changed week 12/13 to sulfiknoghts page

[[Main Page|Biological Databases]]<br>
[[User:Jnimmers | Jnimmers]]
[[Category: Journal Entry]]<br>
'''Assignment Table'''
{|
!Week Number
!Assignment Page
!Individual Journal
!Shared Journal
|-
|1
|[[ Week 1 | Week 1 Assignment Page]]
|N/A
|[[Jnimmers Week 2 Individual Journal | Week 2 Shared Journal]]
|-
|2
|[[Week 2 | Week 2 Assignment Page]]
|[[Jnimmers Week 2 Individual Journal| Week 2 Individual Journal]]
|[[Class Journal Week 2 | Week 2 Shared Journal]]
|-
|3
|[[Week 3 | Week 3 Assignment Page]]
|[[CMR2/YOR093C Week 3]]
|[[Class Journal Week 3 | Week 3 Shared Journal]]
|-
|4
|[[Week 4 | Week 4 Assignment Page]]
|[[Jnimmers Week 4 | Week 4 Individual Journal]]
|[[Class Journal Week 4 | Week 4 Shared Journal]]
|-
|5
|[[Week 5 | Week 5 Assignment Page]]
|[[CRISPRlnc Group Journal | CRISPRlnc Week 5]]
|[[Class Journal Week 5 |Week 5 Shared Journal]]
|-
|6
|[[Week 6 | Week 6 Assignment Page]]
|[[Jnimmers Week 6 | Week 6 Individual Journal]]
|[[Class Journal Week 6 | Week 6 Shared Journal]]
|-
|7
|[[Week 7 | Week 7 Assignment Page]]
|[[Jnimmers Week 7 | Week 7 Individual Journal]]
|[[Class Journal Week 7 | Week 7 Shared Journal]]
|-
|8
|[[Week 8 | Week 8 Assignment Page]]
|[[Jnimmers Week 8 | Week 8 Individual Journal]]
|[[Class Journal Week 8 | Week 8 Shared Journal]]
|-
|9
|[[Week 9 | Week 9 Assignment Page]]
|[[Week 9 Individual Journal]]
|[[Class Journal Week 9 | Week 9 Shared Journal]]
|-
|10
|[[Week 10 | Week 10 Assignment Page]]
|[[Jnimmers Week 10 | Week 10 Individual Journal]]
|[[Class Journal Week 10 | Week 10 Shared Journal]]
|-
|11
|[[Week 11 | Week 11 Assignment Page]]
|[[Jnimmers week 11 | Week 11 Individual Journal]]
|[[Sulfiknights | Sulfiknights Team Page ]]
|-
|12/13
|[[Week 12/13 | Week 12/13 Assignment Page]]
|[[Jnimmers Week 12/13 | Week 12/13 Individual Journal]]
|[[Sulfiknights | Sulfiknights Team Page ]]
|-
|14
|[[Week 14 | Week 14 Assignment Page]]
|[[Week 14 Individual Journal]]
|[[Class Journal Week 14 | Week 14 Shared Journal]]
|-
|15
|[[Week 15 | Week 15 Assignment Page]]
|[[Week 15 Individual Journal]]
|[[Class Journal Week 15 | Week 15 Shared Journal]]
|-

|}

Sulfiknights

2019-11-26T04:14:57Z

Jnimmers: /* Week 12/13 */ Complete team assignment reflection

{{Sulfiknights}}

==Week 12/13 Milestones==

===Project Manager===

Create a schedule by Tuesday, November 26 that has goals for each member of the Sulfiknights team. Though this may not be completely followed day-by-day it is still helpful to have a outline of checkpoints that should be met for completing this assignment.

Check in with the members of the team to assist in making sure the assignment is complete.

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 20:44, 21 November 2019 (PST)

===Quality Assurance===

As on Thursday, November 21st the Quality Assurance guilds were an intermediate for our designer (DeLisa) and our Data Analysts (Marcus and Ivy).

Our goal before Tuesday, November 26 is to assist the Data Analysts in running an ANOVA and running stem. As for Quality Assurance we have completed Milestone 4 and are moving onto Milestone 5 as of Thursday, November 21st.

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:40, 23 November 2019 (PST)

===Data Analysis===

===Coder/Designer===

==Team Journal Assignments==
===Week 12/13===
====Naomi Tesfaiohannes====

Each team member should reflect on the team's progress:

What worked?

What didn't work?

What will I do next to fix what didn't work?

====Ivy Macaraeg====
#What worked?
#*We figured out what we needed to be working on, and that helped get us going even more than before.
#What didn't work?
#*We had some trouble organizing the data in a way that would be clear but compatible with future programs.
#What will I do next to fix what didn't work?
#*I think sticking to the directions and making sure that we are thorough will help us.
====John Nimmers-Minor====
Each team member should reflect on the team's progress:

What worked?

A. Splitting up the work and knowing exactly what each role was in charge of helped tremendously this week.

What didn't work?

A. Having two people work on the exact same task didn't help because one of those two individuals could have potentially been working on a separate piece of the project.

What will I do next to fix what didn't work?

A. Communication throughout the project group will make sure that two people are not doing the same thing at the same time unnecesarily. This will allow us to complete more tasks in a shorter amount of time.

===Week 11===
====Naomi Tesfaiohannes====
Each team member should reflect on the team's progress:

*What worked?
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure.

*What didn't work?
My time management due to other coursework

*What will I do next to fix what didn't work?
Have a better control of what work I put in each day for this assignment

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)
====Joey Nimmers-Minor====
*What worked?
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.
*What didn't work?
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week
*What will I do next to fix what didn't work?
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.

[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)
====Marcus Avila====
# What worked?
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.
# What didn't work?
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.
# What will I do next to fix what didn't work?
#* Next time I will allocate more time to the assignment.
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)
====DeLisa Madere====

'''What Worked?'''
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.

'''What didn't work?'''
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.

