LMU BioDB 2019 - User contributions [en]

Skinny Genes Quality Assurance

2019-12-03T23:03:23Z

Jcowan4: added a reference for the name

==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 Quality Assurance

2019-12-03T22:57:57Z

Jcowan4: added milestone 5

==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===
*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 Quality Assurance

2019-11-26T23:47:52Z

Jcowan4: /* Problems */ added an explanation to file

==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===
*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.

===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

2019-11-26T23:44:53Z

Jcowan4: /* Electronic Lab Notebook */ added a problem header

==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===
*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.

===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)

{{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

2019-11-26T03:45:37Z

Jcowan4: /* Milestone 4 */ added milestone 4

==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===
*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.

{{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

2019-11-26T03:37:28Z

Jcowan4: /* Milestone 2 */ edited and updated what was done

Skinny Genes

2019-11-26T03:25:23Z

Jcowan4: /* Jonar's Reflection */ Reflected

{{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]]) 23:37, 13 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?
*#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?

==Milestones==

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

Skinny Genes

2019-11-21T23:53:44Z

Jcowan4: /* Files */ fixed**

{{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

==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]]) 23:37, 13 November 2019 (PST)

==Milestones==

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

Skinny Genes

2019-11-21T23:53:28Z

Jcowan4: /* Files */ Added and uploaded data

{{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

==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]]) 23:37, 13 November 2019 (PST)

==Milestones==

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

File:Editted Raw Data.xlsx

2019-11-21T23:52:21Z

Jcowan4: Updated Data

== Summary ==
Updated Data

Skinny Genes Quality Assurance

2019-11-21T23:02:41Z

Jcowan4: moved the templates

==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}}
{{jcowan4}}
[[category:Skinny Genes]]
[[category:Group Projects]]

Skinny Genes Quality Assurance

2019-11-21T23:01:58Z

Jcowan4: added template

{{template:cdomin12}}
{{jcowan4}}
[[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===

Skinny Genes Quality Assurance

2019-11-21T23:00:10Z

Jcowan4: /* Electronic Lab Notebook */ added milestone 1 and 2

Skinny Genes Quality Assurance

2019-11-21T22:59:19Z

Jcowan4: /* Electronic Lab Notebook */ Added milestone 4

==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

===Milestone 4===

Template:Jcowan4

2019-11-21T22:58:07Z

Jcowan4: Changed individual data to Skinny Genes Quality Assurance

{| class="wikitable"
|-
! Assignment
! Individual Journal
! Shared Journal
|-
| [[Week 1]]
| [[User:jcowan4 | jcowan4]]
| [[Class Journal Week 1]]
|-
| [[Week 2]]
| [[jcowan4 Journal Week 2]]
| [[Class Journal Week 2]]
|-
| [[Week 3]]
| [[FAS2 Week 3]]
| [[Class Journal Week 3]]
|-
| [[Week 4]]
| [[jcowan4 Journal Week 4]]
| [[Class Journal Week 4]]
|-
| [[Week 5]]
| [[iDog Week 5]]
| [[Class Journal Week 5]]
|-
| [[Week 6]]
| [[jcowan4 Journal Week 6]]
| [[Class Journal Week 6]]
|-
| [[Week 7]]
| [[jcowan4 Journal Week 7]]
| [[Class Journal Week 7]]
|-
| [[Week 8]]
| [[jcowan4 Journal Week 8]]
| [[Class Journal Week 8]]
|-
| [[Week 9]]
| [[jcowan4 Journal Week 9]]
| [[Class Journal Week 9]]
|-
| [[Week 10]]
| [[jcowan4 Journal Week 10]]
| [[Class Journal Week 10]]
|-
| [[Week 11]]
| [[jcowan4 Journal Week 11]]
| [[Skinny Genes]]
|-
| [[Week 12/13]]
| [[Skinny Genes Quality Assurance]]
| [[Skinny Genes]]
|-
| [[Week 15]]
| [[jcowan4 Journal Week 15]]
| [[Class Journal Week 15]]
|}

====Misc. Links====

*[[User:jcowan4]]

*[[Template:jcowan4]]

*[[Main Page|Bio DB Home page]]

*[[Category:Journal Entry]]

Skinny Genes

2019-11-21T22:52:18Z

Jcowan4: /* Milestones */ re-edited the outline

{{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]]

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

==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

==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)

==Milestones==

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

Jcowan4 Journal Week 12/13

2019-11-21T22:50:11Z

Jcowan4: /* Electronic Journal for Quality Assurance */ fixed template link

==Electronic Journal for Quality Assurance==

====Milestone 1====

====Milestone 2====

====Milestone 3====

====Milestone 4====

====Milestone 5====

====Milestone 6====

====Milestone 7====

{{jcowan4}}

Jcowan4 Journal Week 12/13

2019-11-21T22:49:45Z

Jcowan4: /* Electronic Journal for Quality Assurance */ added template

Jcowan4 Journal Week 12/13

2019-11-21T22:49:10Z

Jcowan4: /* Electronic Journal for Quality Assurance */ Added Milestone

==Electronic Journal for Quality Assurance==

====Milestone 1====

====Milestone 2====

====Milestone 3====

====Milestone 4====

====Milestone 5====

====Milestone 6====

====Milestone 7====

Jcowan4 Journal Week 12/13

2019-11-21T22:47:29Z

Jcowan4: Added header

==Electronic Journal for Quality Assurance==

Template:Jcowan4

2019-11-21T22:46:35Z

Jcowan4: changes week12/13 to Skinny Genes

{| class="wikitable"
|-
! Assignment
! Individual Journal
! Shared Journal
|-
| [[Week 1]]
| [[User:jcowan4 | jcowan4]]
| [[Class Journal Week 1]]
|-
| [[Week 2]]
| [[jcowan4 Journal Week 2]]
| [[Class Journal Week 2]]
|-
| [[Week 3]]
| [[FAS2 Week 3]]
| [[Class Journal Week 3]]
|-
| [[Week 4]]
| [[jcowan4 Journal Week 4]]
| [[Class Journal Week 4]]
|-
| [[Week 5]]
| [[iDog Week 5]]
| [[Class Journal Week 5]]
|-
| [[Week 6]]
| [[jcowan4 Journal Week 6]]
| [[Class Journal Week 6]]
|-
| [[Week 7]]
| [[jcowan4 Journal Week 7]]
| [[Class Journal Week 7]]
|-
| [[Week 8]]
| [[jcowan4 Journal Week 8]]
| [[Class Journal Week 8]]
|-
| [[Week 9]]
| [[jcowan4 Journal Week 9]]
| [[Class Journal Week 9]]
|-
| [[Week 10]]
| [[jcowan4 Journal Week 10]]
| [[Class Journal Week 10]]
|-
| [[Week 11]]
| [[jcowan4 Journal Week 11]]
| [[Skinny Genes]]
|-
| [[Week 12/13]]
| [[jcowan4 Journal Week 12/13]]
| [[Skinny Genes]]
|-
| [[Week 15]]
| [[jcowan4 Journal Week 15]]
| [[Class Journal Week 15]]
|}

