LMU BioDB 2019 - User contributions [en]

Template:Cdomin12

2019-12-12T20:00:41Z

Cdomin12: edited week 1

[[User:cdomin12|User Page]]

[[template: cdomin12]]

{| class="wikitable"
|-
!Assignment Page
!Individual Journal Entries
!Class Journal
|-
|[[Week 1]]
|[[cdomin12 Week 1]]
|[[Class Journal Week 1]]
|-
|[[Week 2]]
|[[cdomin12 Week 2]]
|[[Class Journal Week 2]]
|-
|[[Week 3]]
|[[RAD53 / YPL153C Week 3]]
|[[Class Journal Week 3]]
|-
|[[Week 4]]
|[[cdomin12 Week 4]]
|[[Class Journal Week 4]]
|-
|[[Week 5]]
|[[IMG/VR Week 5]]
|[[Class Journal Week 5]]
|-
|[[Week 6]]
|[[cdomin12 Week 6]]
|[[Class Journal Week 6]]
|-
|[[Week 7]]
|[[cdomin12 Week 7]]
|[[Class Journal Week 7]]
|-
|[[Week 8]]
|[[cdomin12 Week 8]]
|[[Class Journal Week 8]]
|-
|[[Week 9]]
|[[cdomin12 Week 9]]
|[[Class Journal Week 9]]
|-
|[[Week 10]]
|[[cdomin12 Week 10]]
|[[Class Journal Week 10]]
|-
|[[Week 11]]
|[[cdomin12 Week 11]]
|[[Skinny Genes]]
|-
|[[Week 12/13]]
|[[Skinny Genes Quality Assurance]]
|[[Skinny Genes]]
|-
|[[Week 15]]
|[[Skinny Genes Deliverables]]
|[[Skinny Genes]]
|}

[[category:Journal Entry]]

Skinny Genes Quality Assurance

2019-12-03T23:45:15Z

Cdomin12: /* Problems */ added milestone 6

==Datas and Files==
[[Media:Skinny Genes Editted Raw Data.xlsx | Skinny Genes Edited Raw Data]]

==Electronic Lab Notebook==

===Milestone 1===
*Annotated Bib completed for Tuesday due date individual journals according to Week 11/12 guidelines

===Milestone 2===
*Created presentation about the article
*We divided up the work into sections and each focused on our assigned task (each was designated a slide(s) and figure(s))
*Also, worked on annotated bibliography

===Milestone 3===
*deleted Gweight and Eweight since not conducive to our dataset
*changed "YORF" to "ID" and "Name" to "Standard Name"
*sample-data relationship table changed categories to "strain_LogFC_timepoint-replicate number"
*Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3, wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4 so that replicates are grouped together

===Milestone 4===
*The QAs worked on organizing the layout and naming the standard names and IDs. (Group worked alongside Prof. Dalquist due to complications)
*In essence, we put in a list of genes into the name translator and found ost of the IDs and standard names, but we had blanks for a good amount of genes.
*We used multiple websites which included: [http://www.yeastract.com/formorftogene.php "ORF List <-> Gene List"], [http://llama.mshri.on.ca/synergizer/translate/ Synergizer], [https://rdrr.io/bioc/ClusterJudge/man/convert_Yeast_SGDId_2_systematic.html Bioconductor package]
*We recently received all the names to move on with our work.
*We spoke with other groups to ensure that column headers were consistent with how other groups structured the data.
*Deleted duplicate data under alias names
*Filled in missing gaps for names

===Milestone 5===
*

===Problems===
*Data set had duplicate data as well as alias for the duplicate data
*Many IDs/Standard names still were missing
*Manual input was needed to resolve (along with Prof. Dalquist)
'''Data was no fully complete and research and conversion was needed to move the database project along'''

===Milestone 6===
*made sure that all of the rows of data were imported into the database for the expression table
*made sure that both the ID (SGD systematic name) and Standard Names were included in each expression table and correct

{{template:cdomin12}}
{{jcowan4}}
[[category:Skinny Genes]]
[[category:Group Projects]]

==Acknowledgments==
1. I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment.

2. "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 14:00, 25 November 2019 (PST)

==References==
*Week 12/13. Retrieved November 25, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Skinny Genes Quality Assurance

2019-12-03T23:21:17Z

Cdomin12: added milestone 4 data

==Datas and Files==
[[Media:Skinny Genes Editted Raw Data.xlsx | Skinny Genes Edited Raw Data]]

==Electronic Lab Notebook==

===Milestone 1===
*Annotated Bib completed for Tuesday due date individual journals according to Week 11/12 guidelines

===Milestone 2===
*Created presentation about the article
*We divided up the work into sections and each focused on our assigned task (each was designated a slide(s) and figure(s))
*Also, worked on annotated bibliography

===Milestone 3===
*deleted Gweight and Eweight since not conducive to our dataset
*changed "YORF" to "ID" and "Name" to "Standard Name"
*sample-data relationship table changed categories to "strain_LogFC_timepoint-replicate number"
*Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3, wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4 so that replicates are grouped together

===Milestone 4===
*The QAs worked on organizing the layout and naming the standard names and IDs. (Group worked alongside Prof. Dalquist due to complications)
*In essence, we put in a list of genes into the name translator and found ost of the IDs and standard names, but we had blanks for a good amount of genes.
*We used multiple websites which included: [http://www.yeastract.com/formorftogene.php "ORF List <-> Gene List"], [http://llama.mshri.on.ca/synergizer/translate/ Synergizer], [https://rdrr.io/bioc/ClusterJudge/man/convert_Yeast_SGDId_2_systematic.html Bioconductor package]
*We recently received all the names to move on with our work.
*We spoke with other groups to ensure that column headers were consistent with how other groups structured the data.
*Deleted duplicate data under alias names
*Filled in missing gaps for names

===Milestone 5===
*

===Problems===
*Data set had duplicate data as well as alias for the duplicate data
*Many IDs/Standard names still were missing
*Manual input was needed to resolve (along with Prof. Dalquist)
'''Data was no fully complete and research and conversion was needed to move the database project along'''

{{template:cdomin12}}
{{jcowan4}}
[[category:Skinny Genes]]
[[category:Group Projects]]

==Acknowledgments==
1. I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment.

2. "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 14:00, 25 November 2019 (PST)

==References==
*Week 12/13. Retrieved November 25, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Skinny Genes Quality Assurance

2019-12-03T23:18:47Z

Cdomin12: /* Milestone 5 */ added bullet

==Datas and Files==
[[Media:Skinny Genes Editted Raw Data.xlsx | Skinny Genes Edited Raw Data]]

==Electronic Lab Notebook==

===Milestone 1===
*Annotated Bib completed for Tuesday due date individual journals according to Week 11/12 guidelines

===Milestone 2===
*Created presentation about the article
*We divided up the work into sections and each focused on our assigned task (each was designated a slide(s) and figure(s))
*Also, worked on annotated bibliography

===Milestone 3===
*deleted Gweight and Eweight since not conducive to our dataset
*changed "YORF" to "ID" and "Name" to "Standard Name"
*sample-data relationship table changed categories to "strain_LogFC_timepoint-replicate number"
*Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3, wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4 so that replicates are grouped together

===Milestone 4===
*The QAs worked on organizing the layout and naming the standard names and IDs. (Group worked alongside Prof. Dalquist due to complications)
*In essence, we put in a list of genes into the name translator and found ost of the IDs and standard names, but we had blanks for a good amount of genes.
*We used multiple websites which included: [http://www.yeastract.com/formorftogene.php "ORF List <-> Gene List"], [http://llama.mshri.on.ca/synergizer/translate/ Synergizer], [https://rdrr.io/bioc/ClusterJudge/man/convert_Yeast_SGDId_2_systematic.html Bioconductor package]
*We recently received all the names to move on with our work.

===Milestone 5===
*

===Problems===
*Data set had duplicate data as well as alias for the duplicate data
*Many IDs/Standard names still were missing
*Manual input was needed to resolve (along with Prof. Dalquist)
'''Data was no fully complete and research and conversion was needed to move the database project along'''

{{template:cdomin12}}
{{jcowan4}}
[[category:Skinny Genes]]
[[category:Group Projects]]

==Acknowledgments==
1. I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment.

2. "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 14:00, 25 November 2019 (PST)

==References==
*Week 12/13. Retrieved November 25, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Skinny Genes

2019-12-03T23:13:14Z

Cdomin12: /* Files */ added file

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Files==
[[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample to Data Relationship Table]]

[[Media: Ymesfin_Yeast_Potassium_Starvation_Journal_Club_2.pdf | Journal Club Presentation]]

[[Media: Ymesfin_Barreto_ANOVA_no_duplicates_-_Copy.xlsx | ANOVA Data (no duplicates)]]

[[Media:Ymesfin Barreto ANOVA no duplicates and revised headers.xlsx | ANOVA Data (most updated no duplicates, new headers)]]

==Annotated Bibliography==
#Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. ''PLoS biology'', ''4''(11), e351. DOI: 10.1371/journal.pbio.0040351
#Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. ''FEMS yeast research'', 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x
#Christina: Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. ''BMC genomics'', ''15''(1), 1040. doi:10.1186/1471-2164-15-1040
#Christina: Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. ''FEMS yeast research'', ''12''(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
#Mihir: Canadell, D., González, A., Casado, C., & Ariño, J. (2015). Functional interactions between potassium and phosphate homeostasis in Saccharomyces cerevisiae. ''Molecular microbiology'', ''95''(3), 555-572. DOI: 10.1111/mmi.12886
#Mihir: Kahm, M., Navarrete, C., Llopis-Torregrosa, V., Herrera, R., Barreto, L., Yenush, L., … Kschischo, M. (2012). Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling. ''PLoS Computational Biology'', ''8''(6). doi: 10.1371/journal.pcbi.1002548
#David: Gladfelter, A.S., Kozubowski, L., Zyla, T.R., and Lew, D.J. (2005) Interplay between septin organization, cell cycle and cell shape in yeast. J Cell Sci 118: 1617–1628. DOI: 10.1242/jcs.02286
#David: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI: 10.1534/genetics.111.128314
#Jonar: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351.
#Jonar: Udensi, U. K., & Tchounwou, P. B. (2017). Potassium Homeostasis, Oxidative Stress, and Human Disease. International journal of clinical and experimental physiology, 4(3), 111–122. doi:10.4103/ijcep.ijcep_43_17

==Schedule==
{| class="wikitable"
|-
! Tasks
! Date
|-
| Team Journal Assignment: Methods and Results thus far
*Project Manager: Create Sample/Data Relationship Table
*Data Analysis: download raw data, run ANOVA
*QA and Coder: standardize the ID and Standard Names of the genes
| 11/21/19
|-
|
| 11/26/19
|-
|
| 11/28/19
|-
|
| 12/03/19
|-
|
| 12/05/19
|-
| Final Presentation
| 12/10/19
|-
| Report submitted
| 12/13/19
|-
|}

==Executive Summaries==
===Week 11===
====Aby's Reflection====
*Progress: This week we created an outline for our presentation and formatted the presentation for the journal club.
*#What worked? Responsibilities for the presentation was delegated well so that everyone contributed an equal share.
*#What didn't work? It was difficult to work around everyone's schedules so that we could meet up and work together.
*#What will I do next to fix what didn't work? We will need to communicate with one another better and anticipate the amount of time necessary to complete the assignment as a group so that our schedules don't interfere with the groupwork.
====Jonar's Reflection====
*Progress:
*#What worked? Everybody in the group was responsive and we were able to agree on and start our presentation early. The delegation of work and support worked well.
*#What didn't work? Due to time constraints with multiple people, finding time for all five members was a little difficult
*#What will I do next to fix what didn't work? We can plan an early meeting time or we can delegate tasks and plan a little meeting just to go over the work.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 23:59, 13 November 2019 (PST)
====Christina's Reflection====
*Progress:
*#What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
*#What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
*#What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.

[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 00:51, 26 November 2019 (PST)

====Mihir's Reflection====
*Progress:
*#What worked?
*#* We were able to communicate well, and we all worked together to help each other understand and excel in our tasks. Furthermore, we figured out methods of communication and how to best work with each other remotely.
*#What didn't work?
*#* Scheduling times to work on this assignment was pretty hectic this week, given that each member of our team had an unusual number of projects, midterms, homework, and extra-curricular activities this week. We could not all meet together outside of class.
*#What will I do next to fix what didn't work?
*#* Hopefully, this was a one-time occurrence and none of us will be as busy as we were this week. However, other than that, we could also improve our responsiveness in our team's group message, as that is our sole method of communication outside of class.
[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 20:16, 13 November 2019 (PST)
====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:01, 26 November 2019 (PST)

===Week 12/13===
====Aby's Reflection====
*Progress: This week David and I statistically analyzed the data using an ANOVA.
*#What worked? The ANOVA was relatively easy to code using Excel.
*#What didn't work? We were hoping to run STEM this week as well but had difficulty creating the ID's and Standard Names for the data.
*#What will I do next to fix what didn't work? We reached out to Dr. Dahlquist in regards to changing the ID's and Standard Names and thus, we should be able to run STEM after a few more edits.
[[User:Ymesfin|Ymesfin]] ([[User talk:Ymesfin|talk]]) 11:10, 25 November 2019 (PST)

====Jonar's Reflection====
*Progress:
*#What worked? What worked was how we divided what needed to be done and how we were in constant communication with each other.
*#What didn't work? Early on we had problems with the standard name and gene ID, which caused us to get a little anxious about what were supposed to do. In essence, we needed to ask for help. (Which was done later on but not early enough)
*#What will I do next to fix what didn't work? Overall, I think we are handling the project well but if we had to work on something it would probably better timing for project management.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 19:25, 25 November 2019 (PST)

====Christina's Reflection====
*Progress:
*#What worked? We were able to communicate in class to effectively figure out what we needs to be done on a timeline.
*#What didn't work? It took a long to get past the step of finalizing the data into columns that had both the IDs and standard names. However, this was due to the fact that the data sheet had many repeated genes and a variety of different names for genes.
*#What will I do next to fix what didn't work? Communicate better on how we can solve this problem as a group.