'''What will I do next to fix what didn't work?'''
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.
====Ivy Macaraeg====
*What worked?
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out.
*What didn't work?
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it.
*What will I do next to fix what didn't work?
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)

==Annotated Bibliography Sources==
===DeLisa Madere===

1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938

2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x
===Naomi Tesfaiohannes===

1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013

2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003
===Ivy Macaraeg===

1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712

2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5
===Marcus Avila===

1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98

2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0
===John Nimmers-Minor===

1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005

2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x

==Data/Files==
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]
*Other files can be found on our [[Sulfiknights Deliverables|deliverables page]]

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006

[[Category:Group Projects]]
[[Category:Sulfiknights]]

Jnimmers Week 12/13

2019-11-26T03:19:00Z

Jnimmers: spelling and deleted extra instructures

Jnimmers Week 12/13

2019-11-26T03:18:11Z

Jnimmers: /* Individual Journal Assignment */ Finished individual journal

==Electronic Lab Notebook==
===Purpose===
This week, [[User:Ntesfaio | Naomi Tesfaiohannes]] and I assisted the Data Analysis team in the creation of the spreadsheet that will be used in the analysis and coding of our groups data work. The purpose of this was to prepare the Excel document for further analysis, understanding and to further the group's project to be worked on by the coding team.

===Methods===
*Create a shared excel sheet online.
*Convert the gene names provided by the paper and convert them to their ORF names through the [http://www.yeastract.com/formorftogene.php "ORF List <-> Gene List"] tool at YEASTRACT.
*Make sure that the Standard ID and Systematic names were both available in the data table
*Next week, the Quality Assurance team will work with the Coder/Designers in order to verify the ANOVA tests and sanity checks done by the Data Analysts
===Data & Files===
[[Media:Thorsendata_sulfiknights.xlsx|Excel Spreadsheet with ANOVA Results]]
===Conclusion===
A number of deliverables were created and started by our group including the Excel spreadsheet and the ANOVA test/sanity check. Next class the ANOVA test will be rechecked for any errors and the process towards creating the GRNMap will begin.
===Ackowledgements===
*I would like to thank [[User:Kdahlquist|Dr. Kam D. Dahlquist]] for her continued support and instruction for this assignment. She assisted my team with the understanding of our paper's data and allowed for us to move forward with our analysis.
*I would like to thank my partners [[Sulfiknights | The Sufiknights]] for working together with me on this assignment as we prepare our deliveribles and our final project presentation.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 19:18, 25 November 2019 (PST)
===References===
*LMU BioDB 2019. (2019). Week 8. Retrieved November 25, 2019, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8 https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8].
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006

* Store this journal entry as "''username'' Week 12/13" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* For your assignment this week document your individual progress in your '''''electronic laboratory notebook'''''.

=== Electronic Lab Notebook ===

Record your progress toward your team's [[Final_Project_Deliverables | deliverables]] for this week in an '''''electronic lab notebook'''''.

[[Category:Journal Entry]]

Jnimmers Week 12/13

2019-11-26T02:32:07Z

Jnimmers: /* Individual Journal Assignment */ formattinf

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 12/13" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* For your assignment this week document your individual progress in your '''''electronic laboratory notebook'''''.

=== Electronic Lab Notebook ===

Record your progress toward your team's [[Final_Project_Deliverables | deliverables]] for this week in an '''''electronic lab notebook'''''.

[[Category:Journal Entry]]

Jnimmers Week 12/13

2019-11-26T02:31:58Z

Jnimmers: /* Individual Journal Assignment */ create category

Jnimmers Week 12/13

2019-11-26T02:31:10Z

Jnimmers: Create page

Template:Jnimmers

2019-11-26T02:30:36Z

Jnimmers: Changed week 12/13 name

[[Main Page|Biological Databases]]<br>
[[User:Jnimmers | Jnimmers]]
[[Category: Journal Entry]]<br>
'''Assignment Table'''
{|
!Week Number
!Assignment Page
!Individual Journal
!Shared Journal
|-
|1
|[[ Week 1 | Week 1 Assignment Page]]
|N/A
|[[Jnimmers Week 2 Individual Journal | Week 2 Shared Journal]]
|-
|2
|[[Week 2 | Week 2 Assignment Page]]
|[[Jnimmers Week 2 Individual Journal| Week 2 Individual Journal]]
|[[Class Journal Week 2 | Week 2 Shared Journal]]
|-
|3
|[[Week 3 | Week 3 Assignment Page]]
|[[CMR2/YOR093C Week 3]]
|[[Class Journal Week 3 | Week 3 Shared Journal]]
|-
|4
|[[Week 4 | Week 4 Assignment Page]]
|[[Jnimmers Week 4 | Week 4 Individual Journal]]
|[[Class Journal Week 4 | Week 4 Shared Journal]]
|-
|5
|[[Week 5 | Week 5 Assignment Page]]
|[[CRISPRlnc Group Journal | CRISPRlnc Week 5]]
|[[Class Journal Week 5 |Week 5 Shared Journal]]
|-
|6
|[[Week 6 | Week 6 Assignment Page]]
|[[Jnimmers Week 6 | Week 6 Individual Journal]]
|[[Class Journal Week 6 | Week 6 Shared Journal]]
|-
|7
|[[Week 7 | Week 7 Assignment Page]]
|[[Jnimmers Week 7 | Week 7 Individual Journal]]
|[[Class Journal Week 7 | Week 7 Shared Journal]]
|-
|8
|[[Week 8 | Week 8 Assignment Page]]
|[[Jnimmers Week 8 | Week 8 Individual Journal]]
|[[Class Journal Week 8 | Week 8 Shared Journal]]
|-
|9
|[[Week 9 | Week 9 Assignment Page]]
|[[Week 9 Individual Journal]]
|[[Class Journal Week 9 | Week 9 Shared Journal]]
|-
|10
|[[Week 10 | Week 10 Assignment Page]]
|[[Jnimmers Week 10 | Week 10 Individual Journal]]
|[[Class Journal Week 10 | Week 10 Shared Journal]]
|-
|11
|[[Week 11 | Week 11 Assignment Page]]
|[[Jnimmers week 11 | Week 11 Individual Journal]]
|[[Sulfiknights | Sulfiknights Team Page ]]
|-
|12/13
|[[Week 12/13 | Week 12/13 Assignment Page]]
|[[Jnimmers Week 12/13 | Week 12/13 Individual Journal]]
|[[Class Journal Week 12/13 | Week 12/13 Shared Journal]]
|-
|14
|[[Week 14 | Week 14 Assignment Page]]
|[[Week 14 Individual Journal]]
|[[Class Journal Week 14 | Week 14 Shared Journal]]
|-
|15
|[[Week 15 | Week 15 Assignment Page]]
|[[Week 15 Individual Journal]]
|[[Class Journal Week 15 | Week 15 Shared Journal]]
|-

|}

Template:Sulfiknights

2019-11-19T23:59:47Z

Jnimmers: edit template

{| class="wikitable" style="width: 100%; text-align: center"
! colspan="8"|Sulfiknight Links
|-
! rowspan="2"|[[Main Page|BIOL Databases Main Page]]
! rowspan="2"|[[Sulfiknights|Sulfiknights Project Overview Page]]
! rowspan="2"|[[Template:Sulfiknights|Sulfiknight Template Page]]
! rowspan="2"|[[Final Project Deliverables| Final Project Deliverables Requirements]]
! Members
| '''Project Manager & Quality Assurance: '''[[User:Ntesfaio|Naomi Tesfaiohannes]]
| '''Quality Assurance:''' [[User:jnimmers|Joey Nimmers-Minor]]
| '''Data Analysis:''' [[User:Imacarae|Ivy-Quynh Macaraeg]] & [[User:Mavila9|Marcus Avila]]
| '''Designer:''' [[User:Dmadere|DeLisa Madere]]
|-
! Assignment Pages
| [[Week 11]]
| [[Week 12/13]]
| [[Week 15]]
|}