====Misc. Links====

*[[User:jcowan4]]

*[[Template:jcowan4]]

*[[Main Page|Bio DB Home page]]

*[[Category:Journal Entry]]

Skinny Genes

2019-11-21T22:45:20Z

Jcowan4: /* Milestones */ layout for milestones

{{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]]

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

==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

==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)

==Milestones==

#Milestones
#Milestones
#Milestones
#Milestones
#Milestones
#Milestones
#Milestones

Skinny Genes

2019-11-19T23:06:22Z

Jcowan4: /* Executive Summaries */ milestones

{{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
#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

==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)

==Milestones==

Jcowan4 Journal Week 11

2019-11-19T07:58:02Z

Jcowan4: /* Annotated Bibliography */ answered

==Biological Terms==

Intracellular: Occurring or being (situated) inside a cell or cells. (Biology Online, 2019)

Transcriptomic: The study of all RNA molecules in a cell. RNA is copied from pieces of DNA and contains information to make proteins and perform other important functions in the cell. Transcriptomics is used to learn more about how genes are turned on in different types of cells and how this may help cause certain diseases, such as cancer.

Extracellular: Occurring or being (situated) outside the cell or cells. (Biology Online, 2019)

Methionine: (Science: biochemistry) Contains the SCH3 group that can act as a methyl donor (see s adenosyl methionine). Common in proteins but at low frequency. The met x linkage is subject to specific cleavage by cyanogen bromide. (Biology Online, 2019)

Biosynthesis: The production of a complex chemical compound from simpler precursors in a living organism, usually involving enzymes (to catalyze the reaction) and energy source (such as ATP). (Biology Online, 2019)

B-galactosidase: A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.

Homocysteine: The chemical reactions and pathways resulting in the formation of homocysteine, 2-amino-4-sulfanylbutanoic acid.

Oxidative: Capable of oxidizing other substances. Of, pertaining to, or produced by oxidation. (Biology Online, 2019)

Glutathione: (Science: biochemistry) The tripeptide _ glutamylcysteinylglycine. It contains an unusual peptide Linkage between the _ carboxyl group of the glutamate side chain and the amine group of cysteine. (Biology Online, 2019)

Substrate: A substratum or an underlying stratum. (Biology Online, 2019)

Transduction: there are a group of viruses called bacteriophages. These bacteriophages inject their viral dna into the host cell of bacteria. The viral dna then becomes incorporated into the chromosome of the bacterium. Thus the viral dna forms part of the bacterial chromosome and will be copied to all daughter cells. Though this viral dna will become active again at low frequency's. (Biology Online, 2019)

==Outline==

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

The main result found in the article was how the Saccharomyces cerevisiae short-term potassium deprivation causes a lack of potassium which affects and changes sulfur metabolism. This leads to an oxidative stress response and activates the retrograde pathway. It is stated that the catalyst could possibly be ammonium accumulation that happens through the Trk1 potassium transporter. Other results include: a halt in gene expression required for ribosome biogenesis and translation, a decrease in the expression of diverse components used in the progression of cell cycle and blockage in septins assembly. Essentially, a shortage of potassium in the environment triggers an acute transcriptional response, which opens up new finds and more areas to be explored.

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

The significance of this work is the new discoveries and pathways involving potassium and its role in cellular life.

===What were the limitations in previous studies that led them to perform this work?===
There were no previous studies that directly correlate to this work. However, there are multiple studies that are able to supplement the work.

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

The yeast cells were put into a YBN growth medium that lacked normal amounts of potassium and ammonium (potassium starvation). The cells were recorded and monitored in time intervals of 0, 10, 20, 30, 40, 60 and 120 minutes.

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

'''Strains:'''

*YNR055.1

*YPC722, YPC723, YPC724,

*BY4741, BY4741 rtg2, BY4741 rtg3, BY4741 fzo1

*BYT1, BYT2, BYT12

*W303-1A

*DBY746

(*The information regarding the if they were haploid or diploid wa not given)

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

*Grown in translucent potassium-free YNB media
*Temperature: 28 Celsius
*Incubator: N/A
*The times used were 0, 10, 20, 40, 60 and 120 minutes

===What controls did they use?===
Controls: wild-type strain BY4741, 50mM KCI added

===How many replicates did they perform per treatment or timepoint?===
4 Replicates per timepoint

===What method did they use to prepare the RNA, label it and hybridize it to the microarray? ===
RNA extraction using the Ribo Pure™-Yeast kit

===What mathematical/statistical method did they use to analyze the data?===
They used GEPAS v3.1

===Are the data publicly available for download? From which web site?===
The data could be found at [https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x Society for Applied Microbiology]

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

'''Table 1''' shows the transcriptional changes between 10, 20, 40, 60, and 120 minutes. It measures the amount of genes that are induced and repressed at each timepoint.

'''Table 2''' shows a list of strains that were used.

'''Figure 1''' shows that the majority of genes were induced/repressed between 60-120 minutes after being transferred to a potassium free media. '''X''' = Timepoint '''Y''' = Genes

'''Figure 2''' '''(A)''' shows the how potassium starvation decreases sulfuric amino acid metabolism. This is seen in the model that depicts the how Met/Cys are metabolized. '''B''' is a graph that shows mRna concentration from the microarray '''X''' = mRna change '''Y''' = Genes. '''C''' shows the concentration of Met and Cys after the procedure. '''X''' = Timepoint '''Y''' = Genes (Met/Cys)

'''Figure 3''' shows the oxidative stress response in genes due to potassium deprivation. '''A''' shows the multiple genes reacting to potassium deprivation and is measured by the levels of oxidative stress. '''B''' shows images of the genes responding to the procedure. '''Y''' = Time intervals. '''C''' shows the change in Glutanione level due to potassium starvation.

'''Figure 4''' shows the effects of methylglyoxal production and treholse production from potassium starvation. '''A''' shows how the production of each is made. '''B''' shows the changes in expression '''X''' = Timepoint '''Y''' = Changes in expression (-fold). '''C''' shows the levels of methyglyoxal when affected by potassium starvation. '''X''' = Timepoint '''Y''' = Methyglyoxal Levels.

'''Figure 5''' shows the a correlation between the expression of CIT2 and DLD3 genes and potassium starvation. '''A''' shows the changes in expression for genes and an image of the changes in CIT2, DLD3 and ACT1. '''B''' shows the changes in mitochondrial change before and after the procedure and images of WT and fzo1. '''C''' & '''D''' shows the graph depicting the relative concentration of intracellular ammonium after treatment.