====Mihir's Reflection====
*Progress:
** This week I worked on creating the format for encoding the entries into the database.

#What worked?
#*This weekend we split up into our different guilds. I think that we worked well in those guilds, and it seemed like the pairs of Jonar and Christina and David and Aby worked well.
#What didn't work?
#*I think that this week, we were a little too fractured because of how immediately we were required to split up following the official beginning of the project. There was a lack of communication when we were discussing how to fix the gene names of the spreadsheet. Even though our communication was good last week, because of a variety of reasons I think that we were not able to effectively relate information regarding our data and formatting to one another.
#What will I do next to fix what didn't work?
#*I think this next week, we should take the time talk to each other regarding what he had accomplished between work sessions and what we planned on working on during the upcoming work session.

====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:02, 26 November 2019 (PST)

==Milestones==

====Milestones 1====
====Milestones 2====
====Milestones 3====
====Milestones 4====
====Milestones 5====
====Milestones 6====
====Milestones 7====

File:Ymesfin Barreto ANOVA no duplicates and revised headers.xlsx

2019-12-03T23:12:10Z

Cdomin12:

Skinny Genes

2019-11-26T08:51:57Z

Cdomin12: /* Christina's Reflection */ added sig

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Files==
[[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample to Data Relationship Table]]

[[Media: Ymesfin_Yeast_Potassium_Starvation_Journal_Club_2.pdf | Journal Club Presentation]]

[[Media:Skinny Genes Editted Raw Data.xlsx | Skinny Genes Edited Raw Data]]

[[Media:Editted_Raw_Data.xlsx | Skinny Genes Raw Data (Updated)]]

==Annotated Bibliography==
#Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. ''PLoS biology'', ''4''(11), e351. DOI: 10.1371/journal.pbio.0040351
#Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. ''FEMS yeast research'', 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x
#Christina: Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. ''BMC genomics'', ''15''(1), 1040. doi:10.1186/1471-2164-15-1040
#Christina: Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. ''FEMS yeast research'', ''12''(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
#Mihir: Canadell, D., González, A., Casado, C., & Ariño, J. (2015). Functional interactions between potassium and phosphate homeostasis in Saccharomyces cerevisiae. ''Molecular microbiology'', ''95''(3), 555-572. DOI: 10.1111/mmi.12886
#Mihir: Kahm, M., Navarrete, C., Llopis-Torregrosa, V., Herrera, R., Barreto, L., Yenush, L., … Kschischo, M. (2012). Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling. ''PLoS Computational Biology'', ''8''(6). doi: 10.1371/journal.pcbi.1002548
#David: Gladfelter, A.S., Kozubowski, L., Zyla, T.R., and Lew, D.J. (2005) Interplay between septin organization, cell cycle and cell shape in yeast. J Cell Sci 118: 1617–1628. DOI: 10.1242/jcs.02286
#David: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI: 10.1534/genetics.111.128314
#Jonar: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351.
#Jonar: Udensi, U. K., & Tchounwou, P. B. (2017). Potassium Homeostasis, Oxidative Stress, and Human Disease. International journal of clinical and experimental physiology, 4(3), 111–122. doi:10.4103/ijcep.ijcep_43_17

==Schedule==
{| class="wikitable"
|-
! Tasks
! Date
|-
| Team Journal Assignment: Methods and Results thus far
*Project Manager: Create Sample/Data Relationship Table
*Data Analysis: download raw data, run ANOVA
*QA and Coder: standardize the ID and Standard Names of the genes
| 11/21/19
|-
|
| 11/26/19
|-
|
| 11/28/19
|-
|
| 12/03/19
|-
|
| 12/05/19
|-
| Final Presentation
| 12/10/19
|-
| Report submitted
| 12/13/19
|-
|}

==Executive Summaries==
===Week 11===
====Aby's Reflection====
*Progress: This week we created an outline for our presentation and formatted the presentation for the journal club.
*#What worked? Responsibilities for the presentation was delegated well so that everyone contributed an equal share.
*#What didn't work? It was difficult to work around everyone's schedules so that we could meet up and work together.
*#What will I do next to fix what didn't work? We will need to communicate with one another better and anticipate the amount of time necessary to complete the assignment as a group so that our schedules don't interfere with the groupwork.
====Jonar's Reflection====
*Progress:
*#What worked? Everybody in the group was responsive and we were able to agree on and start our presentation early. The delegation of work and support worked well.
*#What didn't work? Due to time constraints with multiple people, finding time for all five members was a little difficult
*#What will I do next to fix what didn't work? We can plan an early meeting time or we can delegate tasks and plan a little meeting just to go over the work.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 23:59, 13 November 2019 (PST)
====Christina's Reflection====
*Progress:
*#What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
*#What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
*#What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.

[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 00:51, 26 November 2019 (PST)

====Mihir's Reflection====
*Progress:
*#What worked?
*#* We were able to communicate well, and we all worked together to help each other understand and excel in our tasks. Furthermore, we figured out methods of communication and how to best work with each other remotely.
*#What didn't work?
*#* Scheduling times to work on this assignment was pretty hectic this week, given that each member of our team had an unusual number of projects, midterms, homework, and extra-curricular activities this week. We could not all meet together outside of class.
*#What will I do next to fix what didn't work?
*#* Hopefully, this was a one-time occurrence and none of us will be as busy as we were this week. However, other than that, we could also improve our responsiveness in our team's group message, as that is our sole method of communication outside of class.
[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 20:16, 13 November 2019 (PST)
====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:01, 26 November 2019 (PST)

===Week 12/13===
====Aby's Reflection====
*Progress: This week David and I statistically analyzed the data using an ANOVA.
*#What worked? The ANOVA was relatively easy to code using Excel.
*#What didn't work? We were hoping to run STEM this week as well but had difficulty creating the ID's and Standard Names for the data.
*#What will I do next to fix what didn't work? We reached out to Dr. Dahlquist in regards to changing the ID's and Standard Names and thus, we should be able to run STEM after a few more edits.
[[User:Ymesfin|Ymesfin]] ([[User talk:Ymesfin|talk]]) 11:10, 25 November 2019 (PST)

====Jonar's Reflection====
*Progress:
*#What worked? What worked was how we divided what needed to be done and how we were in constant communication with each other.
*#What didn't work? Early on we had problems with the standard name and gene ID, which caused us to get a little anxious about what were supposed to do. In essence, we needed to ask for help. (Which was done later on but not early enough)
*#What will I do next to fix what didn't work? Overall, I think we are handling the project well but if we had to work on something it would probably better timing for project management.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 19:25, 25 November 2019 (PST)

====Christina's Reflection====
*Progress:
*#What worked? We were able to communicate in class to effectively figure out what we needs to be done on a timeline.
*#What didn't work? It took a long to get past the step of finalizing the data into columns that had both the IDs and standard names. However, this was due to the fact that the data sheet had many repeated genes and a variety of different names for genes.
*#What will I do next to fix what didn't work? Communicate better on how we can solve this problem as a group.

====Mihir's Reflection====
*Progress:
** This week I worked on creating the format for encoding the entries into the database.

#What worked?
#*This weekend we split up into our different guilds. I think that we worked well in those guilds, and it seemed like the pairs of Jonar and Christina and David and Aby worked well.
#What didn't work?
#*I think that this week, we were a little too fractured because of how immediately we were required to split up following the official beginning of the project. There was a lack of communication when we were discussing how to fix the gene names of the spreadsheet. Even though our communication was good last week, because of a variety of reasons I think that we were not able to effectively relate information regarding our data and formatting to one another.
#What will I do next to fix what didn't work?
#*I think this next week, we should take the time talk to each other regarding what he had accomplished between work sessions and what we planned on working on during the upcoming work session.

====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:02, 26 November 2019 (PST)

==Milestones==

====Milestones 1====
====Milestones 2====
====Milestones 3====
====Milestones 4====
====Milestones 5====
====Milestones 6====
====Milestones 7====

Skinny Genes

2019-11-26T08:51:46Z

Cdomin12: /* Christina's Reflection */ added

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Files==
[[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample to Data Relationship Table]]

[[Media: Ymesfin_Yeast_Potassium_Starvation_Journal_Club_2.pdf | Journal Club Presentation]]

[[Media:Skinny Genes Editted Raw Data.xlsx | Skinny Genes Edited Raw Data]]

[[Media:Editted_Raw_Data.xlsx | Skinny Genes Raw Data (Updated)]]

==Annotated Bibliography==
#Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. ''PLoS biology'', ''4''(11), e351. DOI: 10.1371/journal.pbio.0040351
#Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. ''FEMS yeast research'', 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x
#Christina: Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. ''BMC genomics'', ''15''(1), 1040. doi:10.1186/1471-2164-15-1040
#Christina: Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. ''FEMS yeast research'', ''12''(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
#Mihir: Canadell, D., González, A., Casado, C., & Ariño, J. (2015). Functional interactions between potassium and phosphate homeostasis in Saccharomyces cerevisiae. ''Molecular microbiology'', ''95''(3), 555-572. DOI: 10.1111/mmi.12886
#Mihir: Kahm, M., Navarrete, C., Llopis-Torregrosa, V., Herrera, R., Barreto, L., Yenush, L., … Kschischo, M. (2012). Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling. ''PLoS Computational Biology'', ''8''(6). doi: 10.1371/journal.pcbi.1002548
#David: Gladfelter, A.S., Kozubowski, L., Zyla, T.R., and Lew, D.J. (2005) Interplay between septin organization, cell cycle and cell shape in yeast. J Cell Sci 118: 1617–1628. DOI: 10.1242/jcs.02286
#David: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI: 10.1534/genetics.111.128314
#Jonar: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351.
#Jonar: Udensi, U. K., & Tchounwou, P. B. (2017). Potassium Homeostasis, Oxidative Stress, and Human Disease. International journal of clinical and experimental physiology, 4(3), 111–122. doi:10.4103/ijcep.ijcep_43_17

==Schedule==
{| class="wikitable"
|-
! Tasks
! Date
|-
| Team Journal Assignment: Methods and Results thus far
*Project Manager: Create Sample/Data Relationship Table
*Data Analysis: download raw data, run ANOVA
*QA and Coder: standardize the ID and Standard Names of the genes
| 11/21/19
|-
|
| 11/26/19
|-
|
| 11/28/19
|-
|
| 12/03/19
|-
|
| 12/05/19
|-
| Final Presentation
| 12/10/19
|-
| Report submitted
| 12/13/19
|-
|}

==Executive Summaries==
===Week 11===
====Aby's Reflection====
*Progress: This week we created an outline for our presentation and formatted the presentation for the journal club.
*#What worked? Responsibilities for the presentation was delegated well so that everyone contributed an equal share.
*#What didn't work? It was difficult to work around everyone's schedules so that we could meet up and work together.
*#What will I do next to fix what didn't work? We will need to communicate with one another better and anticipate the amount of time necessary to complete the assignment as a group so that our schedules don't interfere with the groupwork.
====Jonar's Reflection====
*Progress:
*#What worked? Everybody in the group was responsive and we were able to agree on and start our presentation early. The delegation of work and support worked well.
*#What didn't work? Due to time constraints with multiple people, finding time for all five members was a little difficult
*#What will I do next to fix what didn't work? We can plan an early meeting time or we can delegate tasks and plan a little meeting just to go over the work.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 23:59, 13 November 2019 (PST)
====Christina's Reflection====
*Progress:
*#What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
*#What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
*#What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.
====Mihir's Reflection====
*Progress:
*#What worked?
*#* We were able to communicate well, and we all worked together to help each other understand and excel in our tasks. Furthermore, we figured out methods of communication and how to best work with each other remotely.
*#What didn't work?
*#* Scheduling times to work on this assignment was pretty hectic this week, given that each member of our team had an unusual number of projects, midterms, homework, and extra-curricular activities this week. We could not all meet together outside of class.
*#What will I do next to fix what didn't work?
*#* Hopefully, this was a one-time occurrence and none of us will be as busy as we were this week. However, other than that, we could also improve our responsiveness in our team's group message, as that is our sole method of communication outside of class.
[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 20:16, 13 November 2019 (PST)
====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:01, 26 November 2019 (PST)

===Week 12/13===
====Aby's Reflection====
*Progress: This week David and I statistically analyzed the data using an ANOVA.
*#What worked? The ANOVA was relatively easy to code using Excel.
*#What didn't work? We were hoping to run STEM this week as well but had difficulty creating the ID's and Standard Names for the data.
*#What will I do next to fix what didn't work? We reached out to Dr. Dahlquist in regards to changing the ID's and Standard Names and thus, we should be able to run STEM after a few more edits.
[[User:Ymesfin|Ymesfin]] ([[User talk:Ymesfin|talk]]) 11:10, 25 November 2019 (PST)

====Jonar's Reflection====
*Progress:
*#What worked? What worked was how we divided what needed to be done and how we were in constant communication with each other.
*#What didn't work? Early on we had problems with the standard name and gene ID, which caused us to get a little anxious about what were supposed to do. In essence, we needed to ask for help. (Which was done later on but not early enough)
*#What will I do next to fix what didn't work? Overall, I think we are handling the project well but if we had to work on something it would probably better timing for project management.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 19:25, 25 November 2019 (PST)

====Christina's Reflection====
*Progress:
*#What worked? We were able to communicate in class to effectively figure out what we needs to be done on a timeline.
*#What didn't work? It took a long to get past the step of finalizing the data into columns that had both the IDs and standard names. However, this was due to the fact that the data sheet had many repeated genes and a variety of different names for genes.
*#What will I do next to fix what didn't work? Communicate better on how we can solve this problem as a group.

====Mihir's Reflection====
*Progress:
** This week I worked on creating the format for encoding the entries into the database.