[[Category: Group Projects]]

Template:Sulfiknights

2019-11-19T23:59:14Z

Jnimmers: Update Template

{| class="wikitable" style="width: 100%; text-align: center"
! colspan="8"|Sulfiknight Links
|-
! rowspan="2"|[[Main Page|BIOL Databases Main Page]]
! rowspan="2"|[[Sulfiknights|Sulfiknights Project Overview Page]]
! rowspan="2"|[[Template:Sulfiknights|Sulfiknight Template Page]]
! rowspan="2"|[[Final Project Deliverables Requirements]]
! Members
| '''Project Manager & Quality Assurance: '''[[User:Ntesfaio|Naomi Tesfaiohannes]]
| '''Quality Assurance:''' [[User:jnimmers|Joey Nimmers-Minor]]
| '''Data Analysis:''' [[User:Imacarae|Ivy-Quynh Macaraeg]] & [[User:Mavila9|Marcus Avila]]
| '''Designer:''' [[User:Dmadere|DeLisa Madere]]
|-
! Assignment Pages
| [[Week 11]]
| [[Week 12/13]]
| [[Week 15]]
|}

[[Category: Group Projects]]

Jnimmers week 11

2019-11-19T23:02:08Z

Jnimmers: update annotated bib cite

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

==Purpose==
*The purpose of this assignment was to further learn how to read a scientific journal and pull pertinent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Annotated Bibliographies==
=== Annotated Bibliography #1===

# Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
# Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
# Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
# Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
# Article is Open Access
# Availability: Online (PubMed,ePub, and PDF)
# Publisher: American Society for Microbiology Journals (scientific society), for-profit, not a member of the OAPA
# The journal began in 1899
# Peer-reviewed articles: Yes
# [https://aem.asm.org/content/board-editors Editorial Board]
# Impact factor: 5.311
# Primary research article
# [https://aem.asm.org/content/71/2/599/figures-only Figures and Data Tab]

===Annotated Bibliography #2===
# Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15526190
# PubMed Central: Not available
# Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s00204-004-0620-x#enumeration
# Publisher Full Text (PDF): https://link.springer.com/content/pdf/10.1007%2Fs00204-004-0620-x.pdf
# Copyright: Springer-Verlag 2004
# Article is open access
# Availability: in print and online
# Publisher: Springer-Verlag (non-scientific society, mass publisher of scientific material,for-profit, not a member of the OAPA
# The Springer-Verlag media company was founded in 1842
# Peer-reviewed articles: yes
# Not Available
# Impact factor: 5.98
# Primary research article
# Data are not available.

==Database Searches==
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science.
# PubMed
#* What original keyword(s) did you use? How many results did you get?
#** I searched "arsenic metabolism and got 13,712 results.
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** I added the keywords yeast and did a search within 10 years and the search narrowed to 111 results
# Google Scholar
#* What original keyword(s) did you use? How many results did you get?
#** I searched for "arsenic metabolism and got 285,000 results
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** After including the keyword "yeast" in the search, I got 41,600 results
# Web of Science
#* What original keyword(s) did you use? How many results did you get?
#** I originally searched "arsenic toxicity yeast" and got 61 results.
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** After that, I searched "arsenic toxicity yeast" within the 61 results and added the "Highly Cited in Field" filter creating a search of 1 result.
* Use the advanced search functions for each of these three databases/tools and answer the following:
# PubMed
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** The most useful search was after setting the publish date range to 5 years.
# Google Scholar
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** Including the search must find a paper betweem 2007 and now because the original paper that my group in analyzing was published in 2007.
# Web of Science
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** I found the "Highly Cited in Field" filter the most useful to narrow down the search to a singular, highly regarded publishing.
Perform a prospective search on your article in the Web of Science and answer the following:
#* How many articles does this article cite?
#** 42 articles
#* How many articles cite this article?
#** 76 articles
===Reflection===
#The choice of keywords in a search has a major impact in the specificity of the results you get. One word can change the results from being as broad as all phylogenetic domains to something as simple as yeast or any other general species type.
#Pubmed is advantageous because most of the articles are from reliable and peer reviewed sources because the credentials required to be put on Pubmed are more stringent than the databases. The problem with PubMed is that it doesn't have very many articles from non-scientific sources, meaning that if one was to do a comparison of understanding between the scientific and commercial field, they would have to go elsewhere.
Google Scholar is good because of the massive selection of information available on the site, however, with such a large database comes the problem of reliability in terms of the journals, authors and articles found.
Web of Science is good because it allows students to access certain journal articles that may be hidden behind a paywall, however, the amount of articles found in Web of Science is very low in comparison to the other two databases simply based on the number of search results using an identical search terms(s)

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Sulfiknights

2019-11-19T22:59:16Z

Jnimmers: /* John Nimmers-Minor */ formatting

{{Sulfiknights}}

==Data/Files==
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]

==Team Feedback==
===Naomi Tesfaiohannes===
Each team member should reflect on the team's progress:

*What worked?
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure.

*What didn't work?
My time management due to other coursework

*What will I do next to fix what didn't work?
Have a better control of what work I put in each day for this assignment

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)

===Joey Nimmers-Minor===
*What worked?
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.
*What didn't work?
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week
*What will I do next to fix what didn't work?
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.

[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)

===Marcus Avila===
# What worked?
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.
# What didn't work?
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.
# What will I do next to fix what didn't work?
#* Next time I will allocate more time to the assignment.
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)

===DeLisa Madere===

'''What Worked?'''
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.

'''What didn't work?'''
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.