'''Figure 6''' shows expression of genes controlling cyclins express various responses to potassium starvation. '''A''' shows a graph demonstrating the change in expression levels of retrograde after potassium starvation. '''X''' = Timepoint '''Y''' = log2 change in expression levels. '''B''' are images depicting relative abundance of cyclin mRNA & '''C''' are images depicting relative abundance of cyclin protein

'''Figure 7''' shows that potassium starvation decreases septin ring formation. '''A''' shows a graph that represents the change in expression levels of septin ring fomration genes after potassium starvation. '''B''' are images depicting the localization of Cdc11-GFP during treatment. '''C''' are images depicting relative abundance of Cdc11 protein. '''D''' are images depicting the localization of Cdc11 protein

===How does this work compare with previous studies?===
No other previous works.

===What are the important implications of this work?===
The important implications of this work are understanding the results from potassium starvation and how it opens up a new study regarding cations starvation or the relationship of cations and cellular life.

===What future directions should the authors take?===
The authors should try to understand how potassium affects other cations or how potassium affects other objects aside from yeast.

===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?===
The author's data supported their conclusion and could be seen when they used analyzing the figures and tables. However, the paper was extremely dense and required more research in order to understand the procedure and results.

==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? Yeast (283103), potassium (259156), potassium and yeast (3055)
*#** 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 (66)
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? Yeast (3090000), potassium (4370000), potassium and yeast (1290000)
*#** 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 (41600)
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get? Yeast (272999), potassium (271094), potassium and yeast (2162)
*#** 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 (60)
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful included: Text availability, most recent, filtering out the older articles. It narrowed down my search to under 100 articles.
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful functions include: time intervals of when the articles were released/updated, date. The result changed from 21600 to 2100.
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful functions included: Times cited, Usage count, date after (year). Results went from 60 to 11

'''REFERENCE 1'''

# 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'''
# https://www.ncbi.nlm.nih.gov/pubmed/17048990
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609136/
# https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0040351
# https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.0040351&type=printable
# Copyright: � 2006 Hess et al
# Article is open to the public
# Availibility: Online
# Publisher: PLOS Biology
# Earliest Publish Date: 2003
# Peer-reviewed: Yes
# https://journals.plos.org/plosbiology/s/editorial-board
# Impact Factor: 8.386 (2018)
# Primary Research article
# https://ndownloader.figshare.com/files/471538

'''REFERENCE 2'''

# 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
# https://www.ncbi.nlm.nih.gov/pubmed/29218312
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716641/
# http://www.ijcep.org/index.php/ijcep/article/view/182
# http://www.ijcep.org/index.php/ijcep/article/view/182/162
# © 2017 International Journal of Clinical and Experimental Physiology
# Open to the public
# Availability: Online
# Published by Wolters Kluwer - Medknow
# Earliest Published Daye: 2014
# Peer-Reviewed
# http://www.ijcep.org/index.php/ijcep/about/editorialTeam
# Impact Factor: 1.706 (2016)
# Review Article
# NA

* Reflect:
*# What impact does the choice of keywords have on your results? The important keywords lone are too broad of a topic. You have to be as specific as possible
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)? Pubmed is very well-rounded. It has open access and is able to locate articles easily. the drawback, however, is the limited data it provides. Google Scholar is very accessible with very basic information and does not always provide a doi. Web of science is closed to the public but the filters and advanced search provides easy access. However, it is aa paid website in comparison to the other two.

==Data/Files==

[[Media:Jonar_Cowan_Team_Skinny_Genes.pdf | Skinny Genes Presentation]]

==Conclusion==

This week, I learned how to reference sources and to look up information to confirm its viability. I also learned how to properly format a presentation.

==Acknowledgements==

This week we were put into teams. The team I was assigned to was Team [[Skinny_Genes|Skinny Genes]]. The other members are [[User:Msamdars|Mihir Samdars]], [[User:Ymesfin|Aby Mesfin]], [[User:Dramir36 |David Ramirez]], [[User:Cdomin12|Christina Dominguez]]. We worked in and out of class together Monday and Wednesday.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

==References==
# LMU BioDB 2019. (2019). Week 11. Retrieved November 7, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
# MediaWiki (2019). Category: Help. Retrieved November 11, 2019, from https://www.mediawiki.org/wiki/Category:Help
# Lagarias, J.C., Duanmu, D., Casero, D., Dent, R.M., Gallaher, S., Yang, W., Rockwell, N.C., Martin, S.S., Pellegrini, M., Niyogi, K.K., Merchant, S.S., Grossman, A.R. (2013). "Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival". Proceedings of the National Academy of Sciences of the United States of America. 110 (9): 3621–3626. doi:10.1073/pnas.1222375110.
# Douglas, L. M., Alvarez, F. J., McCreary, C., & Konopka, J. B. (2005). "Septin function in yeast model systems and pathogenic fungi". Eukaryotic Cell. 4 (9): 1503–12.
# Biology Online. (2019). Retrieved November 7, 2019 from https://biology-online.org
# Smith, A. (2000). Oxford Dictionary of Biochemistry and Molecular Biology: Revised Edition. Oxford University Press.
# Lackie, J. M. (Ed.). (2007). The dictionary of cell & molecular biology. Academic Press. Retrieved November 11, 2019 from http://ebookcentral.proquest.com/lib/lmu/detail.action?docID=311420.
# Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group. AmiGO: online access to ontology and annotation data. Bioinformatics. Jan 2009;25(2):288-289. Retrieved November 11, 2019 from http://amigo.geneontology.org/amigo/
# Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., ... & Fisk, D. G. (2011). Saccharomyces Genome Database: the genomics resource of budding yeast. ''Nucleic Acids Research'', 40(D1), D700-D705.

{{jcowan4}}
(*Participation: Table 2, Introduction (Background Information), Question 1, Question 3)

Jcowan4 Journal Week 11

2019-11-19T06:07:39Z

Jcowan4: /* Conclusion */ conclusion about this week 11/18/2019

==Biological Terms==

Intracellular: Occurring or being (situated) inside a cell or cells. (Biology Online, 2019)

Transcriptomic: The study of all RNA molecules in a cell. RNA is copied from pieces of DNA and contains information to make proteins and perform other important functions in the cell. Transcriptomics is used to learn more about how genes are turned on in different types of cells and how this may help cause certain diseases, such as cancer.