#What worked?
#*This weekend we split up into our different guilds. I think that we worked well in those guilds, and it seemed like the pairs of Jonar and Christina and David and Aby worked well.
#What didn't work?
#*I think that this week, we were a little too fractured because of how immediately we were required to split up following the official beginning of the project. There was a lack of communication when we were discussing how to fix the gene names of the spreadsheet. Even though our communication was good last week, because of a variety of reasons I think that we were not able to effectively relate information regarding our data and formatting to one another.
#What will I do next to fix what didn't work?
#*I think this next week, we should take the time talk to each other regarding what he had accomplished between work sessions and what we planned on working on during the upcoming work session.

====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:02, 26 November 2019 (PST)

==Milestones==

====Milestones 1====
====Milestones 2====
====Milestones 3====
====Milestones 4====
====Milestones 5====
====Milestones 6====
====Milestones 7====

Skinny Genes Quality Assurance

2019-11-25T22:00:53Z

Cdomin12: /* Acknowledgments */ added space

==Datas and Files==

==Electronic Lab Notebook==

===Milestone 1===
*Annotated Bib completed for Tuesday due date individual journals according to Week 11/12 guidelines

===Milestone 2===

===Milestone 3===
*deleted Gweight and Eweight since not conducive to our dataset
*changed "YORF" to "ID" and "Name" to "Standard Name"
*sample-data relationship table changed categories to "strain_LogFC_timepoint-replicate number"
*Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3, wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4 so that replicates are grouped together

===Milestone 4===

{{template:cdomin12}}
{{jcowan4}}
[[category:Skinny Genes]]
[[category:Group Projects]]

==Acknowledgments==
1. I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment.

2. "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 14:00, 25 November 2019 (PST)

==References==
*Week 12/13. Retrieved November 25, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Skinny Genes Quality Assurance

2019-11-25T22:00:41Z

Cdomin12: /* References */ deleted *

==Datas and Files==

==Electronic Lab Notebook==

===Milestone 1===
*Annotated Bib completed for Tuesday due date individual journals according to Week 11/12 guidelines

===Milestone 2===

===Milestone 3===
*deleted Gweight and Eweight since not conducive to our dataset
*changed "YORF" to "ID" and "Name" to "Standard Name"
*sample-data relationship table changed categories to "strain_LogFC_timepoint-replicate number"
*Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3, wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4 so that replicates are grouped together

===Milestone 4===

{{template:cdomin12}}
{{jcowan4}}
[[category:Skinny Genes]]
[[category:Group Projects]]

==Acknowledgments==
1. I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment.
2. "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 14:00, 25 November 2019 (PST)

==References==
*Week 12/13. Retrieved November 25, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Skinny Genes Quality Assurance

2019-11-25T22:00:30Z

Cdomin12: added acknowledgments and references

==Datas and Files==

==Electronic Lab Notebook==

===Milestone 1===
*Annotated Bib completed for Tuesday due date individual journals according to Week 11/12 guidelines

===Milestone 2===

===Milestone 3===
*deleted Gweight and Eweight since not conducive to our dataset
*changed "YORF" to "ID" and "Name" to "Standard Name"
*sample-data relationship table changed categories to "strain_LogFC_timepoint-replicate number"
*Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3, wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4 so that replicates are grouped together

===Milestone 4===

{{template:cdomin12}}
{{jcowan4}}
[[category:Skinny Genes]]
[[category:Group Projects]]

==Acknowledgments==
1. I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment.
2. "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 14:00, 25 November 2019 (PST)

==References==
**Week 12/13. Retrieved November 25, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Skinny Genes Quality Assurance

2019-11-25T21:52:03Z

Cdomin12: datas and files added

Template:Skinny Genes

2019-11-21T23:40:01Z

Cdomin12: added skinny genes quality assurance

{| class="wikitable" style="width: 100%; text-align: center"
! colspan="8"|Skinny Genes Links
|-
! rowspan="2"|[[Main Page|BIOL Databases Main Page]]
! rowspan="2"|[[Skinny Genes|Skinny Genes Project]]
! rowspan="2"|[[Template:Skinny Genes|Skinny Genes Template Page]]
! Members
| '''Project Manager & Data Analysis: '''[[User:ymesfin| Yeabsira Mesfin]]
| '''Quality Assurance:''' [[User:Jcowan4|Jonar Cowan]] & [[User:Cdomin12|Christina Dominguez]]
| '''Data Analysis:''' [[User:dramir36| David Ramirez]]
| '''Coder:''' [[User:msamdars| Mihir Samdarshi]]
|-
! Assignment Pages
| [[Week 11]]
| [[Week 12/13]]
| [[Week 15]]
|}

[[Skinny Genes Quality Assurance]]

[[Category: Group Projects]]

[[Category:Skinny Genes]]

[[Category:Group Projects]]

Skinny Genes Quality Assurance

2019-11-21T23:36:58Z

Cdomin12: /* Milestone 1 */ added description

==Electronic Lab Notebook==

===Milestone 1===
*Annotated Bib completed for Tuesday due date individual journals according to Week 11/12 guidelines

===Milestone 2===

===Milestone 3===
*deleted Gweight and Eweight since not conducive to our dataset
*changed "YORF" to "ID" and "Name" to "Standard Name"
*sample-data relationship table changed categories to "strain_LogFC_timepoint-replicate number"
*Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3, wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4 so that replicates are grouped together

===Milestone 4===

{{template:cdomin12}}
{{jcowan4}}
[[category:Skinny Genes]]
[[category:Group Projects]]

Skinny Genes Quality Assurance

2019-11-21T23:01:03Z

Cdomin12: added categories

{{template:cdomin12}}

[[category:Skinny Genes]]
[[category:Group Projects]]+

==Electronic Lab Notebook==

===Milestone 1===

===Milestone 2===

===Milestone 3===
*deleted Gweight and Eweight since not conducive to our dataset
*changed "YORF" to "ID" and "Name" to "Standard Name"
*sample-data relationship table changed categories to "strain_LogFC_timepoint-replicate number"
*Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3, wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4 so that replicates are grouped together

===Milestone 4===

Template:Cdomin12

2019-11-21T22:59:37Z

Cdomin12: changed week 12/13 and 15

[[User:cdomin12|User Page]]

[[template: cdomin12]]

{| class="wikitable"
|-
!Assignment Page
!Individual Journal Entries
!Class Journal
|-
|[[Week 1]]
|[[cdomin12 Week 1]]
|[[Class Journal Week 1]]
|-
|[[Week 2]]
|[[cdomin12 Week 2]]
|[[Class Journal Week 2]]
|-
|[[Week 3]]
|[[RAD53 / YPL153C Week 3]]
|[[Class Journal Week 3]]
|-
|[[Week 4]]
|[[cdomin12 Week 4]]
|[[Class Journal Week 4]]
|-
|[[Week 5]]
|[[IMG/VR Week 5]]
|[[Class Journal Week 5]]
|-
|[[Week 6]]
|[[cdomin12 Week 6]]
|[[Class Journal Week 6]]
|-
|[[Week 7]]
|[[cdomin12 Week 7]]
|[[Class Journal Week 7]]
|-
|[[Week 8]]
|[[cdomin12 Week 8]]
|[[Class Journal Week 8]]
|-
|[[Week 9]]
|[[cdomin12 Week 9]]
|[[Class Journal Week 9]]
|-
|[[Week 10]]
|[[cdomin12 Week 10]]
|[[Class Journal Week 10]]
|-
|[[Week 11]]
|[[cdomin12 Week 11]]
|[[Skinny Genes]]
|-
|[[Week 12/13]]
|[[Skinny Genes Quality Assurance]]
|[[Skinny Genes]]
|-
|[[Week 15]]
|[[cdomin12 Week 15]]
|[[Skinny Genes]]
|}

[[category:Journal Entry]]

Skinny Genes Quality Assurance

2019-11-21T22:58:37Z

Cdomin12: added milestone 3

==Electronic Lab Notebook==
===Milestone 3===
*deleted Gweight and Eweight since not conducive to our dataset
*changed "YORF" to "ID" and "Name" to "Standard Name"
*sample-data relationship table changed categories to "strain_LogFC_timepoint-replicate number"
*Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3, wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4 so that replicates are grouped together

Cdomin12 Week 12/13

2019-11-21T22:55:30Z

Cdomin12: /* Milestone 3 */ added replicats

{{template:cdomin12}}

[[category:Group Projects]]
[[category:Skinny Genes]]

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 31 results
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" gave 133,000 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" and "yeast" gave 4,560 results
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" which gave 427 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 60 results
*# 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? 31 results with "potassium starvation" in title/abstract search
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? I used "since 2018" to sort more recent studies which gave 9,520 results.
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? searching "potassium starvation" in abstract yielded 27 results.
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite? 41 articles
*#** How many articles cite this article? 13 articles

===Bibliographic Entries===
# Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/
# Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=25432801
# Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/pdf/12864_2014_Article_6863.pdf
# Copyright: BioMed Central. This is an Open Access article.
# Availability: online
# Publisher: BioMedCentral, for profit, not a member of the OAPA, in United Kingdom
# The journal began in 2000
# Peer-reviewed articles: yes
# https://bmcbiol.biomedcentral.com/about/editorial-board
# Impact factor: 7.98
# Primary research article
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/ at bottom of page titled "electronic supplementary material"

# Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. FEMS yeast research, 12(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/22612992
# PubMed Central: N/A
# Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/12/6/651/528233
# Publisher Full Text (PDF): https://watermark.silverchair.com/12-6-651.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAmswggJnBgkqhkiG9w0BBwagggJYMIICVAIBADCCAk0GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMS28Gc_64lo0S5ZOsAgEQgIICHmtxEUsoWIF-rzLhH5zoeHZxIody_Cm7QuaVy4dTveZ3QOXd9gDTSDhNWBw3xiiuZ2pmj64dx5LkWYNWeyP99QGzYAD7PHaKm2l96qRjDZYeD_sfIwSfa9LAXr8olcrLKJPjR4uiZtIy7MXncNkU3991cc7PRZWxnTS994vQd0a5rwVFrrwhR3L7Y77HzHxN8Pza3TSHWhxNVxeV4tMiI9pAkH5wlS_EuqKI_6w8RXRQ6NNnswgPr2ky4pjnPY9GSdpcqSVCFkgkJZG4lvXAb-IoYDdMpnZ-DPXIiwC3cbFXrYso8ie9tX8z7i83vv9Hv9GLaEKy9sWIHOq2ig8O0ihELO_td8YEVW-E4c3C2WJCGlaLRlLRrcCHR395-qHDFjnLHaHgiyzIu6KwxloyUS9iFEqp1oLXses5nD9zE_2145xnfA-741mK-a2YWhitStQjtBp7U4xVXL_gF3vxryGy2GK3Ea6n7nvm8faWZGFyvc89MuerMkH4PiCSD6Rh_vcCpcMkweUzxhtWUlTxbobLWAo3CdbxfwQ4S-8Umwf2QrHd7oC9HywBgyRYa3EKxwRWadK_16F8zBE79qd1yFLZhoKovVza7UAJ-2PcuI3enya1zcND1dt-wU_86hdFsOM8bElprCn9gCI4RImIesFpXLJEuHgmdLVpHBNeLoEqAUQj33bcDfggizIRta4f3npaE_6syWqBesGnKw-g
# Copyright: Federation of European Microbiological Societies
# Article is not Open Access, does not discuss when it becomes available, published in Europe, LMU did pay for the article
# Availability: online
# Publisher: Blackwell Publishing, for profit, not a member of the OAPA
# The journal begain in 1922
# Peer-reviewed articles: yes
# https://fems-microbiology.org/about_fems/organization/
# Impact factor: 1.994 (2019)
# Primary research article

===Reflect===
====1.What impact does the choice of keywords have on your results?====
Adding the type of organism that you want results on makes a major difference in the specificity of the results. I found that there has been a lot of work on plants and less work on yeast. Adding that I wanted it for yeast made a difference to find articles that were more relatable.

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

==Electronic Lab Notebook==
===Milestone 3===
*deleted Gweight and Eweight since not conducive to our dataset
*changed "YORF" to "ID" and "Name" to "Standard Name"
*sample-data relationship table changed categories to "strain_LogFC_timepoint-replicate number"
*Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3, wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4 so that replicates are grouped together

==Acknowledgments==
# I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment.
#"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 08:51, 18 November 2019 (PST)

==References==
*Week 12/13. Retrieved November 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Cdomin12 Week 12/13

2019-11-21T22:52:57Z

Cdomin12: /* Electronic Lab Notebook */ added milestone 3 update

{{template:cdomin12}}

[[category:Group Projects]]
[[category:Skinny Genes]]

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 31 results
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" gave 133,000 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" and "yeast" gave 4,560 results
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" which gave 427 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 60 results
*# 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? 31 results with "potassium starvation" in title/abstract search
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? I used "since 2018" to sort more recent studies which gave 9,520 results.
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? searching "potassium starvation" in abstract yielded 27 results.
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite? 41 articles
*#** How many articles cite this article? 13 articles

===Bibliographic Entries===
# Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/
# Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=25432801
# Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/pdf/12864_2014_Article_6863.pdf
# Copyright: BioMed Central. This is an Open Access article.
# Availability: online
# Publisher: BioMedCentral, for profit, not a member of the OAPA, in United Kingdom
# The journal began in 2000
# Peer-reviewed articles: yes
# https://bmcbiol.biomedcentral.com/about/editorial-board
# Impact factor: 7.98
# Primary research article
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/ at bottom of page titled "electronic supplementary material"

# Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. FEMS yeast research, 12(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/22612992
# PubMed Central: N/A
# Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/12/6/651/528233
# Publisher Full Text (PDF): https://watermark.silverchair.com/12-6-651.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAmswggJnBgkqhkiG9w0BBwagggJYMIICVAIBADCCAk0GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMS28Gc_64lo0S5ZOsAgEQgIICHmtxEUsoWIF-rzLhH5zoeHZxIody_Cm7QuaVy4dTveZ3QOXd9gDTSDhNWBw3xiiuZ2pmj64dx5LkWYNWeyP99QGzYAD7PHaKm2l96qRjDZYeD_sfIwSfa9LAXr8olcrLKJPjR4uiZtIy7MXncNkU3991cc7PRZWxnTS994vQd0a5rwVFrrwhR3L7Y77HzHxN8Pza3TSHWhxNVxeV4tMiI9pAkH5wlS_EuqKI_6w8RXRQ6NNnswgPr2ky4pjnPY9GSdpcqSVCFkgkJZG4lvXAb-IoYDdMpnZ-DPXIiwC3cbFXrYso8ie9tX8z7i83vv9Hv9GLaEKy9sWIHOq2ig8O0ihELO_td8YEVW-E4c3C2WJCGlaLRlLRrcCHR395-qHDFjnLHaHgiyzIu6KwxloyUS9iFEqp1oLXses5nD9zE_2145xnfA-741mK-a2YWhitStQjtBp7U4xVXL_gF3vxryGy2GK3Ea6n7nvm8faWZGFyvc89MuerMkH4PiCSD6Rh_vcCpcMkweUzxhtWUlTxbobLWAo3CdbxfwQ4S-8Umwf2QrHd7oC9HywBgyRYa3EKxwRWadK_16F8zBE79qd1yFLZhoKovVza7UAJ-2PcuI3enya1zcND1dt-wU_86hdFsOM8bElprCn9gCI4RImIesFpXLJEuHgmdLVpHBNeLoEqAUQj33bcDfggizIRta4f3npaE_6syWqBesGnKw-g
# Copyright: Federation of European Microbiological Societies
# Article is not Open Access, does not discuss when it becomes available, published in Europe, LMU did pay for the article
# Availability: online
# Publisher: Blackwell Publishing, for profit, not a member of the OAPA
# The journal begain in 1922
# Peer-reviewed articles: yes
# https://fems-microbiology.org/about_fems/organization/
# Impact factor: 1.994 (2019)
# Primary research article

===Reflect===
====1.What impact does the choice of keywords have on your results?====
Adding the type of organism that you want results on makes a major difference in the specificity of the results. I found that there has been a lot of work on plants and less work on yeast. Adding that I wanted it for yeast made a difference to find articles that were more relatable.