'''What will I do next to fix what didn't work?'''
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.

===Ivy Macaraeg===
*What worked?
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out.
*What didn't work?
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it.
*What will I do next to fix what didn't work?
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)

==Annotated Bibliography Sources==

===DeLisa Madere===

1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938

2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x

===Naomi Tesfaiohannes===

1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013

2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003

===Ivy Macaraeg===

1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712

2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5

===Marcus Avila===

1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98

2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0

===John Nimmers-Minor===

1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005

2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006

[[Category:Group Projects]]
[[Category:Sulfiknights]]

Sulfiknights

2019-11-19T22:59:06Z

Jnimmers: /* Annotated Bibliography Sources */ Updated sources for annotated bib

{{Sulfiknights}}

==Data/Files==
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]

==Team Feedback==
===Naomi Tesfaiohannes===
Each team member should reflect on the team's progress:

*What worked?
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure.

*What didn't work?
My time management due to other coursework

*What will I do next to fix what didn't work?
Have a better control of what work I put in each day for this assignment

[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)

===Joey Nimmers-Minor===
*What worked?
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.
*What didn't work?
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week
*What will I do next to fix what didn't work?
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.

[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)

===Marcus Avila===
# What worked?
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.
# What didn't work?
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.
# What will I do next to fix what didn't work?
#* Next time I will allocate more time to the assignment.
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)

===DeLisa Madere===

'''What Worked?'''
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.

'''What didn't work?'''
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.

'''What will I do next to fix what didn't work?'''
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.

===Ivy Macaraeg===
*What worked?
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out.
*What didn't work?
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it.
*What will I do next to fix what didn't work?
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)

==Annotated Bibliography Sources==

===DeLisa Madere===

1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938

2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x

===Naomi Tesfaiohannes===

1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013

2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003

===Ivy Macaraeg===

1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712

2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5

===Marcus Avila===

1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98

2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0

===John Nimmers-Minor===

1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006

[[Category:Group Projects]]
[[Category:Sulfiknights]]

Jnimmers week 11

2019-11-19T02:31:51Z

Jnimmers: formatting

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

==Purpose==
*The purpose of this assignment was to further learn how to read a scientific journal and pull pertinent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Annotated Bibliographies==
=== Annotated Bibliography #1===

# Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
# Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
# Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
# Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
# Article is Open Access
# Availability: Online (PubMed,ePub, and PDF)
# Publisher: American Society for Microbiology Journals (scientific society), for-profit, not a member of the OAPA
# The journal began in 1899
# Peer-reviewed articles: Yes
# [https://aem.asm.org/content/board-editors Editorial Board]
# Impact factor: 5.311
# Primary research article
# [https://aem.asm.org/content/71/2/599/figures-only Figures and Data Tab]

===Annotated Bibliography #2===
# A new metabolic pathway of arsenite: arsenic-glutathione complexes are substrates for human arsenic methyltransferase Cyt19. DOI: 10.1007/s00204-004-0620-x
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15526190
# PubMed Central: Not available
# Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s00204-004-0620-x#enumeration
# Publisher Full Text (PDF): https://link.springer.com/content/pdf/10.1007%2Fs00204-004-0620-x.pdf
# Copyright: Springer-Verlag 2004
# Article is open access
# Availability: in print and online
# Publisher: Springer-Verlag (non-scientific society, mass publisher of scientific material,for-profit, not a member of the OAPA
# The Springer-Verlag media company was founded in 1842
# Peer-reviewed articles: yes
# Not Available
# Impact factor: 5.98
# Primary research article
# Data are not available.

==Database Searches==
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science.
# PubMed
#* What original keyword(s) did you use? How many results did you get?
#** I searched "arsenic metabolism and got 13,712 results.
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** I added the keywords yeast and did a search within 10 years and the search narrowed to 111 results
# Google Scholar
#* What original keyword(s) did you use? How many results did you get?
#** I searched for "arsenic metabolism and got 285,000 results
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** After including the keyword "yeast" in the search, I got 41,600 results
# Web of Science
#* What original keyword(s) did you use? How many results did you get?
#** I originally searched "arsenic toxicity yeast" and got 61 results.
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** After that, I searched "arsenic toxicity yeast" within the 61 results and added the "Highly Cited in Field" filter creating a search of 1 result.
* Use the advanced search functions for each of these three databases/tools and answer the following:
# PubMed
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** The most useful search was after setting the publish date range to 5 years.
# Google Scholar
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** Including the search must find a paper betweem 2007 and now because the original paper that my group in analyzing was published in 2007.
# Web of Science
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** I found the "Highly Cited in Field" filter the most useful to narrow down the search to a singular, highly regarded publishing.
Perform a prospective search on your article in the Web of Science and answer the following:
#* How many articles does this article cite?
#** 42 articles
#* How many articles cite this article?
#** 76 articles
===Reflection===
#The choice of keywords in a search has a major impact in the specificity of the results you get. One word can change the results from being as broad as all phylogenetic domains to something as simple as yeast or any other general species type.
#Pubmed is advantageous because most of the articles are from reliable and peer reviewed sources because the credentials required to be put on Pubmed are more stringent than the databases. The problem with PubMed is that it doesn't have very many articles from non-scientific sources, meaning that if one was to do a comparison of understanding between the scientific and commercial field, they would have to go elsewhere.
Google Scholar is good because of the massive selection of information available on the site, however, with such a large database comes the problem of reliability in terms of the journals, authors and articles found.
Web of Science is good because it allows students to access certain journal articles that may be hidden behind a paywall, however, the amount of articles found in Web of Science is very low in comparison to the other two databases simply based on the number of search results using an identical search terms(s)

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-19T02:26:47Z

Jnimmers: /* Database Searches */ finish reflection

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Annotated Bibliography #1====

# Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
# Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
# Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
# Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
# Article is Open Access
# Availability: Online (PubMed,ePub, and PDF)
# Publisher: American Society for Microbiology Journals (scientific society), for-profit, not a member of the OAPA
# The journal began in 1899
# Peer-reviewed articles: Yes
# [https://aem.asm.org/content/board-editors Editorial Board]
# Impact factor: 5.311
# Primary research article
# [https://aem.asm.org/content/71/2/599/figures-only Figures and Data Tab]

====Annotated Bibliography #2====
# A new metabolic pathway of arsenite: arsenic-glutathione complexes are substrates for human arsenic methyltransferase Cyt19. DOI: 10.1007/s00204-004-0620-x
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15526190
# PubMed Central: Not available
# Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s00204-004-0620-x#enumeration
# Publisher Full Text (PDF): https://link.springer.com/content/pdf/10.1007%2Fs00204-004-0620-x.pdf
# Copyright: Springer-Verlag 2004
# Article is open access
# Availability: in print and online
# Publisher: Springer-Verlag (non-scientific society, mass publisher of scientific material,for-profit, not a member of the OAPA
# The Springer-Verlag media company was founded in 1842
# Peer-reviewed articles: yes
# Not Available
# Impact factor: 5.98
# Primary research article
# Data are not available.