Extracellular: Occurring or being (situated) outside the cell or cells. (Biology Online, 2019)

Methionine: (Science: biochemistry) Contains the SCH3 group that can act as a methyl donor (see s adenosyl methionine). Common in proteins but at low frequency. The met x linkage is subject to specific cleavage by cyanogen bromide. (Biology Online, 2019)

Biosynthesis: The production of a complex chemical compound from simpler precursors in a living organism, usually involving enzymes (to catalyze the reaction) and energy source (such as ATP). (Biology Online, 2019)

B-galactosidase: A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.

Homocysteine: The chemical reactions and pathways resulting in the formation of homocysteine, 2-amino-4-sulfanylbutanoic acid.

Oxidative: Capable of oxidizing other substances. Of, pertaining to, or produced by oxidation. (Biology Online, 2019)

Glutathione: (Science: biochemistry) The tripeptide _ glutamylcysteinylglycine. It contains an unusual peptide Linkage between the _ carboxyl group of the glutamate side chain and the amine group of cysteine. (Biology Online, 2019)

Substrate: A substratum or an underlying stratum. (Biology Online, 2019)

Transduction: there are a group of viruses called bacteriophages. These bacteriophages inject their viral dna into the host cell of bacteria. The viral dna then becomes incorporated into the chromosome of the bacterium. Thus the viral dna forms part of the bacterial chromosome and will be copied to all daughter cells. Though this viral dna will become active again at low frequency's. (Biology Online, 2019)

==Outline==

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

The main result found in the article was how the Saccharomyces cerevisiae short-term potassium deprivation causes a lack of potassium which affects and changes sulfur metabolism. This leads to an oxidative stress response and activates the retrograde pathway. It is stated that the catalyst could possibly be ammonium accumulation that happens through the Trk1 potassium transporter. Other results include: a halt in gene expression required for ribosome biogenesis and translation, a decrease in the expression of diverse components used in the progression of cell cycle and blockage in septins assembly. Essentially, a shortage of potassium in the environment triggers an acute transcriptional response, which opens up new finds and more areas to be explored.

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

The significance of this work is the new discoveries and pathways involving potassium and its role in cellular life.

===What were the limitations in previous studies that led them to perform this work?===
There were no previous studies that directly correlate to this work. However, there are multiple studies that are able to supplement the work.

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

The yeast cells were put into a YBN growth medium that lacked normal amounts of potassium and ammonium (potassium starvation). The cells were recorded and monitored in time intervals of 0, 10, 20, 30, 40, 60 and 120 minutes.

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

'''Strains:'''

*YNR055.1

*YPC722, YPC723, YPC724,

*BY4741, BY4741 rtg2, BY4741 rtg3, BY4741 fzo1

*BYT1, BYT2, BYT12

*W303-1A

*DBY746

(*The information regarding the if they were haploid or diploid wa not given)

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

*Grown in translucent potassium-free YNB media
*Temperature: 28 Celsius
*Incubator: N/A
*The times used were 0, 10, 20, 40, 60 and 120 minutes

===What controls did they use?===
Controls: wild-type strain BY4741, 50mM KCI added

===How many replicates did they perform per treatment or timepoint?===
4 Replicates per timepoint

===What method did they use to prepare the RNA, label it and hybridize it to the microarray? ===
RNA extraction using the Ribo Pure™-Yeast kit

===What mathematical/statistical method did they use to analyze the data?===
They used GEPAS v3.1

===Are the data publicly available for download? From which web site?===
The data could be found at [https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x Society for Applied Microbiology]

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

'''Table 1''' shows the transcriptional changes between 10, 20, 40, 60, and 120 minutes. It measures the amount of genes that are induced and repressed at each timepoint.

'''Table 2''' shows a list of strains that were used.

'''Figure 1''' shows that the majority of genes were induced/repressed between 60-120 minutes after being transferred to a potassium free media. '''X''' = Timepoint '''Y''' = Genes

'''Figure 2''' '''(A)''' shows the how potassium starvation decreases sulfuric amino acid metabolism. This is seen in the model that depicts the how Met/Cys are metabolized. '''B''' is a graph that shows mRna concentration from the microarray '''X''' = mRna change '''Y''' = Genes. '''C''' shows the concentration of Met and Cys after the procedure. '''X''' = Timepoint '''Y''' = Genes (Met/Cys)

'''Figure 3''' shows the oxidative stress response in genes due to potassium deprivation. '''A''' shows the multiple genes reacting to potassium deprivation and is measured by the levels of oxidative stress. '''B''' shows images of the genes responding to the procedure. '''Y''' = Time intervals. '''C''' shows the change in Glutanione level due to potassium starvation.

'''Figure 4''' shows the effects of methylglyoxal production and treholse production from potassium starvation. '''A''' shows how the production of each is made. '''B''' shows the changes in expression '''X''' = Timepoint '''Y''' = Changes in expression (-fold). '''C''' shows the levels of methyglyoxal when affected by potassium starvation. '''X''' = Timepoint '''Y''' = Methyglyoxal Levels.

'''Figure 5''' shows the a correlation between the expression of CIT2 and DLD3 genes and potassium starvation. '''A''' shows the changes in expression for genes and an image of the changes in CIT2, DLD3 and ACT1. '''B''' shows the changes in mitochondrial change before and after the procedure and images of WT and fzo1. '''C''' & '''D''' shows the graph depicting the relative concentration of intracellular ammonium after treatment.

'''Figure 6''' shows expression of genes controlling cyclins express various responses to potassium starvation. '''A''' shows a graph demonstrating the change in expression levels of retrograde after potassium starvation. '''X''' = Timepoint '''Y''' = log2 change in expression levels. '''B''' are images depicting relative abundance of cyclin mRNA & '''C''' are images depicting relative abundance of cyclin protein

'''Figure 7''' shows that potassium starvation decreases septin ring formation. '''A''' shows a graph that represents the change in expression levels of septin ring fomration genes after potassium starvation. '''B''' are images depicting the localization of Cdc11-GFP during treatment. '''C''' are images depicting relative abundance of Cdc11 protein. '''D''' are images depicting the localization of Cdc11 protein

===How does this work compare with previous studies?===
No other previous works.

===What are the important implications of this work?===
The important implications of this work are understanding the results from potassium starvation and how it opens up a new study regarding cations starvation or the relationship of cations and cellular life.

===What future directions should the authors take?===
The authors should try to understand how potassium affects other cations or how potassium affects other objects aside from yeast.

===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?===
The author's data supported their conclusion and could be seen when they used analyzing the figures and tables. However, the paper was extremely dense and required more research in order to understand the procedure and results.