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

==Electronic Lab Notebook==
===Milestone 3===
*deleted Gweight and Eweight since not conducive to our dataset
*changed "YORF" to "ID" and "Name" to "Standard Name"
*sample-data relationship table changed categories to "strain_LogFC_timepoint-replicate number"
*Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3, wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4

==Acknowledgments==
# I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment.
#"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 08:51, 18 November 2019 (PST)

==References==
*Week 12/13. Retrieved November 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Cdomin12 Week 12/13

2019-11-21T22:43:06Z

Cdomin12: /* Acknowledgments */ added user names

{{template:cdomin12}}

[[category:Group Projects]]
[[category:Skinny Genes]]

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 31 results
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" gave 133,000 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" and "yeast" gave 4,560 results
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" which gave 427 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 60 results
*# 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? 31 results with "potassium starvation" in title/abstract search
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? I used "since 2018" to sort more recent studies which gave 9,520 results.
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? searching "potassium starvation" in abstract yielded 27 results.
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite? 41 articles
*#** How many articles cite this article? 13 articles

===Bibliographic Entries===
# Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/
# Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=25432801
# Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/pdf/12864_2014_Article_6863.pdf
# Copyright: BioMed Central. This is an Open Access article.
# Availability: online
# Publisher: BioMedCentral, for profit, not a member of the OAPA, in United Kingdom
# The journal began in 2000
# Peer-reviewed articles: yes
# https://bmcbiol.biomedcentral.com/about/editorial-board
# Impact factor: 7.98
# Primary research article
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/ at bottom of page titled "electronic supplementary material"

# Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. FEMS yeast research, 12(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/22612992
# PubMed Central: N/A
# Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/12/6/651/528233
# Publisher Full Text (PDF): https://watermark.silverchair.com/12-6-651.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAmswggJnBgkqhkiG9w0BBwagggJYMIICVAIBADCCAk0GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMS28Gc_64lo0S5ZOsAgEQgIICHmtxEUsoWIF-rzLhH5zoeHZxIody_Cm7QuaVy4dTveZ3QOXd9gDTSDhNWBw3xiiuZ2pmj64dx5LkWYNWeyP99QGzYAD7PHaKm2l96qRjDZYeD_sfIwSfa9LAXr8olcrLKJPjR4uiZtIy7MXncNkU3991cc7PRZWxnTS994vQd0a5rwVFrrwhR3L7Y77HzHxN8Pza3TSHWhxNVxeV4tMiI9pAkH5wlS_EuqKI_6w8RXRQ6NNnswgPr2ky4pjnPY9GSdpcqSVCFkgkJZG4lvXAb-IoYDdMpnZ-DPXIiwC3cbFXrYso8ie9tX8z7i83vv9Hv9GLaEKy9sWIHOq2ig8O0ihELO_td8YEVW-E4c3C2WJCGlaLRlLRrcCHR395-qHDFjnLHaHgiyzIu6KwxloyUS9iFEqp1oLXses5nD9zE_2145xnfA-741mK-a2YWhitStQjtBp7U4xVXL_gF3vxryGy2GK3Ea6n7nvm8faWZGFyvc89MuerMkH4PiCSD6Rh_vcCpcMkweUzxhtWUlTxbobLWAo3CdbxfwQ4S-8Umwf2QrHd7oC9HywBgyRYa3EKxwRWadK_16F8zBE79qd1yFLZhoKovVza7UAJ-2PcuI3enya1zcND1dt-wU_86hdFsOM8bElprCn9gCI4RImIesFpXLJEuHgmdLVpHBNeLoEqAUQj33bcDfggizIRta4f3npaE_6syWqBesGnKw-g
# Copyright: Federation of European Microbiological Societies
# Article is not Open Access, does not discuss when it becomes available, published in Europe, LMU did pay for the article
# Availability: online
# Publisher: Blackwell Publishing, for profit, not a member of the OAPA
# The journal begain in 1922
# Peer-reviewed articles: yes
# https://fems-microbiology.org/about_fems/organization/
# Impact factor: 1.994 (2019)
# Primary research article

===Reflect===
====1.What impact does the choice of keywords have on your results?====
Adding the type of organism that you want results on makes a major difference in the specificity of the results. I found that there has been a lot of work on plants and less work on yeast. Adding that I wanted it for yeast made a difference to find articles that were more relatable.

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

==Electronic Lab Notebook==

==Acknowledgments==
# I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment.
#"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 08:51, 18 November 2019 (PST)

==References==
*Week 12/13. Retrieved November 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Cdomin12 Week 12/13

2019-11-21T22:42:32Z

Cdomin12: /* Acknowledgments */ added section

{{template:cdomin12}}

[[category:Group Projects]]
[[category:Skinny Genes]]

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 31 results
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" gave 133,000 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" and "yeast" gave 4,560 results
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" which gave 427 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 60 results
*# 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? 31 results with "potassium starvation" in title/abstract search
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? I used "since 2018" to sort more recent studies which gave 9,520 results.
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? searching "potassium starvation" in abstract yielded 27 results.
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite? 41 articles
*#** How many articles cite this article? 13 articles

===Bibliographic Entries===
# Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/
# Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=25432801
# Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/pdf/12864_2014_Article_6863.pdf
# Copyright: BioMed Central. This is an Open Access article.
# Availability: online
# Publisher: BioMedCentral, for profit, not a member of the OAPA, in United Kingdom
# The journal began in 2000
# Peer-reviewed articles: yes
# https://bmcbiol.biomedcentral.com/about/editorial-board
# Impact factor: 7.98
# Primary research article
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/ at bottom of page titled "electronic supplementary material"

# Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. FEMS yeast research, 12(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/22612992
# PubMed Central: N/A
# Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/12/6/651/528233
# Publisher Full Text (PDF): https://watermark.silverchair.com/12-6-651.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAmswggJnBgkqhkiG9w0BBwagggJYMIICVAIBADCCAk0GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMS28Gc_64lo0S5ZOsAgEQgIICHmtxEUsoWIF-rzLhH5zoeHZxIody_Cm7QuaVy4dTveZ3QOXd9gDTSDhNWBw3xiiuZ2pmj64dx5LkWYNWeyP99QGzYAD7PHaKm2l96qRjDZYeD_sfIwSfa9LAXr8olcrLKJPjR4uiZtIy7MXncNkU3991cc7PRZWxnTS994vQd0a5rwVFrrwhR3L7Y77HzHxN8Pza3TSHWhxNVxeV4tMiI9pAkH5wlS_EuqKI_6w8RXRQ6NNnswgPr2ky4pjnPY9GSdpcqSVCFkgkJZG4lvXAb-IoYDdMpnZ-DPXIiwC3cbFXrYso8ie9tX8z7i83vv9Hv9GLaEKy9sWIHOq2ig8O0ihELO_td8YEVW-E4c3C2WJCGlaLRlLRrcCHR395-qHDFjnLHaHgiyzIu6KwxloyUS9iFEqp1oLXses5nD9zE_2145xnfA-741mK-a2YWhitStQjtBp7U4xVXL_gF3vxryGy2GK3Ea6n7nvm8faWZGFyvc89MuerMkH4PiCSD6Rh_vcCpcMkweUzxhtWUlTxbobLWAo3CdbxfwQ4S-8Umwf2QrHd7oC9HywBgyRYa3EKxwRWadK_16F8zBE79qd1yFLZhoKovVza7UAJ-2PcuI3enya1zcND1dt-wU_86hdFsOM8bElprCn9gCI4RImIesFpXLJEuHgmdLVpHBNeLoEqAUQj33bcDfggizIRta4f3npaE_6syWqBesGnKw-g
# Copyright: Federation of European Microbiological Societies
# Article is not Open Access, does not discuss when it becomes available, published in Europe, LMU did pay for the article
# Availability: online
# Publisher: Blackwell Publishing, for profit, not a member of the OAPA
# The journal begain in 1922
# Peer-reviewed articles: yes
# https://fems-microbiology.org/about_fems/organization/
# Impact factor: 1.994 (2019)
# Primary research article

===Reflect===
====1.What impact does the choice of keywords have on your results?====
Adding the type of organism that you want results on makes a major difference in the specificity of the results. I found that there has been a lot of work on plants and less work on yeast. Adding that I wanted it for yeast made a difference to find articles that were more relatable.

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

==Electronic Lab Notebook==

==Acknowledgments==
# "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 08:51, 18 November 2019 (PST)

==References==
*Week 12/13. Retrieved November 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Cdomin12 Week 12/13

2019-11-21T22:40:18Z

Cdomin12: /* Acknowledgments */ added electronic lab notebook section

{{template:cdomin12}}

[[category:Group Projects]]
[[category:Skinny Genes]]

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 31 results
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" gave 133,000 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" and "yeast" gave 4,560 results
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" which gave 427 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 60 results
*# 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? 31 results with "potassium starvation" in title/abstract search
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? I used "since 2018" to sort more recent studies which gave 9,520 results.
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? searching "potassium starvation" in abstract yielded 27 results.
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite? 41 articles
*#** How many articles cite this article? 13 articles

===Bibliographic Entries===
# Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/
# Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=25432801
# Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/pdf/12864_2014_Article_6863.pdf
# Copyright: BioMed Central. This is an Open Access article.
# Availability: online
# Publisher: BioMedCentral, for profit, not a member of the OAPA, in United Kingdom
# The journal began in 2000
# Peer-reviewed articles: yes
# https://bmcbiol.biomedcentral.com/about/editorial-board
# Impact factor: 7.98
# Primary research article
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/ at bottom of page titled "electronic supplementary material"

# Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. FEMS yeast research, 12(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/22612992
# PubMed Central: N/A
# Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/12/6/651/528233
# Publisher Full Text (PDF): https://watermark.silverchair.com/12-6-651.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAmswggJnBgkqhkiG9w0BBwagggJYMIICVAIBADCCAk0GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMS28Gc_64lo0S5ZOsAgEQgIICHmtxEUsoWIF-rzLhH5zoeHZxIody_Cm7QuaVy4dTveZ3QOXd9gDTSDhNWBw3xiiuZ2pmj64dx5LkWYNWeyP99QGzYAD7PHaKm2l96qRjDZYeD_sfIwSfa9LAXr8olcrLKJPjR4uiZtIy7MXncNkU3991cc7PRZWxnTS994vQd0a5rwVFrrwhR3L7Y77HzHxN8Pza3TSHWhxNVxeV4tMiI9pAkH5wlS_EuqKI_6w8RXRQ6NNnswgPr2ky4pjnPY9GSdpcqSVCFkgkJZG4lvXAb-IoYDdMpnZ-DPXIiwC3cbFXrYso8ie9tX8z7i83vv9Hv9GLaEKy9sWIHOq2ig8O0ihELO_td8YEVW-E4c3C2WJCGlaLRlLRrcCHR395-qHDFjnLHaHgiyzIu6KwxloyUS9iFEqp1oLXses5nD9zE_2145xnfA-741mK-a2YWhitStQjtBp7U4xVXL_gF3vxryGy2GK3Ea6n7nvm8faWZGFyvc89MuerMkH4PiCSD6Rh_vcCpcMkweUzxhtWUlTxbobLWAo3CdbxfwQ4S-8Umwf2QrHd7oC9HywBgyRYa3EKxwRWadK_16F8zBE79qd1yFLZhoKovVza7UAJ-2PcuI3enya1zcND1dt-wU_86hdFsOM8bElprCn9gCI4RImIesFpXLJEuHgmdLVpHBNeLoEqAUQj33bcDfggizIRta4f3npaE_6syWqBesGnKw-g
# Copyright: Federation of European Microbiological Societies
# Article is not Open Access, does not discuss when it becomes available, published in Europe, LMU did pay for the article
# Availability: online
# Publisher: Blackwell Publishing, for profit, not a member of the OAPA
# The journal begain in 1922
# Peer-reviewed articles: yes
# https://fems-microbiology.org/about_fems/organization/
# Impact factor: 1.994 (2019)
# Primary research article

===Reflect===
====1.What impact does the choice of keywords have on your results?====
Adding the type of organism that you want results on makes a major difference in the specificity of the results. I found that there has been a lot of work on plants and less work on yeast. Adding that I wanted it for yeast made a difference to find articles that were more relatable.