===Database Searches===
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science.
# PubMed
#* What original keyword(s) did you use? How many results did you get?
#** I searched "arsenic metabolism and got 13,712 results.
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** I added the keywords yeast and did a search within 10 years and the search narrowed to 111 results
# Google Scholar
#* What original keyword(s) did you use? How many results did you get?
#** I searched for "arsenic metabolism and got 285,000 results
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** After including the keyword "yeast" in the search, I got 41,600 results
# Web of Science
#* What original keyword(s) did you use? How many results did you get?
#** I originally searched "arsenic toxicity yeast" and got 61 results.
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** After that, I searched "arsenic toxicity yeast" within the 61 results and added the "Highly Cited in Field" filter creating a search of 1 result.
* Use the advanced search functions for each of these three databases/tools and answer the following:
# PubMed
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** The most useful search was after setting the publish date range to 5 years.
# Google Scholar
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** Including the search must find a paper betweem 2007 and now because the original paper that my group in analyzing was published in 2007.
# Web of Science
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** I found the "Highly Cited in Field" filter the most useful to narrow down the search to a singular, highly regarded publishing.
Perform a prospective search on your article in the Web of Science and answer the following:
#* How many articles does this article cite?
#** 42 articles
#* How many articles cite this article?
#** 76 articles
====Reflection====
#The choice of keywords in a search has a major impact in the specificity of the results you get. One word can change the results from being as broad as all phylogenetic domains to something as simple as yeast or any other general species type.
#Pubmed is advantageous because most of the articles are from reliable and peer reviewed sources because the credentials required to be put on Pubmed are more stringent than the databases. The problem with PubMed is that it doesn't have very many articles from non-scientific sources, meaning that if one was to do a comparison of understanding between the scientific and commercial field, they would have to go elsewhere.
Google Scholar is good because of the massive selection of information available on the site, however, with such a large database comes the problem of reliability in terms of the journals, authors and articles found.
Web of Science is good because it allows students to access certain journal articles that may be hidden behind a paywall, however, the amount of articles found in Web of Science is very low in comparison to the other two databases simply based on the number of search results using an identical search terms(s)

==Purpose==
*The purpose of this assignment was to further learn how to read a scientific journal and pull pertinent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-19T02:16:27Z

Jnimmers: update database answers

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Annotated Bibliography #1====

# Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
# Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
# Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
# Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
# Article is Open Access
# Availability: Online (PubMed,ePub, and PDF)
# Publisher: American Society for Microbiology Journals (scientific society), for-profit, not a member of the OAPA
# The journal began in 1899
# Peer-reviewed articles: Yes
# [https://aem.asm.org/content/board-editors Editorial Board]
# Impact factor: 5.311
# Primary research article
# [https://aem.asm.org/content/71/2/599/figures-only Figures and Data Tab]

====Annotated Bibliography #2====
# A new metabolic pathway of arsenite: arsenic-glutathione complexes are substrates for human arsenic methyltransferase Cyt19. DOI: 10.1007/s00204-004-0620-x
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15526190
# PubMed Central: Not available
# Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s00204-004-0620-x#enumeration
# Publisher Full Text (PDF): https://link.springer.com/content/pdf/10.1007%2Fs00204-004-0620-x.pdf
# Copyright: Springer-Verlag 2004
# Article is open access
# Availability: in print and online
# Publisher: Springer-Verlag (non-scientific society, mass publisher of scientific material,for-profit, not a member of the OAPA
# The Springer-Verlag media company was founded in 1842
# Peer-reviewed articles: yes
# Not Available
# Impact factor: 5.98
# Primary research article
# Data are not available.

===Database Searches===
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science.
# PubMed
#* What original keyword(s) did you use? How many results did you get?
#** I searched "arsenic metabolism and got 13,712 results.
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** I added the keywords yeast and did a search within 10 years and the search narrowed to 111 results
# Google Scholar
#* What original keyword(s) did you use? How many results did you get?
#** I searched for "arsenic metabolism and got 285,000 results
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** After including the keyword "yeast" in the search, I got 41,600 results
# Web of Science
#* What original keyword(s) did you use? How many results did you get?
#** I originally searched "arsenic toxicity yeast" and got 61 results.
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** After that, I searched "arsenic toxicity yeast" within the 61 results and added the "Highly Cited in Field" filter creating a search of 1 result.
* Use the advanced search functions for each of these three databases/tools and answer the following:
# PubMed
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** The most useful search was after setting the publish date range to 5 years.
# Google Scholar
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** Including the search must find a paper betweem 2007 and now because the original paper that my group in analyzing was published in 2007.
# Web of Science
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** I found the "Highly Cited in Field" filter the most useful to narrow down the search to a singular, highly regarded publishing.
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
====Reflection====
*The primary site used in order to find these articles was Google Scholar by searching the keywords: Arsenic Metabolism, which produced a total of 285,000 results. In order to specify my results, I then searched with the keywords: "Arsenic metabolism yeast"; in order to better find papers that shared greater similarity to the original, assigned paper. This search produced ~41,600results.
#The choice of keywords in a search has a major impact in the specificity of the results you get. One word can change the results from being as broad as all phylogenetic domains to something as simple as yeast or any other general species type.
#Pubmed is ad
==Purpose==
*The purpose of this assignment was to further learn how to read a scientific journal and pull pertinent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-19T02:11:16Z

Jnimmers: updated database search answers

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Annotated Bibliography #1====

# Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
# Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
# Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
# Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
# Article is Open Access
# Availability: Online (PubMed,ePub, and PDF)
# Publisher: American Society for Microbiology Journals (scientific society), for-profit, not a member of the OAPA
# The journal began in 1899
# Peer-reviewed articles: Yes
# [https://aem.asm.org/content/board-editors Editorial Board]
# Impact factor: 5.311
# Primary research article
# [https://aem.asm.org/content/71/2/599/figures-only Figures and Data Tab]

====Annotated Bibliography #2====
# A new metabolic pathway of arsenite: arsenic-glutathione complexes are substrates for human arsenic methyltransferase Cyt19. DOI: 10.1007/s00204-004-0620-x
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15526190
# PubMed Central: Not available
# Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s00204-004-0620-x#enumeration
# Publisher Full Text (PDF): https://link.springer.com/content/pdf/10.1007%2Fs00204-004-0620-x.pdf
# Copyright: Springer-Verlag 2004
# Article is open access
# Availability: in print and online
# Publisher: Springer-Verlag (non-scientific society, mass publisher of scientific material,for-profit, not a member of the OAPA
# The Springer-Verlag media company was founded in 1842
# Peer-reviewed articles: yes
# Not Available
# Impact factor: 5.98
# Primary research article
# Data are not available.