==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? Yeast (283103), potassium (259156), potassium and yeast (3055)
*#** 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 (66)
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? Yeast (3090000), potassium (4370000), potassium and yeast (1290000)
*#** 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 (41600)
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get? Yeast (272999), potassium (271094), potassium and yeast (2162)
*#** 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 (60)
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful included: Text availability, most recent, filtering out the older articles. It narrowed down my search to under 100 articles.
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful functions include: time intervals of when the articles were released/updated, date. The result changed from 21600 to 2100.
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful functions included: Times cited, Usage count, date after (year). Results went from 60 to 11

'''REFERENCE 1'''

# 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'''
# https://www.ncbi.nlm.nih.gov/pubmed/17048990
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609136/
# https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0040351
# https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.0040351&type=printable
# Copyright: � 2006 Hess et al
# Article is open to the public
# Availibility: Online
# Publisher: PLOS Biology
# Earliest Publish Date: 2003
# Peer-reviewed: Yes
# https://journals.plos.org/plosbiology/s/editorial-board
# Impact Factor: 8.386 (2018)
# Primary Research article
# https://ndownloader.figshare.com/files/471538

'''REFERENCE 2'''

# 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
# https://www.ncbi.nlm.nih.gov/pubmed/29218312
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716641/
# http://www.ijcep.org/index.php/ijcep/article/view/182
# http://www.ijcep.org/index.php/ijcep/article/view/182/162
# © 2017 International Journal of Clinical and Experimental Physiology
# Open to the public
# Availability: Online
# Published by Wolters Kluwer - Medknow
# Earliest Published Daye: 2014
# Peer-Reviewed
# http://www.ijcep.org/index.php/ijcep/about/editorialTeam
# Impact Factor: 1.706 (2016)
# Review Article
# NA

==Data/Files==

[[Media:Jonar_Cowan_Team_Skinny_Genes.pdf | Skinny Genes Presentation]]

==Conclusion==

This week, I learned how to reference sources and to look up information to confirm its viability. I also learned how to properly format a presentation.

==Acknowledgements==

This week we were put into teams. The team I was assigned to was Team [[Skinny_Genes|Skinny Genes]]. The other members are [[User:Msamdars|Mihir Samdars]], [[User:Ymesfin|Aby Mesfin]], [[User:Dramir36 |David Ramirez]], [[User:Cdomin12|Christina Dominguez]]. We worked in and out of class together Monday and Wednesday.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

==References==
# LMU BioDB 2019. (2019). Week 11. Retrieved November 7, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
# MediaWiki (2019). Category: Help. Retrieved November 11, 2019, from https://www.mediawiki.org/wiki/Category:Help
# Lagarias, J.C., Duanmu, D., Casero, D., Dent, R.M., Gallaher, S., Yang, W., Rockwell, N.C., Martin, S.S., Pellegrini, M., Niyogi, K.K., Merchant, S.S., Grossman, A.R. (2013). "Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival". Proceedings of the National Academy of Sciences of the United States of America. 110 (9): 3621–3626. doi:10.1073/pnas.1222375110.
# Douglas, L. M., Alvarez, F. J., McCreary, C., & Konopka, J. B. (2005). "Septin function in yeast model systems and pathogenic fungi". Eukaryotic Cell. 4 (9): 1503–12.
# Biology Online. (2019). Retrieved November 7, 2019 from https://biology-online.org
# Smith, A. (2000). Oxford Dictionary of Biochemistry and Molecular Biology: Revised Edition. Oxford University Press.
# Lackie, J. M. (Ed.). (2007). The dictionary of cell & molecular biology. Academic Press. Retrieved November 11, 2019 from http://ebookcentral.proquest.com/lib/lmu/detail.action?docID=311420.
# Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group. AmiGO: online access to ontology and annotation data. Bioinformatics. Jan 2009;25(2):288-289. Retrieved November 11, 2019 from http://amigo.geneontology.org/amigo/
# Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., ... & Fisk, D. G. (2011). Saccharomyces Genome Database: the genomics resource of budding yeast. ''Nucleic Acids Research'', 40(D1), D700-D705.

{{jcowan4}}
(*Participation: Table 2, Introduction (Background Information), Question 1, Question 3)

Jcowan4 Journal Week 11

2019-11-19T06:04:46Z

Jcowan4: /* Annotated Bibliography */ answered ref 2

==Biological Terms==

Intracellular: Occurring or being (situated) inside a cell or cells. (Biology Online, 2019)

Transcriptomic: The study of all RNA molecules in a cell. RNA is copied from pieces of DNA and contains information to make proteins and perform other important functions in the cell. Transcriptomics is used to learn more about how genes are turned on in different types of cells and how this may help cause certain diseases, such as cancer.

Extracellular: Occurring or being (situated) outside the cell or cells. (Biology Online, 2019)

Methionine: (Science: biochemistry) Contains the SCH3 group that can act as a methyl donor (see s adenosyl methionine). Common in proteins but at low frequency. The met x linkage is subject to specific cleavage by cyanogen bromide. (Biology Online, 2019)

Biosynthesis: The production of a complex chemical compound from simpler precursors in a living organism, usually involving enzymes (to catalyze the reaction) and energy source (such as ATP). (Biology Online, 2019)

B-galactosidase: A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.

Homocysteine: The chemical reactions and pathways resulting in the formation of homocysteine, 2-amino-4-sulfanylbutanoic acid.

Oxidative: Capable of oxidizing other substances. Of, pertaining to, or produced by oxidation. (Biology Online, 2019)

Glutathione: (Science: biochemistry) The tripeptide _ glutamylcysteinylglycine. It contains an unusual peptide Linkage between the _ carboxyl group of the glutamate side chain and the amine group of cysteine. (Biology Online, 2019)

Substrate: A substratum or an underlying stratum. (Biology Online, 2019)

Transduction: there are a group of viruses called bacteriophages. These bacteriophages inject their viral dna into the host cell of bacteria. The viral dna then becomes incorporated into the chromosome of the bacterium. Thus the viral dna forms part of the bacterial chromosome and will be copied to all daughter cells. Though this viral dna will become active again at low frequency's. (Biology Online, 2019)

==Outline==

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

The main result found in the article was how the Saccharomyces cerevisiae short-term potassium deprivation causes a lack of potassium which affects and changes sulfur metabolism. This leads to an oxidative stress response and activates the retrograde pathway. It is stated that the catalyst could possibly be ammonium accumulation that happens through the Trk1 potassium transporter. Other results include: a halt in gene expression required for ribosome biogenesis and translation, a decrease in the expression of diverse components used in the progression of cell cycle and blockage in septins assembly. Essentially, a shortage of potassium in the environment triggers an acute transcriptional response, which opens up new finds and more areas to be explored.

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

The significance of this work is the new discoveries and pathways involving potassium and its role in cellular life.

===What were the limitations in previous studies that led them to perform this work?===
There were no previous studies that directly correlate to this work. However, there are multiple studies that are able to supplement the work.