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

==Electronic Lab Notebook==

==Acknowledgments==
# "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 08:51, 18 November 2019 (PST)

Cdomin12 Week 12/13

2019-11-21T22:39:44Z

Cdomin12: added categories

{{template:cdomin12}}

[[category:Group Projects]]
[[category:Skinny Genes]]

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 31 results
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" gave 133,000 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" and "yeast" gave 4,560 results
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" which gave 427 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 60 results
*# 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? 31 results with "potassium starvation" in title/abstract search
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? I used "since 2018" to sort more recent studies which gave 9,520 results.
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? searching "potassium starvation" in abstract yielded 27 results.
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite? 41 articles
*#** How many articles cite this article? 13 articles

===Bibliographic Entries===
# Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/
# Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=25432801
# Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/pdf/12864_2014_Article_6863.pdf
# Copyright: BioMed Central. This is an Open Access article.
# Availability: online
# Publisher: BioMedCentral, for profit, not a member of the OAPA, in United Kingdom
# The journal began in 2000
# Peer-reviewed articles: yes
# https://bmcbiol.biomedcentral.com/about/editorial-board
# Impact factor: 7.98
# Primary research article
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/ at bottom of page titled "electronic supplementary material"

# Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. FEMS yeast research, 12(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/22612992
# PubMed Central: N/A
# Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/12/6/651/528233
# Publisher Full Text (PDF): https://watermark.silverchair.com/12-6-651.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAmswggJnBgkqhkiG9w0BBwagggJYMIICVAIBADCCAk0GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMS28Gc_64lo0S5ZOsAgEQgIICHmtxEUsoWIF-rzLhH5zoeHZxIody_Cm7QuaVy4dTveZ3QOXd9gDTSDhNWBw3xiiuZ2pmj64dx5LkWYNWeyP99QGzYAD7PHaKm2l96qRjDZYeD_sfIwSfa9LAXr8olcrLKJPjR4uiZtIy7MXncNkU3991cc7PRZWxnTS994vQd0a5rwVFrrwhR3L7Y77HzHxN8Pza3TSHWhxNVxeV4tMiI9pAkH5wlS_EuqKI_6w8RXRQ6NNnswgPr2ky4pjnPY9GSdpcqSVCFkgkJZG4lvXAb-IoYDdMpnZ-DPXIiwC3cbFXrYso8ie9tX8z7i83vv9Hv9GLaEKy9sWIHOq2ig8O0ihELO_td8YEVW-E4c3C2WJCGlaLRlLRrcCHR395-qHDFjnLHaHgiyzIu6KwxloyUS9iFEqp1oLXses5nD9zE_2145xnfA-741mK-a2YWhitStQjtBp7U4xVXL_gF3vxryGy2GK3Ea6n7nvm8faWZGFyvc89MuerMkH4PiCSD6Rh_vcCpcMkweUzxhtWUlTxbobLWAo3CdbxfwQ4S-8Umwf2QrHd7oC9HywBgyRYa3EKxwRWadK_16F8zBE79qd1yFLZhoKovVza7UAJ-2PcuI3enya1zcND1dt-wU_86hdFsOM8bElprCn9gCI4RImIesFpXLJEuHgmdLVpHBNeLoEqAUQj33bcDfggizIRta4f3npaE_6syWqBesGnKw-g
# Copyright: Federation of European Microbiological Societies
# Article is not Open Access, does not discuss when it becomes available, published in Europe, LMU did pay for the article
# Availability: online
# Publisher: Blackwell Publishing, for profit, not a member of the OAPA
# The journal begain in 1922
# Peer-reviewed articles: yes
# https://fems-microbiology.org/about_fems/organization/
# Impact factor: 1.994 (2019)
# Primary research article

===Reflect===
====1.What impact does the choice of keywords have on your results?====
Adding the type of organism that you want results on makes a major difference in the specificity of the results. I found that there has been a lot of work on plants and less work on yeast. Adding that I wanted it for yeast made a difference to find articles that were more relatable.

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

==Acknowledgments==
# "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 08:51, 18 November 2019 (PST)

Cdomin12 Week 12/13

2019-11-18T16:51:00Z

Cdomin12: /* 2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)? */ added acknowledmens section

{{template:cdomin12}}

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 31 results
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" gave 133,000 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" and "yeast" gave 4,560 results
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" which gave 427 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 60 results
*# 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? 31 results with "potassium starvation" in title/abstract search
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? I used "since 2018" to sort more recent studies which gave 9,520 results.
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? searching "potassium starvation" in abstract yielded 27 results.
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite? 41 articles
*#** How many articles cite this article? 13 articles

===Bibliographic Entries===
# Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/
# Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=25432801
# Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/pdf/12864_2014_Article_6863.pdf
# Copyright: BioMed Central. This is an Open Access article.
# Availability: online
# Publisher: BioMedCentral, for profit, not a member of the OAPA, in United Kingdom
# The journal began in 2000
# Peer-reviewed articles: yes
# https://bmcbiol.biomedcentral.com/about/editorial-board
# Impact factor: 7.98
# Primary research article
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/ at bottom of page titled "electronic supplementary material"

# Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. FEMS yeast research, 12(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/22612992
# PubMed Central: N/A
# Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/12/6/651/528233
# Publisher Full Text (PDF): https://watermark.silverchair.com/12-6-651.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAmswggJnBgkqhkiG9w0BBwagggJYMIICVAIBADCCAk0GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMS28Gc_64lo0S5ZOsAgEQgIICHmtxEUsoWIF-rzLhH5zoeHZxIody_Cm7QuaVy4dTveZ3QOXd9gDTSDhNWBw3xiiuZ2pmj64dx5LkWYNWeyP99QGzYAD7PHaKm2l96qRjDZYeD_sfIwSfa9LAXr8olcrLKJPjR4uiZtIy7MXncNkU3991cc7PRZWxnTS994vQd0a5rwVFrrwhR3L7Y77HzHxN8Pza3TSHWhxNVxeV4tMiI9pAkH5wlS_EuqKI_6w8RXRQ6NNnswgPr2ky4pjnPY9GSdpcqSVCFkgkJZG4lvXAb-IoYDdMpnZ-DPXIiwC3cbFXrYso8ie9tX8z7i83vv9Hv9GLaEKy9sWIHOq2ig8O0ihELO_td8YEVW-E4c3C2WJCGlaLRlLRrcCHR395-qHDFjnLHaHgiyzIu6KwxloyUS9iFEqp1oLXses5nD9zE_2145xnfA-741mK-a2YWhitStQjtBp7U4xVXL_gF3vxryGy2GK3Ea6n7nvm8faWZGFyvc89MuerMkH4PiCSD6Rh_vcCpcMkweUzxhtWUlTxbobLWAo3CdbxfwQ4S-8Umwf2QrHd7oC9HywBgyRYa3EKxwRWadK_16F8zBE79qd1yFLZhoKovVza7UAJ-2PcuI3enya1zcND1dt-wU_86hdFsOM8bElprCn9gCI4RImIesFpXLJEuHgmdLVpHBNeLoEqAUQj33bcDfggizIRta4f3npaE_6syWqBesGnKw-g
# Copyright: Federation of European Microbiological Societies
# Article is not Open Access, does not discuss when it becomes available, published in Europe, LMU did pay for the article
# Availability: online
# Publisher: Blackwell Publishing, for profit, not a member of the OAPA
# The journal begain in 1922
# Peer-reviewed articles: yes
# https://fems-microbiology.org/about_fems/organization/
# Impact factor: 1.994 (2019)
# Primary research article

===Reflect===
====1.What impact does the choice of keywords have on your results?====
Adding the type of organism that you want results on makes a major difference in the specificity of the results. I found that there has been a lot of work on plants and less work on yeast. Adding that I wanted it for yeast made a difference to find articles that were more relatable.

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

==Acknowledgments==
# "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 08:51, 18 November 2019 (PST)

Cdomin12 Week 12/13

2019-11-16T01:39:34Z

Cdomin12: /* 1.What impact does the choice of keywords have on your results? */ answer

Skinny Genes

2019-11-16T01:38:21Z

Cdomin12: /* Annotated Bibliography */ added mine

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Files==
[[Media: Ymesfin_Yeast_Potassium_Starvation_Journal_Club_2.pdf | Journal Club Presentation]]

==Annotated Bibliography==
#Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351. DOI: 10.1371/journal.pbio.0040351
#Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. FEMS yeast research, 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x
#Christina: Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
#Christina: Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. FEMS yeast research, 12(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x

==Executive Summaries==
===Aby's Reflection===
*Progress: This week we created an outline for our presentation and formatted the presentation for the journal club.
*#What worked? Responsibilities for the presentation was delegated well so that everyone contributed an equal share.
*#What didn't work? It was difficult to work around everyone's schedules so that we could meet up and work together.
*#What will I do next to fix what didn't work? We will need to communicate with one another better and anticipate the amount of time necessary to complete the assignment as a group so that our schedules don't interfere with the groupwork.

===Jonar's Reflection===
*Progress:
*#What worked? Everybody in the group was responsive and we were able to agree on and start our presentation early. The delegation of work and support worked well.
*#What didn't work? Due to time constraints with multiple people, finding time for all five members was a little difficult
*#What will I do next to fix what didn't work? We can plan an early meeting time or we can delegate tasks and plan a little meeting just to go over the work.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 23:59, 13 November 2019 (PST)

===Christina's Reflection===
*Progress:
*#What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
*#What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
*#What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.

===Mihir's Reflection===
*Progress:
*#What worked?
*#* We were able to communicate well, and we all worked together to help each other understand and excel in our tasks. Furthermore, we figured out methods of communication and how to best work with each other remotely.
*#What didn't work?
*#* Scheduling times to work on this assignment was pretty hectic this week, given that each member of our team had an unusual number of projects, midterms, homework, and extra-curricular activities this week. We could not all meet together outside of class.
*#What will I do next to fix what didn't work?
*#* Hopefully, this was a one-time occurrence and none of us will be as busy as we were this week. However, other than that, we could also improve our responsiveness in our team's group message, as that is our sole method of communication outside of class.
[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 20:16, 13 November 2019 (PST)

===David's Reflection===
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 23:37, 13 November 2019 (PST)

Cdomin12 Week 12/13

2019-11-16T01:37:40Z

Cdomin12: /* Bibliographic Entries */ added second journal

{{template:cdomin12}}

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 31 results
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" gave 133,000 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" and "yeast" gave 4,560 results
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" which gave 427 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 60 results
*# 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? 31 results with "potassium starvation" in title/abstract search
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? I used "since 2018" to sort more recent studies which gave 9,520 results.
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? searching "potassium starvation" in abstract yielded 27 results.
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite? 41 articles
*#** How many articles cite this article? 13 articles

===Bibliographic Entries===
# Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/
# Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=25432801
# Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/pdf/12864_2014_Article_6863.pdf
# Copyright: BioMed Central. This is an Open Access article.
# Availability: online
# Publisher: BioMedCentral, for profit, not a member of the OAPA, in United Kingdom
# The journal began in 2000
# Peer-reviewed articles: yes
# https://bmcbiol.biomedcentral.com/about/editorial-board
# Impact factor: 7.98
# Primary research article
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/ at bottom of page titled "electronic supplementary material"

# Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. FEMS yeast research, 12(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/22612992
# PubMed Central: N/A
# Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/12/6/651/528233
# Publisher Full Text (PDF): https://watermark.silverchair.com/12-6-651.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAmswggJnBgkqhkiG9w0BBwagggJYMIICVAIBADCCAk0GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMS28Gc_64lo0S5ZOsAgEQgIICHmtxEUsoWIF-rzLhH5zoeHZxIody_Cm7QuaVy4dTveZ3QOXd9gDTSDhNWBw3xiiuZ2pmj64dx5LkWYNWeyP99QGzYAD7PHaKm2l96qRjDZYeD_sfIwSfa9LAXr8olcrLKJPjR4uiZtIy7MXncNkU3991cc7PRZWxnTS994vQd0a5rwVFrrwhR3L7Y77HzHxN8Pza3TSHWhxNVxeV4tMiI9pAkH5wlS_EuqKI_6w8RXRQ6NNnswgPr2ky4pjnPY9GSdpcqSVCFkgkJZG4lvXAb-IoYDdMpnZ-DPXIiwC3cbFXrYso8ie9tX8z7i83vv9Hv9GLaEKy9sWIHOq2ig8O0ihELO_td8YEVW-E4c3C2WJCGlaLRlLRrcCHR395-qHDFjnLHaHgiyzIu6KwxloyUS9iFEqp1oLXses5nD9zE_2145xnfA-741mK-a2YWhitStQjtBp7U4xVXL_gF3vxryGy2GK3Ea6n7nvm8faWZGFyvc89MuerMkH4PiCSD6Rh_vcCpcMkweUzxhtWUlTxbobLWAo3CdbxfwQ4S-8Umwf2QrHd7oC9HywBgyRYa3EKxwRWadK_16F8zBE79qd1yFLZhoKovVza7UAJ-2PcuI3enya1zcND1dt-wU_86hdFsOM8bElprCn9gCI4RImIesFpXLJEuHgmdLVpHBNeLoEqAUQj33bcDfggizIRta4f3npaE_6syWqBesGnKw-g
# Copyright: Federation of European Microbiological Societies
# Article is not Open Access, does not discuss when it becomes available, published in Europe, LMU did pay for the article
# Availability: online
# Publisher: Blackwell Publishing, for profit, not a member of the OAPA
# The journal begain in 1922
# Peer-reviewed articles: yes
# https://fems-microbiology.org/about_fems/organization/
# Impact factor: 1.994 (2019)
# Primary research article

===Reflect===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

Cdomin12 Week 12/13

2019-11-16T01:20:12Z

Cdomin12: /* Annotated Bibliography */ answered top questions

{{template:cdomin12}}

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 31 results
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" gave 133,000 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" and "yeast" gave 4,560 results
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" which gave 427 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 60 results
*# 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? 31 results with "potassium starvation" in title/abstract search
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? I used "since 2018" to sort more recent studies which gave 9,520 results.
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? searching "potassium starvation" in abstract yielded 27 results.
*#* Perform a prospective search on your article in the Web of Science and answer the following:
*#** How many articles does this article cite? 41 articles
*#** How many articles cite this article? 13 articles

===Bibliographic Entries===
# Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/
# Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=25432801
# Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/pdf/12864_2014_Article_6863.pdf
# Copyright: BioMed Central. This is an Open Access article.
# Availability: online
# Publisher: BioMedCentral, for profit, not a member of the OAPA, in United Kingdom
# The journal began in 2000
# Peer-reviewed articles: yes
# https://bmcbiol.biomedcentral.com/about/editorial-board
# Impact factor: 7.98
# Primary research article
# [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/] at bottom of page titled "electronic supplementary material"

# 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
#

===Reflect===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

Cdomin12 Week 12/13

2019-11-16T01:10:19Z

Cdomin12: /* Annotated Bibliography */ google scholar answers

{{template:cdomin12}}

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 31 results
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? "potassium starvation" gave 133,000 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" and "yeast" gave 4,560 results
*#* 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? 31 results with "potassium starvation" in title/abstract search
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? I used "since 2018" to sort more recent studies which gave 9,520 results.
*#* 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?