===Database Searches===
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science.
# PubMed
#* What original keyword(s) did you use? How many results did you get?
#** I searched "arsenic metabolism and got 13,712 results.
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** I added the keywords yeast and did a search within 10 years and the search narrowed to 111 results
# Google Scholar
#* What original keyword(s) did you use? How many results did you get?
#** I searched for "arsenic metabolism and got 285,000 results
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** After including the keyword "yeast" in the search, I got 41,600 results
# Web of Science
#* What original keyword(s) did you use? How many results did you get?
#** I originally searched "arsenic toxicity yeast" and got 61 results.
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** After that, I searched "arsenic toxicity yeast" within the 61 results and added the "Highly Cited in Field" filter creating a search of 1 result.
* Use the advanced search functions for each of these three databases/tools and answer the following:
# PubMed
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** The most useful search was after setting the publish date range to 5 years.
# Google Scholar
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** Including the search must find a paper betweem 2007 and now because the original paper that my group in analyzing was published in 2007.
# Web of Science
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** I found the "Highly Cited in Field" filter the most useful to narrow down the search to a singular, highly regarded publishing.

====Reflection====
*The primary site used in order to find these articles was Google Scholar by searching the keywords: Arsenic Metabolism, which produced a total of 285,000 results. In order to specify my results, I then searched with the keywords: "Arsenic metabolism yeast"; in order to better find papers that shared greater similarity to the original, assigned paper. This search produced ~41,600results.
#The choice of keywords in a search has a major impact in the specificity of the results you get. One word can change the results from being as broad as all phylogenetic domains to something as simple as yeast or any other general species type.
#Pubmed is ad
==Purpose==
*The purpose of this assignment was to further learn how to read a scientific journal and pull pertinent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-19T01:46:10Z

Jnimmers: /* Annotated Bibliography #2 */ Create second annotated bibliography

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Annotated Bibliography #1====

# Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
# Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
# Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
# Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
# Article is Open Access
# Availability: Online (PubMed,ePub, and PDF)
# Publisher: American Society for Microbiology Journals (scientific society), for-profit, not a member of the OAPA
# The journal began in 1899
# Peer-reviewed articles: Yes
# [https://aem.asm.org/content/board-editors Editorial Board]
# Impact factor: 5.311
# Primary research article
# [https://aem.asm.org/content/71/2/599/figures-only Figures and Data Tab]

====Annotated Bibliography #2====
# A new metabolic pathway of arsenite: arsenic-glutathione complexes are substrates for human arsenic methyltransferase Cyt19. DOI: 10.1007/s00204-004-0620-x
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15526190
# PubMed Central: Not available
# Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s00204-004-0620-x#enumeration
# Publisher Full Text (PDF): https://link.springer.com/content/pdf/10.1007%2Fs00204-004-0620-x.pdf
# Copyright: Springer-Verlag 2004
# Article is open access
# Availability: in print and online
# Publisher: Springer-Verlag (non-scientific society, mass publisher of scientific material,for-profit, not a member of the OAPA
# The Springer-Verlag media company was founded in 1842
# Peer-reviewed articles: yes
# Not Available
# Impact factor: 5.98
# Primary research article
# Data are not available.

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-19T01:35:19Z

Jnimmers: Created 2nd annotated bib

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Annotated Bibliography #1====

# Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
# Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
# Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
# Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
# Article is Open Access
# Availability: Online (PubMed,ePub, and PDF)
# Publisher: American Society for Microbiology Journals (scientific society), for-profit, not a member of the OAPA
# The journal began in 1899
# Peer-reviewed articles: Yes
# [https://aem.asm.org/content/board-editors Editorial Board]
# Impact factor: 5.311
# Primary research article
# [https://aem.asm.org/content/71/2/599/figures-only Figures and Data Tab]

====Annotated Bibliography #2====
# A new metabolic pathway of arsenite: arsenic-glutathione complexes are substrates for human arsenic methyltransferase Cyt19. DOI: 10.1007/s00204-004-0620-x
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15526190
# PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
# Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
# Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
# Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article);
# Article is not Open Access, but is freely available 2 months after publication, published in the United States, LMU did not pay for the article
# Availability: in print and online
# Publisher: American Society for Cell Biology (scientific society), non-profit, not a member of the OAPA
# The journal begain in 1989
# Peer-reviewed articles: yest
# [https://www.molbiolcell.org/editorial-board Editorial board].
# Impact factor: 3.512 (2017)
# Primary research article
# Data are not available (dead hyperlink)

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-19T01:23:25Z

Jnimmers: /* = Annotated Bibliography #2 */ delete section

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Annotated Bibliography #1====

# Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
# Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
# Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
# Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
# Article is Open Access
# Availability: Online (PubMed,ePub, and PDF)
# Publisher: American Society for Microbiology Journals (scientific society), for-profit, not a member of the OAPA
# The journal began in 1899
# Peer-reviewed articles: Yes
# [https://aem.asm.org/content/board-editors Editorial Board]
# Impact factor: 5.311
# Primary research article
# [https://aem.asm.org/content/71/2/599/figures-only Figures and Data Tab]

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Annotated Bibliography==
==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-19T01:23:07Z

Jnimmers: Added second annotated bib

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Annotated Bibliography #1====

# Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
# Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
# Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
# Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
# Article is Open Access
# Availability: Online (PubMed,ePub, and PDF)
# Publisher: American Society for Microbiology Journals (scientific society), for-profit, not a member of the OAPA
# The journal began in 1899
# Peer-reviewed articles: Yes
# [https://aem.asm.org/content/board-editors Editorial Board]
# Impact factor: 5.311
# Primary research article
# [https://aem.asm.org/content/71/2/599/figures-only Figures and Data Tab]