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

The yeast cells were put into a YBN growth medium that lacked normal amounts of potassium and ammonium (potassium starvation). The cells were recorded and monitored in time intervals of 0, 10, 20, 30, 40, 60 and 120 minutes.

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

'''Strains:'''

*YNR055.1

*YPC722, YPC723, YPC724,

*BY4741, BY4741 rtg2, BY4741 rtg3, BY4741 fzo1

*BYT1, BYT2, BYT12

*W303-1A

*DBY746

(*The information regarding the if they were haploid or diploid wa not given)

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

*Grown in translucent potassium-free YNB media
*Temperature: 28 Celsius
*Incubator: N/A
*The times used were 0, 10, 20, 40, 60 and 120 minutes

===What controls did they use?===
Controls: wild-type strain BY4741, 50mM KCI added

===How many replicates did they perform per treatment or timepoint?===
4 Replicates per timepoint

===What method did they use to prepare the RNA, label it and hybridize it to the microarray? ===
RNA extraction using the Ribo Pure™-Yeast kit

===What mathematical/statistical method did they use to analyze the data?===
They used GEPAS v3.1

===Are the data publicly available for download? From which web site?===
The data could be found at [https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x Society for Applied Microbiology]

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

'''Table 1''' shows the transcriptional changes between 10, 20, 40, 60, and 120 minutes. It measures the amount of genes that are induced and repressed at each timepoint.

'''Table 2''' shows a list of strains that were used.

'''Figure 1''' shows that the majority of genes were induced/repressed between 60-120 minutes after being transferred to a potassium free media. '''X''' = Timepoint '''Y''' = Genes

'''Figure 2''' '''(A)''' shows the how potassium starvation decreases sulfuric amino acid metabolism. This is seen in the model that depicts the how Met/Cys are metabolized. '''B''' is a graph that shows mRna concentration from the microarray '''X''' = mRna change '''Y''' = Genes. '''C''' shows the concentration of Met and Cys after the procedure. '''X''' = Timepoint '''Y''' = Genes (Met/Cys)

'''Figure 3''' shows the oxidative stress response in genes due to potassium deprivation. '''A''' shows the multiple genes reacting to potassium deprivation and is measured by the levels of oxidative stress. '''B''' shows images of the genes responding to the procedure. '''Y''' = Time intervals. '''C''' shows the change in Glutanione level due to potassium starvation.

'''Figure 4''' shows the effects of methylglyoxal production and treholse production from potassium starvation. '''A''' shows how the production of each is made. '''B''' shows the changes in expression '''X''' = Timepoint '''Y''' = Changes in expression (-fold). '''C''' shows the levels of methyglyoxal when affected by potassium starvation. '''X''' = Timepoint '''Y''' = Methyglyoxal Levels.

'''Figure 5''' shows the a correlation between the expression of CIT2 and DLD3 genes and potassium starvation. '''A''' shows the changes in expression for genes and an image of the changes in CIT2, DLD3 and ACT1. '''B''' shows the changes in mitochondrial change before and after the procedure and images of WT and fzo1. '''C''' & '''D''' shows the graph depicting the relative concentration of intracellular ammonium after treatment.

'''Figure 6''' shows expression of genes controlling cyclins express various responses to potassium starvation. '''A''' shows a graph demonstrating the change in expression levels of retrograde after potassium starvation. '''X''' = Timepoint '''Y''' = log2 change in expression levels. '''B''' are images depicting relative abundance of cyclin mRNA & '''C''' are images depicting relative abundance of cyclin protein

'''Figure 7''' shows that potassium starvation decreases septin ring formation. '''A''' shows a graph that represents the change in expression levels of septin ring fomration genes after potassium starvation. '''B''' are images depicting the localization of Cdc11-GFP during treatment. '''C''' are images depicting relative abundance of Cdc11 protein. '''D''' are images depicting the localization of Cdc11 protein

===How does this work compare with previous studies?===
No other previous works.

===What are the important implications of this work?===
The important implications of this work are understanding the results from potassium starvation and how it opens up a new study regarding cations starvation or the relationship of cations and cellular life.

===What future directions should the authors take?===
The authors should try to understand how potassium affects other cations or how potassium affects other objects aside from yeast.

===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?===
The author's data supported their conclusion and could be seen when they used analyzing the figures and tables. However, the paper was extremely dense and required more research in order to understand the procedure and results.

==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? Yeast (283103), potassium (259156), potassium and yeast (3055)
*#** 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 (66)
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? Yeast (3090000), potassium (4370000), potassium and yeast (1290000)
*#** 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 (41600)
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get? Yeast (272999), potassium (271094), potassium and yeast (2162)
*#** 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 (60)
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful included: Text availability, most recent, filtering out the older articles. It narrowed down my search to under 100 articles.
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful functions include: time intervals of when the articles were released/updated, date. The result changed from 21600 to 2100.
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful functions included: Times cited, Usage count, date after (year). Results went from 60 to 11

'''REFERENCE 1'''

# 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'''
# https://www.ncbi.nlm.nih.gov/pubmed/17048990
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609136/
# https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0040351
# https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.0040351&type=printable
# Copyright: � 2006 Hess et al
# Article is open to the public
# Availibility: Online
# Publisher: PLOS Biology
# Earliest Publish Date: 2003
# Peer-reviewed: Yes
# https://journals.plos.org/plosbiology/s/editorial-board
# Impact Factor: 8.386 (2018)
# Primary Research article
# https://ndownloader.figshare.com/files/471538

'''REFERENCE 2'''

# 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
# https://www.ncbi.nlm.nih.gov/pubmed/29218312
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716641/
# http://www.ijcep.org/index.php/ijcep/article/view/182
# http://www.ijcep.org/index.php/ijcep/article/view/182/162
# © 2017 International Journal of Clinical and Experimental Physiology
# Open to the public
# Availability: Online
# Published by Wolters Kluwer - Medknow
# Earliest Published Daye: 2014
# Peer-Reviewed
# http://www.ijcep.org/index.php/ijcep/about/editorialTeam
# Impact Factor: 1.706 (2016)
# Review Article
# NA

==Data/Files==

[[Media:Jonar_Cowan_Team_Skinny_Genes.pdf | Skinny Genes Presentation]]

==Conclusion==

==Acknowledgements==

This week we were put into teams. The team I was assigned to was Team [[Skinny_Genes|Skinny Genes]]. The other members are [[User:Msamdars|Mihir Samdars]], [[User:Ymesfin|Aby Mesfin]], [[User:Dramir36 |David Ramirez]], [[User:Cdomin12|Christina Dominguez]]. We worked in and out of class together Monday and Wednesday.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