===Bibliographic Entries===
# Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/
# Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=25432801
# Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/pdf/12864_2014_Article_6863.pdf
# Copyright: BioMed Central. This is an Open Access article.
# Availability: online
# Publisher: BioMedCentral, for profit, not a member of the OAPA, in United Kingdom
# The journal began in 2000
# Peer-reviewed articles: yes
# https://bmcbiol.biomedcentral.com/about/editorial-board
# Impact factor: 7.98
# Primary research article
# [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/] at bottom of page titled "electronic supplementary material"

# 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
#

===Reflect===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

Cdomin12 Week 12/13

2019-11-16T01:03:17Z

Cdomin12: /* Annotated Bibliography */ added pubmed question

{{template:cdomin12}}

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" and "yeast" gave 31 results
*#* 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? 31 results with "potassium starvation" in title/abstract search
*#* 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?

===Bibliographic Entries===
# Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/
# Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=25432801
# Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/pdf/12864_2014_Article_6863.pdf
# Copyright: BioMed Central. This is an Open Access article.
# Availability: online
# Publisher: BioMedCentral, for profit, not a member of the OAPA, in United Kingdom
# The journal began in 2000
# Peer-reviewed articles: yes
# https://bmcbiol.biomedcentral.com/about/editorial-board
# Impact factor: 7.98
# Primary research article
# [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/] at bottom of page titled "electronic supplementary material"

# 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
#

===Reflect===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

Cdomin12 Week 12/13

2019-11-16T01:01:40Z

Cdomin12: /* Bibliographic Entries */ edit

{{template:cdomin12}}

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" in the title/abstract, I got 31 results
*#* 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?

===Bibliographic Entries===
# Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/
# Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=25432801
# Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/pdf/12864_2014_Article_6863.pdf
# Copyright: BioMed Central. This is an Open Access article.
# Availability: online
# Publisher: BioMedCentral, for profit, not a member of the OAPA, in United Kingdom
# The journal began in 2000
# Peer-reviewed articles: yes
# https://bmcbiol.biomedcentral.com/about/editorial-board
# Impact factor: 7.98
# Primary research article
# [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/] at bottom of page titled "electronic supplementary material"

# 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
#

===Reflect===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

Cdomin12 Week 12/13

2019-11-16T01:01:07Z

Cdomin12: /* Bibliographic Entries */ added one bib

{{template:cdomin12}}

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" in the title/abstract, I got 31 results
*#* 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?

===Bibliographic Entries===
# Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/
# Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=25432801
# Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/pdf/12864_2014_Article_6863.pdf
# Copyright: BioMed Central. This is an Open Access article.
# Availability: online
# Publisher: BioMedCentral, for profit, not a member of the OAPA, in United Kingdom
# The journal began in 2000
# Peer-reviewed articles: yes
# [https://bmcbiol.biomedcentral.com/about/editorial-board]
# Impact factor: 7.98
# Primary research article
# Data are not available (dead hyperlink)

# 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
# [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/] at bottom of page titled "electronic supplementary material"

===Reflect===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

Cdomin12 Week 12/13

2019-11-16T00:47:22Z

Cdomin12: /* Bibliographic Entries */ question 6

{{template:cdomin12}}

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" in the title/abstract, I got 31 results
*#* 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?

===Bibliographic Entries===
# Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
# PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/
# Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=25432801
# Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/pdf/12864_2014_Article_6863.pdf
# Copyright: Anemaet and van Heusden. This is an Open Access 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)

# 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)

===Reflect===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

Cdomin12 Week 12/13

2019-11-16T00:38:48Z

Cdomin12: /* Bibliographic Entries */ added pubmed q 1 and 2

{{template:cdomin12}}

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" in the title/abstract, I got 31 results
*#* 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?

===Bibliographic Entries===
# Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
# 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)

# 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)

===Reflect===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

Skinny Genes

2019-11-16T00:37:34Z

Cdomin12: /* Annotated Bibliography */ added bib

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Files==
[[Media: Ymesfin_Yeast_Potassium_Starvation_Journal_Club_2.pdf | Journal Club Presentation]]

==Annotated Bibliography==
#Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351. DOI: 10.1371/journal.pbio.0040351
#Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. FEMS yeast research, 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x
#Christina: Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040

==Executive Summaries==
===Aby's Reflection===
*Progress: This week we created an outline for our presentation and formatted the presentation for the journal club.
*#What worked? Responsibilities for the presentation was delegated well so that everyone contributed an equal share.
*#What didn't work? It was difficult to work around everyone's schedules so that we could meet up and work together.
*#What will I do next to fix what didn't work? We will need to communicate with one another better and anticipate the amount of time necessary to complete the assignment as a group so that our schedules don't interfere with the groupwork.

===Jonar's Reflection===
*Progress:
*#What worked? Everybody in the group was responsive and we were able to agree on and start our presentation early. The delegation of work and support worked well.
*#What didn't work? Due to time constraints with multiple people, finding time for all five members was a little difficult
*#What will I do next to fix what didn't work? We can plan an early meeting time or we can delegate tasks and plan a little meeting just to go over the work.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 23:59, 13 November 2019 (PST)

===Christina's Reflection===
*Progress:
*#What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
*#What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
*#What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.

===Mihir's Reflection===
*Progress:
*#What worked?
*#* We were able to communicate well, and we all worked together to help each other understand and excel in our tasks. Furthermore, we figured out methods of communication and how to best work with each other remotely.
*#What didn't work?
*#* Scheduling times to work on this assignment was pretty hectic this week, given that each member of our team had an unusual number of projects, midterms, homework, and extra-curricular activities this week. We could not all meet together outside of class.
*#What will I do next to fix what didn't work?
*#* Hopefully, this was a one-time occurrence and none of us will be as busy as we were this week. However, other than that, we could also improve our responsiveness in our team's group message, as that is our sole method of communication outside of class.
[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 20:16, 13 November 2019 (PST)

===David's Reflection===
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 23:37, 13 November 2019 (PST)

Cdomin12 Week 12/13

2019-11-16T00:33:39Z

Cdomin12: /* Annotated Bibliography */ added potassium starvation

{{template:cdomin12}}

==Annotated Bibliography==

*# 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? "potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" in the title/abstract, I got 31 results
*#* 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?

===Bibliographic Entries===
# 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)

# 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)

===Reflect===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

Cdomin12 Week 12/13

2019-11-16T00:32:11Z

Cdomin12: /* Annotated Bibliography */ pub med

{{template:cdomin12}}

==Annotated Bibliography==

*# 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?
"potassium starvation" which got 521 results
*#** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
By doing an advanced search of "potassium starvation" in the title/abstract, I got 31 results
*#* 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?

===Bibliographic Entries===
# 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)

# 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)

===Reflect===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

Cdomin12 Week 12/13

2019-11-16T00:25:30Z

Cdomin12: added annotated bib

{{template:cdomin12}}

==Annotated Bibliography==

*# 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?

===Bibliographic Entries===
# 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)

# 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)

===Reflect===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

Skinny Genes

2019-11-14T01:32:44Z

Cdomin12: /* Christina's Reflection */ added answrs

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Annotated Bibliography==
#Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351. DOI: 10.1371/journal.pbio.0040351
#Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. FEMS yeast research, 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x

==Executive Summaries==
===Aby's Reflection===
*Progress:
*#What worked?
*#What didn't work?
*#What will I do next to fix what didn't work?
===Jonar's Reflection===
*Progress:
*#What worked?
*#What didn't work?
*#What will I do next to fix what didn't work?
===Christina's Reflection===
*Progress:
*#What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
*#What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
*#What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.

===Mihir's Reflection===
*Progress:
*#What worked?
*#What didn't work?
*#What will I do next to fix what didn't work?
===David's Reflection===
*Progress:
*#What worked?
*#What didn't work?
*#What will I do next to fix what didn't work?

Cdomin12 Week 11

2019-11-14T01:25:38Z

Cdomin12: purpose and conclusion added

{{template:cdomin12}}

==Purpose==
To analyze an article for its results, data, and authenticity in terms of how the experiment was conducted and critical analysis.

==Outline==
===1. Ten Biological Terms===
*septin: a protein involved in cytokinesis and also functions in maintaining cell morphology (https://www.biology-online.org/dictionary/Septin, Biology Online, 2019)
*retrograde: Moving backward or against the usual direction of flow (https://www.biology-online.org/dictionary/Retrograde, Biology Online, 2019)
*assimilation:The conversion of nutriment into a useable form (e.g. liquid or solid) that is incorporated into the tissues and organs following the processes of digestion. (https://www.biology-online.org/dictionary/Assimilation, Biology Online, 2019)
*attenuated: to reduce the virulence (infectivity) of a pathogenic microorganism.(https://www.biology-online.org/dictionary/Attenuated, Biology Online, 2019)
*autotrophy: The state of being self-sustaining and being able to produce food from inorganic compounds.(https://www.biology-online.org/dictionary/Autotrophy, Biology Online, 2019)
*trehalose:disaccharide carbohydrate. (https://www.biology-online.org/dictionary/Trehalose, Biology Online, 2019)
*homocysteine: amino acid cysteine (https://www.biology-online.org/dictionary/Main_Page, Biology Online, 2019)
*chemostat:experimental apparatus where the chemical environment can be maintained static and nutrient availability can be controlled by the experimenter.(https://www.sciencedirect.com/topics/neuroscience/chemostat, ScienceDirect, 2019)
*methylglyoxal: organic compound; reduced derivate of pyruvic acid (https://www.biology-online.org/dictionary/Main_Page, Biology Online, 2019)
*Trk1: potassium transport protein (http://amigo.geneontology.org/amigo/search/bioentity?q=trk1, GeneOntology, 2019)

===2. Outline of Article===

====1. What is the main result presented in this paper?====
The paper showed that there was an impact on gene expression with potassium starvation. It was shown that sulfur metabolism is affected which starts a cascade of events that eventually leads to ammonium accumulation. Ribosome biogenesis and translation decrease expression causing a halt in the cell cycle.

====2. What is the importance or significance of this work?====
This is important to uncover more about how the role of potassium in the cell and gene expression. This remains mostly unexplored and can reveal pathways in whi

====3. What were the limitations in previous studies that led them to perform this work?====
Although there have been similar studies conducted before, there is little known about the cellular level in potassium starvation. Due to this, the authors decided to perform this work in order to understand what parts of the cells and function pertain to potassium levels using a newly developed YNB based growth medium and in short term time intervals.

====4. How did they treat the yeast cells (what experiment were they doing?)====
The yeast cells underwent different amounts of time of potassium starvation in order to access gene expression and cellular function.

====5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?====
Saccharomyces cerevisiae. Haploid or diploid was not mentioned.

====6. What media did they grow them in? What temperature? What type of incubator? For how long?====
Grown in YNB-based growth medium which has only trace amounts of potassium. Grown at 28 degrees C

====7. What controls did they use?====
Wild-type BY4741 non-stressed cells.

====8. How many replicates did they perform per treatment or timepoint?====
Four replicates for each timepoint- 10, 20, 40, 60, and 120 minutes.

====9. What method did they use to prepare the RNA, label it and hybridize it to the microarray?====
They used wildtype and the experimental and grew them in medium with KCL to 0.8 density. After centrifuging, they then resuspended them into the same media with, and potassium or without. They then took the samples for the microarray at time 10, 20, 40, 60, and 120 minutes.

====10. What mathematical/statistical method did they use to analyze the data?====
Data Analysis 3.4 software (Bruker Biospion) was used.

====11. Are the data publicly available for download? From which web site?====
Yes through Society for Applied Microbiology.

====12. Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.====

Figure 1: This represents induced or expressed gene expression grown on the potassium free medium at the relative time points. These measurements were made through RT-PCR assays. There is a pretty even amount of induced and repressed genes

Table 1: This table shows the transcriptional changes at minutes 10, 20, 40, 60, and 120. It measured induction/repression also measured through RT-PCR assays. No trend to show here.

Table 2: Where the strains were taken from in regard to work from other papers.

Figure 2: This pertains to the cellular function of sulfur amino acid metabolism. It has three parts to it. A shows the mechanism of how potassium starvation effects metabolism. B with the X axis representing mRNA change and Y axis being different genes shows the mRNA change in the different time intervals. C (x axis as time min and Y as intracellular levels of methionine and cysteine) shows.

Figure 3: One graph (x axis- time in minutes and y axis changes in expression) shows different genes and their change in expression over time. The other graph (x axis- time in minutes and y axis glutathione levels) shows glutathione levels over time. Both of these show that there is no general stress response to potassium starvation.