==== Annotated Bibliography #2===

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Annotated Bibliography==
==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-19T01:16:31Z

Jnimmers: /* Sample Bibliographic Entry */ updated title

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Annotated Bibliography #1====

# Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
# Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
# Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
# Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
# Article is Open Access
# Availability: Online (PubMed,ePub, and PDF)
# Publisher: American Society for Microbiology Journals (scientific society), for-profit, not a member of the OAPA
# The journal began in 1899
# Peer-reviewed articles: Yes
# [https://aem.asm.org/content/board-editors Editorial Board]
# Impact factor: 5.311
# Primary research article
# [https://aem.asm.org/content/71/2/599/figures-only Figures and Data Tab]

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Annotated Bibliography==
==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-19T01:16:02Z

Jnimmers: /* Sample Bibliographic Entry */ Updated data

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Sample Bibliographic Entry ====

# Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
# Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
# Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
# Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
# Article is Open Access
# Availability: Online (PubMed,ePub, and PDF)
# Publisher: American Society for Microbiology Journals (scientific society), for-profit, not a member of the OAPA
# The journal began in 1899
# Peer-reviewed articles: Yes
# [https://aem.asm.org/content/board-editors Editorial Board]
# Impact factor: 5.311
# Primary research article
# [https://aem.asm.org/content/71/2/599/figures-only Figures and Data Tab]

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Annotated Bibliography==
==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-19T01:14:00Z

Jnimmers: /* Sample Bibliographic Entry */ edit editorial board

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Sample Bibliographic Entry ====

# Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
# Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
# Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
# Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
# Article is Open Access
# Availability: Online (PubMed,ePub, and PDF)
# Publisher: American Society for Microbiology Journals (scientific society), for-profit, not a member of the OAPA
# The journal began in 1899
# Peer-reviewed articles: Yes
# [https://aem.asm.org/content/board-editors Editorial Board]
# Impact factor: Not found
# Primary research article
# Data are not available (dead hyperlink)

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Annotated Bibliography==
==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-19T01:11:53Z

Jnimmers: /* Sample Bibliographic Entry */ update impact factor

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Sample Bibliographic Entry ====

# Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
# Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
# Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
# Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
# Article is Open Access
# Availability: Online (PubMed,ePub, and PDF)
# Publisher: American Society for Microbiology Journals (scientific society), for-profit, not a member of the OAPA
# The journal began in 1899
# Peer-reviewed articles: Yes
# [https://www.ascb.org/about-ascb/staff/ Staff List]
# Impact factor: Not found
# Primary research article
# Data are not available (dead hyperlink)

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Annotated Bibliography==
==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-15T23:02:14Z

Jnimmers: /* Sample Bibliographic Entry */ updated 1st anotated bib

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Sample Bibliographic Entry ====

# Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
# Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
# Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
# Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
# Article is Open Access
# Availability: Online (PubMed,ePub, and PDF)
# Publisher: American Society for Microbiology Journals (scientific society), for-profit, not a member of the OAPA
# The journal began in 1899
# Peer-reviewed articles: Yes
# [https://www.molbiolcell.org/editorial-board Editorial board].
# Impact factor: 3.512 (2017)
# Primary research article
# Data are not available (dead hyperlink)

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Annotated Bibliography==
==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-15T22:23:51Z

Jnimmers: /* Sample Bibliographic Entry */ Update annotated bib

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Sample Bibliographic Entry ====

# Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
# Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
# Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
# Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
# Article is Open Access,
# Availability: in print and online
# Publisher: American Society for Cell Biology (scientific society), non-profit, not a member of the OAPA
# The journal begain in 1989
# Peer-reviewed articles: yest
# [https://www.molbiolcell.org/editorial-board Editorial board].
# Impact factor: 3.512 (2017)
# Primary research article
# Data are not available (dead hyperlink)

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Annotated Bibliography==
==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Sulfiknights

2019-11-14T08:08:30Z

Jnimmers: /* Joey Nimmers-Minor */ submit team jounral

Jnimmers week 11

2019-11-14T08:02:40Z

Jnimmers: invoke

{{Jnimmers}}

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Sample Bibliographic Entry ====

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

# Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. ''Molecular Biology of the Cell'', 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
# PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
# PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
# Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
# Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
# Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article);
# Article is not Open Access, but is freely available 2 months after publication, published in the United States, LMU did not pay for the article
# Availability: in print and online
# Publisher: American Society for Cell Biology (scientific society), non-profit, not a member of the OAPA
# The journal begain in 1989
# Peer-reviewed articles: yest
# [https://www.molbiolcell.org/editorial-board Editorial board].
# Impact factor: 3.512 (2017)
# Primary research article
# Data are not available (dead hyperlink)

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Annotated Bibliography==
==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-14T08:02:14Z

Jnimmers: added file

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Sample Bibliographic Entry ====

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

# Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. ''Molecular Biology of the Cell'', 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
# PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
# PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
# Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
# Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
# Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article);
# Article is not Open Access, but is freely available 2 months after publication, published in the United States, LMU did not pay for the article
# Availability: in print and online
# Publisher: American Society for Cell Biology (scientific society), non-profit, not a member of the OAPA
# The journal begain in 1989
# Peer-reviewed articles: yest
# [https://www.molbiolcell.org/editorial-board Editorial board].
# Impact factor: 3.512 (2017)
# Primary research article
# Data are not available (dead hyperlink)

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Annotated Bibliography==
==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Data and Files==
*[[Media: Biological_Databases_Presentation_-2.pptx]]

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

File:Biological Databases Presentation -2.pptx

2019-11-14T08:01:49Z

Jnimmers:

Jnimmers week 11

2019-11-14T07:26:36Z

Jnimmers: /* Outline of your journal article */ formatting

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Sample Bibliographic Entry ====

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

# Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. ''Molecular Biology of the Cell'', 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
# PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
# PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
# Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
# Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
# Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article);
# Article is not Open Access, but is freely available 2 months after publication, published in the United States, LMU did not pay for the article
# Availability: in print and online
# Publisher: American Society for Cell Biology (scientific society), non-profit, not a member of the OAPA
# The journal begain in 1989
# Peer-reviewed articles: yest
# [https://www.molbiolcell.org/editorial-board Editorial board].
# Impact factor: 3.512 (2017)
# Primary research article
# Data are not available (dead hyperlink)

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Annotated Bibliography==
==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-14T07:17:46Z

Jnimmers: Edit to conclusions

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Sample Bibliographic Entry ====