==References==
# LMU BioDB 2019. (2019). Week 11. Retrieved November 7, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
# MediaWiki (2019). Category: Help. Retrieved November 11, 2019, from https://www.mediawiki.org/wiki/Category:Help
# Lagarias, J.C., Duanmu, D., Casero, D., Dent, R.M., Gallaher, S., Yang, W., Rockwell, N.C., Martin, S.S., Pellegrini, M., Niyogi, K.K., Merchant, S.S., Grossman, A.R. (2013). "Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival". Proceedings of the National Academy of Sciences of the United States of America. 110 (9): 3621–3626. doi:10.1073/pnas.1222375110.
# Douglas, L. M., Alvarez, F. J., McCreary, C., & Konopka, J. B. (2005). "Septin function in yeast model systems and pathogenic fungi". Eukaryotic Cell. 4 (9): 1503–12.
# Biology Online. (2019). Retrieved November 7, 2019 from https://biology-online.org
# Smith, A. (2000). Oxford Dictionary of Biochemistry and Molecular Biology: Revised Edition. Oxford University Press.
# Lackie, J. M. (Ed.). (2007). The dictionary of cell & molecular biology. Academic Press. Retrieved November 11, 2019 from http://ebookcentral.proquest.com/lib/lmu/detail.action?docID=311420.
# Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group. AmiGO: online access to ontology and annotation data. Bioinformatics. Jan 2009;25(2):288-289. Retrieved November 11, 2019 from http://amigo.geneontology.org/amigo/
# Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., ... & Fisk, D. G. (2011). Saccharomyces Genome Database: the genomics resource of budding yeast. ''Nucleic Acids Research'', 40(D1), D700-D705.

{{jcowan4}}
(*Participation: Table 2, Introduction (Background Information), Question 1, Question 3)

Jcowan4 Journal Week 11

2019-11-19T05:44:08Z

Jcowan4: /* Annotated Bibliography */ header

==Biological Terms==

Intracellular: Occurring or being (situated) inside a cell or cells. (Biology Online, 2019)

Transcriptomic: The study of all RNA molecules in a cell. RNA is copied from pieces of DNA and contains information to make proteins and perform other important functions in the cell. Transcriptomics is used to learn more about how genes are turned on in different types of cells and how this may help cause certain diseases, such as cancer.

Extracellular: Occurring or being (situated) outside the cell or cells. (Biology Online, 2019)

Methionine: (Science: biochemistry) Contains the SCH3 group that can act as a methyl donor (see s adenosyl methionine). Common in proteins but at low frequency. The met x linkage is subject to specific cleavage by cyanogen bromide. (Biology Online, 2019)

Biosynthesis: The production of a complex chemical compound from simpler precursors in a living organism, usually involving enzymes (to catalyze the reaction) and energy source (such as ATP). (Biology Online, 2019)

B-galactosidase: A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.

Homocysteine: The chemical reactions and pathways resulting in the formation of homocysteine, 2-amino-4-sulfanylbutanoic acid.

Oxidative: Capable of oxidizing other substances. Of, pertaining to, or produced by oxidation. (Biology Online, 2019)

Glutathione: (Science: biochemistry) The tripeptide _ glutamylcysteinylglycine. It contains an unusual peptide Linkage between the _ carboxyl group of the glutamate side chain and the amine group of cysteine. (Biology Online, 2019)

Substrate: A substratum or an underlying stratum. (Biology Online, 2019)

Transduction: there are a group of viruses called bacteriophages. These bacteriophages inject their viral dna into the host cell of bacteria. The viral dna then becomes incorporated into the chromosome of the bacterium. Thus the viral dna forms part of the bacterial chromosome and will be copied to all daughter cells. Though this viral dna will become active again at low frequency's. (Biology Online, 2019)

==Outline==

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

The main result found in the article was how the Saccharomyces cerevisiae short-term potassium deprivation causes a lack of potassium which affects and changes sulfur metabolism. This leads to an oxidative stress response and activates the retrograde pathway. It is stated that the catalyst could possibly be ammonium accumulation that happens through the Trk1 potassium transporter. Other results include: a halt in gene expression required for ribosome biogenesis and translation, a decrease in the expression of diverse components used in the progression of cell cycle and blockage in septins assembly. Essentially, a shortage of potassium in the environment triggers an acute transcriptional response, which opens up new finds and more areas to be explored.

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

The significance of this work is the new discoveries and pathways involving potassium and its role in cellular life.

===What were the limitations in previous studies that led them to perform this work?===
There were no previous studies that directly correlate to this work. However, there are multiple studies that are able to supplement the work.

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

The yeast cells were put into a YBN growth medium that lacked normal amounts of potassium and ammonium (potassium starvation). The cells were recorded and monitored in time intervals of 0, 10, 20, 30, 40, 60 and 120 minutes.

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

'''Strains:'''

*YNR055.1

*YPC722, YPC723, YPC724,

*BY4741, BY4741 rtg2, BY4741 rtg3, BY4741 fzo1

*BYT1, BYT2, BYT12

*W303-1A

*DBY746

(*The information regarding the if they were haploid or diploid wa not given)

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

*Grown in translucent potassium-free YNB media
*Temperature: 28 Celsius
*Incubator: N/A
*The times used were 0, 10, 20, 40, 60 and 120 minutes

===What controls did they use?===
Controls: wild-type strain BY4741, 50mM KCI added

===How many replicates did they perform per treatment or timepoint?===
4 Replicates per timepoint

===What method did they use to prepare the RNA, label it and hybridize it to the microarray? ===
RNA extraction using the Ribo Pure™-Yeast kit

===What mathematical/statistical method did they use to analyze the data?===
They used GEPAS v3.1

===Are the data publicly available for download? From which web site?===
The data could be found at [https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x Society for Applied Microbiology]

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

'''Table 1''' shows the transcriptional changes between 10, 20, 40, 60, and 120 minutes. It measures the amount of genes that are induced and repressed at each timepoint.

'''Table 2''' shows a list of strains that were used.

'''Figure 1''' shows that the majority of genes were induced/repressed between 60-120 minutes after being transferred to a potassium free media. '''X''' = Timepoint '''Y''' = Genes

'''Figure 2''' '''(A)''' shows the how potassium starvation decreases sulfuric amino acid metabolism. This is seen in the model that depicts the how Met/Cys are metabolized. '''B''' is a graph that shows mRna concentration from the microarray '''X''' = mRna change '''Y''' = Genes. '''C''' shows the concentration of Met and Cys after the procedure. '''X''' = Timepoint '''Y''' = Genes (Met/Cys)

'''Figure 3''' shows the oxidative stress response in genes due to potassium deprivation. '''A''' shows the multiple genes reacting to potassium deprivation and is measured by the levels of oxidative stress. '''B''' shows images of the genes responding to the procedure. '''Y''' = Time intervals. '''C''' shows the change in Glutanione level due to potassium starvation.