Figure 4: (A) This demonstrates the effect of methylglyoxal production as well as trehalose metabolism from potassium starvation. (B) Two graphs (x axis- time in min and y axis- changes in expression fold) shows the change in expression specifically for genes related to trehalose metabolism and methylglyoxal. Measurements were made through the microarray data. (C) A graph (x axis- time in min and y axis- methylglyoxal concentration) showing MG levels remaining higher after 20 minutes potentially linked to genes induced in trehalose metabolism.

Figure 5: (A) Graph (x axis- time in min and y axis- change in expression) shows genes seen in mitochondrial retrograde response. Measurements made through microarray data. DIT2 and DLD2 response done through measurements of microarray data. This shows electrophoresis data for it. (B) mitochondria morphology picture with mutant showing different morphology. Measured through GFP microscopy. (C) Graph (x axis- time min and y axis- ammonium concentration) shows concentration increase after being put in potassium free medium. (D) Graph (x axis- time in min and y axis- ammonium concentration) showing mutated Trk1 or Trk2 did not have more concentration. Measured through samples taken with transformed plasmids.

Figure 6: (A) Graph (x axis- time in min and y axis- changes in expression) shows different genes during potassium starvation. Measured through microarray experiments. (B) mRNA abundance shows of different cyclins measured through RT-PCR. (C) Demonstrates the cyclin data showing that they are almost undetectable. Measured through immunoblot analysis.

Figure 7: (A) Graph (x axis- time in min and y axis- change in expression) of genes that are involved in septin ring formation. Measured through microarray data. (B) Pictures showing + or – potassium after different amounts of time. (C) Measured through immunoblot analysis shows levels of Cdc11 protein. (D) wildtype measured through immunofluorescence with and without KCl.

====13. How does this work compare with previous studies?====
They wanted to specifically examine cellular functions of potassium related to time points in short-term starvation. They also were able to use a newly developed YNB based growth medium which had not been used in previous studies before. This allowed them to grow strains that were not exposed to any potassium.

====14. What are the important implications of this work?====
To learn more about the cellular function of potassium, why it is important and how it can be affected. It is clear that there are connections to other parts of cellular function that cannot perform or do as it should without potassium in the cell.

====15. What future directions should the authors take?====
They should look more closely at the pathways that were affected and the relative transcription factors. They were able to more closely characterize more of cellular functions effected by potassium; however, now they are more aware of which are effected they can dive deeper into why and how it plays a role.

====16. 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?====
They had a lot of data to support what they were concluding. They were able to have the evidence for everything conclusion that they made. Saying that, I found the paper to be confusing with the ample amounts of results that they had and I did not know exactly why they performed certain experiments or could not figure out the methodology as to how it related to their question.

==Annotated Bibliography==

*# 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?

===Bibliographic Entries===
# 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)

# 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)

===Reflect===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

==Conclusion==
While working through the outline, this paper had a lot of results and figures to represent the data. It was a bit confusing and misleading at times, where I had to reread the article multiple times. I felt that this article could have been explained better in a manner that led better into the results and figures. It was difficult to work with, but it did have findings that seemed promising in the field of research.

==Acknowledgments==
1. I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment.

2."Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 19:53, 11 November 2019 (PST)

==References==
*Biology Online. 2019. Accessed November 11, 2019, from https://biology-online.org
*GeneOntology. 2019. Accessed November 11, 2019, from http://geneontology.org
*ScienceDirect. 2019. Accessed November 11, 2019, from https://www.sciencedirect.com/topics/neuroscience/chemostat
*Week 11. Retrieved November 11, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_10

Cdomin12 Week 11

2019-11-13T07:54:40Z

Cdomin12: /* 5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid? */ hap

{{template:cdomin12}}

==Outline==
===1. Ten Biological Terms===
*septin: a protein involved in cytokinesis and also functions in maintaining cell morphology (https://www.biology-online.org/dictionary/Septin, Biology Online, 2019)
*retrograde: Moving backward or against the usual direction of flow (https://www.biology-online.org/dictionary/Retrograde, Biology Online, 2019)
*assimilation:The conversion of nutriment into a useable form (e.g. liquid or solid) that is incorporated into the tissues and organs following the processes of digestion. (https://www.biology-online.org/dictionary/Assimilation, Biology Online, 2019)
*attenuated: to reduce the virulence (infectivity) of a pathogenic microorganism.(https://www.biology-online.org/dictionary/Attenuated, Biology Online, 2019)
*autotrophy: The state of being self-sustaining and being able to produce food from inorganic compounds.(https://www.biology-online.org/dictionary/Autotrophy, Biology Online, 2019)
*trehalose:disaccharide carbohydrate. (https://www.biology-online.org/dictionary/Trehalose, Biology Online, 2019)
*homocysteine: amino acid cysteine (https://www.biology-online.org/dictionary/Main_Page, Biology Online, 2019)
*chemostat:experimental apparatus where the chemical environment can be maintained static and nutrient availability can be controlled by the experimenter.(https://www.sciencedirect.com/topics/neuroscience/chemostat, ScienceDirect, 2019)
*methylglyoxal: organic compound; reduced derivate of pyruvic acid (https://www.biology-online.org/dictionary/Main_Page, Biology Online, 2019)
*Trk1: potassium transport protein (http://amigo.geneontology.org/amigo/search/bioentity?q=trk1, GeneOntology, 2019)

===2. Outline of Article===

====1. What is the main result presented in this paper?====
The paper showed that there was an impact on gene expression with potassium starvation. It was shown that sulfur metabolism is affected which starts a cascade of events that eventually leads to ammonium accumulation. Ribosome biogenesis and translation decrease expression causing a halt in the cell cycle.

====2. What is the importance or significance of this work?====
This is important to uncover more about how the role of potassium in the cell and gene expression. This remains mostly unexplored and can reveal pathways in whi

====3. What were the limitations in previous studies that led them to perform this work?====
Although there have been similar studies conducted before, there is little known about the cellular level in potassium starvation. Due to this, the authors decided to perform this work in order to understand what parts of the cells and function pertain to potassium levels using a newly developed YNB based growth medium and in short term time intervals.

====4. How did they treat the yeast cells (what experiment were they doing?)====
The yeast cells underwent different amounts of time of potassium starvation in order to access gene expression and cellular function.

====5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?====
Saccharomyces cerevisiae. Haploid or diploid was not mentioned.

====6. What media did they grow them in? What temperature? What type of incubator? For how long?====
Grown in YNB-based growth medium which has only trace amounts of potassium. Grown at 28 degrees C

====7. What controls did they use?====
Wild-type BY4741 non-stressed cells.

====8. How many replicates did they perform per treatment or timepoint?====
Four replicates for each timepoint- 10, 20, 40, 60, and 120 minutes.

====9. What method did they use to prepare the RNA, label it and hybridize it to the microarray?====
They used wildtype and the experimental and grew them in medium with KCL to 0.8 density. After centrifuging, they then resuspended them into the same media with, and potassium or without. They then took the samples for the microarray at time 10, 20, 40, 60, and 120 minutes.

====10. What mathematical/statistical method did they use to analyze the data?====
Data Analysis 3.4 software (Bruker Biospion) was used.

====11. Are the data publicly available for download? From which web site?====
Yes through Society for Applied Microbiology.

====12. Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.====

Figure 1: This represents induced or expressed gene expression grown on the potassium free medium at the relative time points. These measurements were made through RT-PCR assays. There is a pretty even amount of induced and repressed genes

Table 1: This table shows the transcriptional changes at minutes 10, 20, 40, 60, and 120. It measured induction/repression also measured through RT-PCR assays. No trend to show here.

Table 2: Where the strains were taken from in regard to work from other papers.

Figure 2: This pertains to the cellular function of sulfur amino acid metabolism. It has three parts to it. A shows the mechanism of how potassium starvation effects metabolism. B with the X axis representing mRNA change and Y axis being different genes shows the mRNA change in the different time intervals. C (x axis as time min and Y as intracellular levels of methionine and cysteine) shows.

Figure 3: One graph (x axis- time in minutes and y axis changes in expression) shows different genes and their change in expression over time. The other graph (x axis- time in minutes and y axis glutathione levels) shows glutathione levels over time. Both of these show that there is no general stress response to potassium starvation.

Figure 4: (A) This demonstrates the effect of methylglyoxal production as well as trehalose metabolism from potassium starvation. (B) Two graphs (x axis- time in min and y axis- changes in expression fold) shows the change in expression specifically for genes related to trehalose metabolism and methylglyoxal. Measurements were made through the microarray data. (C) A graph (x axis- time in min and y axis- methylglyoxal concentration) showing MG levels remaining higher after 20 minutes potentially linked to genes induced in trehalose metabolism.

Figure 5: (A) Graph (x axis- time in min and y axis- change in expression) shows genes seen in mitochondrial retrograde response. Measurements made through microarray data. DIT2 and DLD2 response done through measurements of microarray data. This shows electrophoresis data for it. (B) mitochondria morphology picture with mutant showing different morphology. Measured through GFP microscopy. (C) Graph (x axis- time min and y axis- ammonium concentration) shows concentration increase after being put in potassium free medium. (D) Graph (x axis- time in min and y axis- ammonium concentration) showing mutated Trk1 or Trk2 did not have more concentration. Measured through samples taken with transformed plasmids.

Figure 6: (A) Graph (x axis- time in min and y axis- changes in expression) shows different genes during potassium starvation. Measured through microarray experiments. (B) mRNA abundance shows of different cyclins measured through RT-PCR. (C) Demonstrates the cyclin data showing that they are almost undetectable. Measured through immunoblot analysis.

Figure 7: (A) Graph (x axis- time in min and y axis- change in expression) of genes that are involved in septin ring formation. Measured through microarray data. (B) Pictures showing + or – potassium after different amounts of time. (C) Measured through immunoblot analysis shows levels of Cdc11 protein. (D) wildtype measured through immunofluorescence with and without KCl.

====13. How does this work compare with previous studies?====
They wanted to specifically examine cellular functions of potassium related to time points in short-term starvation. They also were able to use a newly developed YNB based growth medium which had not been used in previous studies before. This allowed them to grow strains that were not exposed to any potassium.

====14. What are the important implications of this work?====
To learn more about the cellular function of potassium, why it is important and how it can be affected. It is clear that there are connections to other parts of cellular function that cannot perform or do as it should without potassium in the cell.

====15. What future directions should the authors take?====
They should look more closely at the pathways that were affected and the relative transcription factors. They were able to more closely characterize more of cellular functions effected by potassium; however, now they are more aware of which are effected they can dive deeper into why and how it plays a role.

====16. 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?====
They had a lot of data to support what they were concluding. They were able to have the evidence for everything conclusion that they made. Saying that, I found the paper to be confusing with the ample amounts of results that they had and I did not know exactly why they performed certain experiments or could not figure out the methodology as to how it related to their question.

==Annotated Bibliography==

*# 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?

===Bibliographic Entries===
# 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)

# 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)

===Reflect===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

==Acknowledgments==
1. I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment.

2."Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 19:53, 11 November 2019 (PST)

==References==
*Biology Online. 2019. Accessed November 11, 2019, from https://biology-online.org
*GeneOntology. 2019. Accessed November 11, 2019, from http://geneontology.org
*ScienceDirect. 2019. Accessed November 11, 2019, from https://www.sciencedirect.com/topics/neuroscience/chemostat
*Week 11. Retrieved November 11, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_10

Cdomin12 Week 11

2019-11-13T07:49:53Z

Cdomin12: /* 2. Outline of Article */ answers

{{template:cdomin12}}

==Outline==
===1. Ten Biological Terms===
*septin: a protein involved in cytokinesis and also functions in maintaining cell morphology (https://www.biology-online.org/dictionary/Septin, Biology Online, 2019)
*retrograde: Moving backward or against the usual direction of flow (https://www.biology-online.org/dictionary/Retrograde, Biology Online, 2019)
*assimilation:The conversion of nutriment into a useable form (e.g. liquid or solid) that is incorporated into the tissues and organs following the processes of digestion. (https://www.biology-online.org/dictionary/Assimilation, Biology Online, 2019)
*attenuated: to reduce the virulence (infectivity) of a pathogenic microorganism.(https://www.biology-online.org/dictionary/Attenuated, Biology Online, 2019)
*autotrophy: The state of being self-sustaining and being able to produce food from inorganic compounds.(https://www.biology-online.org/dictionary/Autotrophy, Biology Online, 2019)
*trehalose:disaccharide carbohydrate. (https://www.biology-online.org/dictionary/Trehalose, Biology Online, 2019)
*homocysteine: amino acid cysteine (https://www.biology-online.org/dictionary/Main_Page, Biology Online, 2019)
*chemostat:experimental apparatus where the chemical environment can be maintained static and nutrient availability can be controlled by the experimenter.(https://www.sciencedirect.com/topics/neuroscience/chemostat, ScienceDirect, 2019)
*methylglyoxal: organic compound; reduced derivate of pyruvic acid (https://www.biology-online.org/dictionary/Main_Page, Biology Online, 2019)
*Trk1: potassium transport protein (http://amigo.geneontology.org/amigo/search/bioentity?q=trk1, GeneOntology, 2019)

===2. Outline of Article===

====1. What is the main result presented in this paper?====
The paper showed that there was an impact on gene expression with potassium starvation. It was shown that sulfur metabolism is affected which starts a cascade of events that eventually leads to ammonium accumulation. Ribosome biogenesis and translation decrease expression causing a halt in the cell cycle.

====2. What is the importance or significance of this work?====
This is important to uncover more about how the role of potassium in the cell and gene expression. This remains mostly unexplored and can reveal pathways in whi

====3. What were the limitations in previous studies that led them to perform this work?====
Although there have been similar studies conducted before, there is little known about the cellular level in potassium starvation. Due to this, the authors decided to perform this work in order to understand what parts of the cells and function pertain to potassium levels using a newly developed YNB based growth medium and in short term time intervals.

====4. How did they treat the yeast cells (what experiment were they doing?)====
The yeast cells underwent different amounts of time of potassium starvation in order to access gene expression and cellular function.