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

# Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. ''Molecular Biology of the Cell'', 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
# PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
# PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
# Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
# Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
# Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article);
# Article is not Open Access, but is freely available 2 months after publication, published in the United States, LMU did not pay for the article
# Availability: in print and online
# Publisher: American Society for Cell Biology (scientific society), non-profit, not a member of the OAPA
# The journal begain in 1989
# Peer-reviewed articles: yest
# [https://www.molbiolcell.org/editorial-board Editorial board].
# Impact factor: 3.512 (2017)
# Primary research article
# Data are not available (dead hyperlink)

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, the authors did not specify whether this particular strain was haploid or diploid.
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Annotated Bibliography==
==Conclusion==
*I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-14T07:09:51Z

Jnimmers: /* Acknowledgments */ Added quote

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Sample Bibliographic Entry ====

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

# Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. ''Molecular Biology of the Cell'', 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
# PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
# PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
# Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
# Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
# Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article);
# Article is not Open Access, but is freely available 2 months after publication, published in the United States, LMU did not pay for the article
# Availability: in print and online
# Publisher: American Society for Cell Biology (scientific society), non-profit, not a member of the OAPA
# The journal begain in 1989
# Peer-reviewed articles: yest
# [https://www.molbiolcell.org/editorial-board Editorial board].
# Impact factor: 3.512 (2017)
# Primary research article
# Data are not available (dead hyperlink)

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, the authors did not specify whether this particular strain was haploid or diploid.
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Annotated Bibliography==
==Conclusion==
==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:09, 13 November 2019 (PST)

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.

Jnimmers week 11

2019-11-14T06:57:39Z

Jnimmers: /* Outline of your journal article */ added figure 1

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).

=== Presentation Prep: Individual Journal Pages ===

In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.

# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own citation, to a book or URL.''''' Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
#* Online Biological Dictionaries
#** Web sites
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
#*** [http://www.geneontology.org Gene Ontology]
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
#** eBooks
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
## What is the main result presented in this paper?
## What is the importance or significance of this work?
## What were the limitations in previous studies that led them to perform this work?
## How did they treat the yeast cells (what experiment were they doing?)
## What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
## What media did they grow them in? What temperature? What type of incubator? For how long?
## What controls did they use?
## How many replicates did they perform per treatment or timepoint?
## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
## What mathematical/statistical method did they use to analyze the data?
## Are the data publicly available for download? From which web site?
##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
##* What do the X and Y axes represent?
##* How were the measurements made?
##* What trends are shown by the plots and what conclusions can you draw from the data?
## How does this work compare with previous studies?
## What are the important implications of this work?
## What future directions should the authors take?
## Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

=== Journal Club Presentation ===

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
** Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
** Outline slide (list of key ''messages'' for the talk)
** One or more introduction slides
** A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
** A summary/conclusion slide that is a reflection of the outline.
** Acknowledgments slide
** References slide
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

=== Annotated Bibliography ===

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

==== Resources ====

* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
* [http://scholar.google.com/ Google Scholar]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link]
* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
* [http://www.yeastgenome.org SGD]

==== Assignment ====

* Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
** Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
**# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
**# The link to the abstract from PubMed.
**# The link to the full text of the article in PubMedCentral (if not available, write N/A).
**# The link to the full text of the article (HTML format) from the publisher web site.
**# The link to the full PDF version of the article from the publisher web site.
**# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
**# How is the article available to you?
**#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
**#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
**#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
**#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
**# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
**# Who is the publisher of the journal?
**#* Is the publisher for-profit or non-profit?
**#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
**#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
**#* What country is the journal published in?
**# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
**# Are the articles in this journal peer-reviewed?
**# Provide a link to the scientific advisory board/editorial board of the journal.
**# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
**# Is the article a review or primary research article?
**# Are the data associated with this article available? If so, provide a link to the dataset.
* You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
*# Use a keyword search for the first three databases/tools and answer the following:
*#* PubMed
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get?
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite?
*#** How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==== Sample Bibliographic Entry ====

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

# Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. ''Molecular Biology of the Cell'', 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
# PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
# PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
# Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
# Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
# Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article);
# Article is not Open Access, but is freely available 2 months after publication, published in the United States, LMU did not pay for the article
# Availability: in print and online
# Publisher: American Society for Cell Biology (scientific society), non-profit, not a member of the OAPA
# The journal begain in 1989
# Peer-reviewed articles: yest
# [https://www.molbiolcell.org/editorial-board Editorial board].
# Impact factor: 3.512 (2017)
# Primary research article
# Data are not available (dead hyperlink)

==Purpose==
*The purpose of this assignment was to futher learn how to read a scientific journal and pull pertainent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

==10 definitions of terms==
# Concomitant
#* At the same time: describing drugs that are administered together or symptoms that occur during the same period.
# Promyelocyte,
#* A cell intermediate in development between a myeloblast and a myelocyte.
#GSH
#* Reduced glutathione
# Proteome
#* The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
# Basal
#* At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
# Thiol
#* An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
# Antimony/Antimonite (Sb)
#* The chemical element of atomic number 51, a brittle silvery-white metalloid.
# Isoenzyme
#* Each of two or more enzymes with identical function but different structure.
# Ubiquitinated
#* Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
# Motif
#* A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

*Definitions for all unknown/defined words were found on https://www.oxfordreference.com/
**Oxford Reference. (1970, January 1). Retrieved November 12, 2019, from https://www.oxfordreference.com/.

==Outline of your journal article==
# Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
#What is the main result presented in this paper?
#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
#What is the importance or significance of this work?
#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
#What were the limitations of previous studies that led them to perform this work?
#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
#How did they treat the yeast cells (what experiment were they doing?)
#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, the authors did not specify whether this particular strain was haploid or diploid.
#What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
#What controls did they use?
#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
#How many replicates did they perform per treatment or timepoint?
#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
#What mathematical/statistical method did they use to analyze the data?
#* The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
#Are the data publicly available for download? From which web site?
#* The data is publicly available for download [https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 here] doi: 10.1152
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. (What do the X and Y axes represent? How were the measurements made? What trends are shown by the plots and what conclusions) can you draw from the data?
#*Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
#*Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
#*Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
#*Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
#*Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
#*Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
#How does this work compare with previous studies?
#*This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
#What are the important implications of this work?
#* This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
#What future directions should the authors take?
#* Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
#Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

==Annotated Bibliography==
==Conclusion==
==Acknowledgments==
*I would like to acknowledge [[User:Kdahlquist | Dr. Kam D. Dahlquist]]
*Thank you to my group: the [[Sulfiknights]] | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.

==References==
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
* (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.