====5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?====
Saccharomyces cerevisiae

====6. What media did they grow them in? What temperature? What type of incubator? For how long?====
Grown in YNB-based growth medium which has only trace amounts of potassium. Grown at 28 degrees C

====7. What controls did they use?====
Wild-type BY4741 non-stressed cells.

====8. How many replicates did they perform per treatment or timepoint?====
Four replicates for each timepoint- 10, 20, 40, 60, and 120 minutes.

====9. What method did they use to prepare the RNA, label it and hybridize it to the microarray?====
They used wildtype and the experimental and grew them in medium with KCL to 0.8 density. After centrifuging, they then resuspended them into the same media with, and potassium or without. They then took the samples for the microarray at time 10, 20, 40, 60, and 120 minutes.

====10. What mathematical/statistical method did they use to analyze the data?====
Data Analysis 3.4 software (Bruker Biospion) was used.

====11. Are the data publicly available for download? From which web site?====
Yes through Society for Applied Microbiology.

====12. Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.====

Figure 1: This represents induced or expressed gene expression grown on the potassium free medium at the relative time points. These measurements were made through RT-PCR assays. There is a pretty even amount of induced and repressed genes

Table 1: This table shows the transcriptional changes at minutes 10, 20, 40, 60, and 120. It measured induction/repression also measured through RT-PCR assays. No trend to show here.

Table 2: Where the strains were taken from in regard to work from other papers.

Figure 2: This pertains to the cellular function of sulfur amino acid metabolism. It has three parts to it. A shows the mechanism of how potassium starvation effects metabolism. B with the X axis representing mRNA change and Y axis being different genes shows the mRNA change in the different time intervals. C (x axis as time min and Y as intracellular levels of methionine and cysteine) shows.

Figure 3: One graph (x axis- time in minutes and y axis changes in expression) shows different genes and their change in expression over time. The other graph (x axis- time in minutes and y axis glutathione levels) shows glutathione levels over time. Both of these show that there is no general stress response to potassium starvation.

Figure 4: (A) This demonstrates the effect of methylglyoxal production as well as trehalose metabolism from potassium starvation. (B) Two graphs (x axis- time in min and y axis- changes in expression fold) shows the change in expression specifically for genes related to trehalose metabolism and methylglyoxal. Measurements were made through the microarray data. (C) A graph (x axis- time in min and y axis- methylglyoxal concentration) showing MG levels remaining higher after 20 minutes potentially linked to genes induced in trehalose metabolism.

Figure 5: (A) Graph (x axis- time in min and y axis- change in expression) shows genes seen in mitochondrial retrograde response. Measurements made through microarray data. DIT2 and DLD2 response done through measurements of microarray data. This shows electrophoresis data for it. (B) mitochondria morphology picture with mutant showing different morphology. Measured through GFP microscopy. (C) Graph (x axis- time min and y axis- ammonium concentration) shows concentration increase after being put in potassium free medium. (D) Graph (x axis- time in min and y axis- ammonium concentration) showing mutated Trk1 or Trk2 did not have more concentration. Measured through samples taken with transformed plasmids.

Figure 6: (A) Graph (x axis- time in min and y axis- changes in expression) shows different genes during potassium starvation. Measured through microarray experiments. (B) mRNA abundance shows of different cyclins measured through RT-PCR. (C) Demonstrates the cyclin data showing that they are almost undetectable. Measured through immunoblot analysis.

Figure 7: (A) Graph (x axis- time in min and y axis- change in expression) of genes that are involved in septin ring formation. Measured through microarray data. (B) Pictures showing + or – potassium after different amounts of time. (C) Measured through immunoblot analysis shows levels of Cdc11 protein. (D) wildtype measured through immunofluorescence with and without KCl.

====13. How does this work compare with previous studies?====
They wanted to specifically examine cellular functions of potassium related to time points in short-term starvation. They also were able to use a newly developed YNB based growth medium which had not been used in previous studies before. This allowed them to grow strains that were not exposed to any potassium.

====14. What are the important implications of this work?====
To learn more about the cellular function of potassium, why it is important and how it can be affected. It is clear that there are connections to other parts of cellular function that cannot perform or do as it should without potassium in the cell.

====15. What future directions should the authors take?====
They should look more closely at the pathways that were affected and the relative transcription factors. They were able to more closely characterize more of cellular functions effected by potassium; however, now they are more aware of which are effected they can dive deeper into why and how it plays a role.

====16. 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?====
They had a lot of data to support what they were concluding. They were able to have the evidence for everything conclusion that they made. Saying that, I found the paper to be confusing with the ample amounts of results that they had and I did not know exactly why they performed certain experiments or could not figure out the methodology as to how it related to their question.

==Annotated Bibliography==

*# 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?

===Bibliographic Entries===
# 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)

# 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)

===Reflect===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

==Acknowledgments==
1. I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment.

2."Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 19:53, 11 November 2019 (PST)

==References==
*Biology Online. 2019. Accessed November 11, 2019, from https://biology-online.org
*GeneOntology. 2019. Accessed November 11, 2019, from http://geneontology.org
*ScienceDirect. 2019. Accessed November 11, 2019, from https://www.sciencedirect.com/topics/neuroscience/chemostat
*Week 11. Retrieved November 11, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_10

Skinny Genes

2019-11-12T23:24:38Z

Cdomin12: /* Week 11 Reflection */ deleted

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Annotated Bibliography==
#Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351. DOI: 10.1371/journal.pbio.0040351
#Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. FEMS yeast research, 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x

==Executive Summaries==
===Aby's Reflection===
*Progress:
*#What worked?
*#What didn't work?
*#What will I do next to fix what didn't work?
===Jonar's Reflection===
*Progress:
*#What worked?
*#What didn't work?
*#What will I do next to fix what didn't work?
===Christina's Reflection===
*Progress:
*#What worked?
*#What didn't work?
*#What will I do next to fix what didn't work?
===Mihir's Reflection===
*Progress:
*#What worked?
*#What didn't work?
*#What will I do next to fix what didn't work?
===David's Reflection===
*Progress:
*#What worked?
*#What didn't work?
*#What will I do next to fix what didn't work?

Cdomin12 Week 11

2019-11-12T23:23:25Z

Cdomin12: added outline

Cdomin12 Week 11

2019-11-12T23:22:58Z

Cdomin12: /* Bibliographic Entries */

{{template:cdomin12}}

===1. Ten Biological Terms===
*septin: a protein involved in cytokinesis and also functions in maintaining cell morphology (https://www.biology-online.org/dictionary/Septin, Biology Online, 2019)
*retrograde: Moving backward or against the usual direction of flow (https://www.biology-online.org/dictionary/Retrograde, Biology Online, 2019)
*assimilation:The conversion of nutriment into a useable form (e.g. liquid or solid) that is incorporated into the tissues and organs following the processes of digestion. (https://www.biology-online.org/dictionary/Assimilation, Biology Online, 2019)
*attenuated: to reduce the virulence (infectivity) of a pathogenic microorganism.(https://www.biology-online.org/dictionary/Attenuated, Biology Online, 2019)
*autotrophy: The state of being self-sustaining and being able to produce food from inorganic compounds.(https://www.biology-online.org/dictionary/Autotrophy, Biology Online, 2019)
*trehalose:disaccharide carbohydrate. (https://www.biology-online.org/dictionary/Trehalose, Biology Online, 2019)
*homocysteine: amino acid cysteine (https://www.biology-online.org/dictionary/Main_Page, Biology Online, 2019)
*chemostat:experimental apparatus where the chemical environment can be maintained static and nutrient availability can be controlled by the experimenter.(https://www.sciencedirect.com/topics/neuroscience/chemostat, ScienceDirect, 2019)
*methylglyoxal: organic compound; reduced derivate of pyruvic acid (https://www.biology-online.org/dictionary/Main_Page, Biology Online, 2019)
*Trk1: potassium transport protein (http://amigo.geneontology.org/amigo/search/bioentity?q=trk1, GeneOntology, 2019)

===2. Outline of Article===

====1. What is the main result presented in this paper?====

====2. What is the importance or significance of this work?====

====3. What were the limitations in previous studies that led them to perform this work?====

====4. How did they treat the yeast cells (what experiment were they doing?)====

====5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?====

====6. What media did they grow them in? What temperature? What type of incubator? For how long?====

====7. What controls did they use?====

====8. How many replicates did they perform per treatment or timepoint?====

====9. What method did they use to prepare the RNA, label it and hybridize it to the microarray?====

====10. What mathematical/statistical method did they use to analyze the data?====

====11. Are the data publicly available for download? From which web site?====

====12. Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.====

Figure 4: (A) This demonstrates the effect of methylglyoxal production as well as trehalose metabolism from potassium starvation. (B) Two graphs (x axis- time in min and y axis- changes in expression fold) shows the change in expression specifically for genes related to trehalose metabolism and methylglyoxal. Measurements were made through the microarray data. (C) A graph (x axis- time in min and y axis- methylglyoxal concentration) showing MG levels remaining higher after 20 minutes potentially linked to genes induced in trehalose metabolism.

====13. What do the X and Y axes represent?====

====14. How were the measurements made?====

====15. What trends are shown by the plots and what conclusions can you draw from the data?====

====16. How does this work compare with previous studies?====

====17. What are the important implications of this work?====

====18. What future directions should the authors take?====

====19. 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?====

==Annotated Bibliography==

*# 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?

===Bibliographic Entries===
# 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)

# 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)

===Reflect===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

==Acknowledgments==
1. I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment.

2."Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 19:53, 11 November 2019 (PST)

==References==
*Biology Online. 2019. Accessed November 11, 2019, from https://biology-online.org
*GeneOntology. 2019. Accessed November 11, 2019, from http://geneontology.org
*ScienceDirect. 2019. Accessed November 11, 2019, from https://www.sciencedirect.com/topics/neuroscience/chemostat
*Week 11. Retrieved November 11, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_10

Cdomin12 Week 11

2019-11-12T23:22:49Z

Cdomin12: /* Reflect */ added entries

Cdomin12 Week 11

2019-11-12T23:20:19Z

Cdomin12: /* Annotated Bibliography */ added search questions

{{template:cdomin12}}

===1. Ten Biological Terms===
*septin: a protein involved in cytokinesis and also functions in maintaining cell morphology (https://www.biology-online.org/dictionary/Septin, Biology Online, 2019)
*retrograde: Moving backward or against the usual direction of flow (https://www.biology-online.org/dictionary/Retrograde, Biology Online, 2019)
*assimilation:The conversion of nutriment into a useable form (e.g. liquid or solid) that is incorporated into the tissues and organs following the processes of digestion. (https://www.biology-online.org/dictionary/Assimilation, Biology Online, 2019)
*attenuated: to reduce the virulence (infectivity) of a pathogenic microorganism.(https://www.biology-online.org/dictionary/Attenuated, Biology Online, 2019)
*autotrophy: The state of being self-sustaining and being able to produce food from inorganic compounds.(https://www.biology-online.org/dictionary/Autotrophy, Biology Online, 2019)
*trehalose:disaccharide carbohydrate. (https://www.biology-online.org/dictionary/Trehalose, Biology Online, 2019)
*homocysteine: amino acid cysteine (https://www.biology-online.org/dictionary/Main_Page, Biology Online, 2019)
*chemostat:experimental apparatus where the chemical environment can be maintained static and nutrient availability can be controlled by the experimenter.(https://www.sciencedirect.com/topics/neuroscience/chemostat, ScienceDirect, 2019)
*methylglyoxal: organic compound; reduced derivate of pyruvic acid (https://www.biology-online.org/dictionary/Main_Page, Biology Online, 2019)
*Trk1: potassium transport protein (http://amigo.geneontology.org/amigo/search/bioentity?q=trk1, GeneOntology, 2019)

===2. Outline of Article===

====1. What is the main result presented in this paper?====

====2. What is the importance or significance of this work?====

====3. What were the limitations in previous studies that led them to perform this work?====

====4. How did they treat the yeast cells (what experiment were they doing?)====

====5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?====

====6. What media did they grow them in? What temperature? What type of incubator? For how long?====

====7. What controls did they use?====

====8. How many replicates did they perform per treatment or timepoint?====

====9. What method did they use to prepare the RNA, label it and hybridize it to the microarray?====

====10. What mathematical/statistical method did they use to analyze the data?====

====11. Are the data publicly available for download? From which web site?====

====12. Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.====

Figure 4: (A) This demonstrates the effect of methylglyoxal production as well as trehalose metabolism from potassium starvation. (B) Two graphs (x axis- time in min and y axis- changes in expression fold) shows the change in expression specifically for genes related to trehalose metabolism and methylglyoxal. Measurements were made through the microarray data. (C) A graph (x axis- time in min and y axis- methylglyoxal concentration) showing MG levels remaining higher after 20 minutes potentially linked to genes induced in trehalose metabolism.

====13. What do the X and Y axes represent?====

====14. How were the measurements made?====

====15. What trends are shown by the plots and what conclusions can you draw from the data?====

====16. How does this work compare with previous studies?====

====17. What are the important implications of this work?====

====18. What future directions should the authors take?====

====19. 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?====

==Annotated Bibliography==

*# 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===
====1.What impact does the choice of keywords have on your results?====

====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

==Acknowledgments==
1. I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment.

2."Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 19:53, 11 November 2019 (PST)

==References==
*Biology Online. 2019. Accessed November 11, 2019, from https://biology-online.org
*GeneOntology. 2019. Accessed November 11, 2019, from http://geneontology.org
*ScienceDirect. 2019. Accessed November 11, 2019, from https://www.sciencedirect.com/topics/neuroscience/chemostat
*Week 11. Retrieved November 11, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_10

Cdomin12 Week 11

2019-11-12T23:16:35Z

Cdomin12: /* 2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)? */ adv

Cdomin12 Week 11

2019-11-12T23:15:35Z

Cdomin12: /* 2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)? */ added adv and disadv

Cdomin12 Week 11

2019-11-12T23:05:24Z

Cdomin12: /* 19. 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? */ added adv and disadv