'''Figure 4''' shows the effects of methylglyoxal production and treholse production from potassium starvation. '''A''' shows how the production of each is made. '''B''' shows the changes in expression '''X''' = Timepoint '''Y''' = Changes in expression (-fold). '''C''' shows the levels of methyglyoxal when affected by potassium starvation. '''X''' = Timepoint '''Y''' = Methyglyoxal Levels.

'''Figure 5''' shows the a correlation between the expression of CIT2 and DLD3 genes and potassium starvation. '''A''' shows the changes in expression for genes and an image of the changes in CIT2, DLD3 and ACT1. '''B''' shows the changes in mitochondrial change before and after the procedure and images of WT and fzo1. '''C''' & '''D''' shows the graph depicting the relative concentration of intracellular ammonium after treatment.

'''Figure 6''' shows expression of genes controlling cyclins express various responses to potassium starvation. '''A''' shows a graph demonstrating the change in expression levels of retrograde after potassium starvation. '''X''' = Timepoint '''Y''' = log2 change in expression levels. '''B''' are images depicting relative abundance of cyclin mRNA & '''C''' are images depicting relative abundance of cyclin protein

'''Figure 7''' shows that potassium starvation decreases septin ring formation. '''A''' shows a graph that represents the change in expression levels of septin ring fomration genes after potassium starvation. '''B''' are images depicting the localization of Cdc11-GFP during treatment. '''C''' are images depicting relative abundance of Cdc11 protein. '''D''' are images depicting the localization of Cdc11 protein

===How does this work compare with previous studies?===
No other previous works.

===What are the important implications of this work?===
The important implications of this work are understanding the results from potassium starvation and how it opens up a new study regarding cations starvation or the relationship of cations and cellular life.

===What future directions should the authors take?===
The authors should try to understand how potassium affects other cations or how potassium affects other objects aside from yeast.

===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?===
The author's data supported their conclusion and could be seen when they used analyzing the figures and tables. However, the paper was extremely dense and required more research in order to understand the procedure and results.

==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? Yeast (283103), potassium (259156), potassium and yeast (3055)
*#** 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 (66)
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? Yeast (3090000), potassium (4370000), potassium and yeast (1290000)
*#** 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 (41600)
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get? Yeast (272999), potassium (271094), potassium and yeast (2162)
*#** 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 (60)
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful included: Text availability, most recent, filtering out the older articles. It narrowed down my search to under 100 articles.
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful functions include: time intervals of when the articles were released/updated, date. The result changed from 21600 to 2100.
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful functions included: Times cited, Usage count, date after (year). Results went from 60 to 11
*#* 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?

# 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)

'''REFERENCE 1'''

# 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'''
# https://www.ncbi.nlm.nih.gov/pubmed/17048990
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609136/
# https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0040351
# https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.0040351&type=printable
# Copyright: � 2006 Hess et al
# Article is open to the public
# Availibility: Online
# Publisher: POS Biology
# Earliest Publish Date: 2003
# Peer-reviewed: Yes
# https://journals.plos.org/plosbiology/s/editorial-board
# Impact Factor: 8.386 (2018)
# Primary Research article
# https://ndownloader.figshare.com/files/471538

==Data/Files==

[[Media:Jonar_Cowan_Team_Skinny_Genes.pdf | Skinny Genes Presentation]]

==Conclusion==

==Acknowledgements==

This week we were put into teams. The team I was assigned to was Team [[Skinny_Genes|Skinny Genes]]. The other members are [[User:Msamdars|Mihir Samdars]], [[User:Ymesfin|Aby Mesfin]], [[User:Dramir36 |David Ramirez]], [[User:Cdomin12|Christina Dominguez]]. We worked in and out of class together Monday and Wednesday.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

==References==
# LMU BioDB 2019. (2019). Week 11. Retrieved November 7, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
# MediaWiki (2019). Category: Help. Retrieved November 11, 2019, from https://www.mediawiki.org/wiki/Category:Help
# Lagarias, J.C., Duanmu, D., Casero, D., Dent, R.M., Gallaher, S., Yang, W., Rockwell, N.C., Martin, S.S., Pellegrini, M., Niyogi, K.K., Merchant, S.S., Grossman, A.R. (2013). "Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival". Proceedings of the National Academy of Sciences of the United States of America. 110 (9): 3621–3626. doi:10.1073/pnas.1222375110.
# Douglas, L. M., Alvarez, F. J., McCreary, C., & Konopka, J. B. (2005). "Septin function in yeast model systems and pathogenic fungi". Eukaryotic Cell. 4 (9): 1503–12.
# Biology Online. (2019). Retrieved November 7, 2019 from https://biology-online.org
# Smith, A. (2000). Oxford Dictionary of Biochemistry and Molecular Biology: Revised Edition. Oxford University Press.
# Lackie, J. M. (Ed.). (2007). The dictionary of cell & molecular biology. Academic Press. Retrieved November 11, 2019 from http://ebookcentral.proquest.com/lib/lmu/detail.action?docID=311420.
# Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group. AmiGO: online access to ontology and annotation data. Bioinformatics. Jan 2009;25(2):288-289. Retrieved November 11, 2019 from http://amigo.geneontology.org/amigo/
# Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., ... & Fisk, D. G. (2011). Saccharomyces Genome Database: the genomics resource of budding yeast. ''Nucleic Acids Research'', 40(D1), D700-D705.

{{jcowan4}}
(*Participation: Table 2, Introduction (Background Information), Question 1, Question 3)

Jcowan4 Journal Week 11

2019-11-19T05:39:46Z

Jcowan4: /* Annotated Bibliography */ Finished reference 1

==Biological Terms==

Intracellular: Occurring or being (situated) inside a cell or cells. (Biology Online, 2019)

Transcriptomic: The study of all RNA molecules in a cell. RNA is copied from pieces of DNA and contains information to make proteins and perform other important functions in the cell. Transcriptomics is used to learn more about how genes are turned on in different types of cells and how this may help cause certain diseases, such as cancer.

Extracellular: Occurring or being (situated) outside the cell or cells. (Biology Online, 2019)

Methionine: (Science: biochemistry) Contains the SCH3 group that can act as a methyl donor (see s adenosyl methionine). Common in proteins but at low frequency. The met x linkage is subject to specific cleavage by cyanogen bromide. (Biology Online, 2019)

Biosynthesis: The production of a complex chemical compound from simpler precursors in a living organism, usually involving enzymes (to catalyze the reaction) and energy source (such as ATP). (Biology Online, 2019)

B-galactosidase: A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.

Homocysteine: The chemical reactions and pathways resulting in the formation of homocysteine, 2-amino-4-sulfanylbutanoic acid.

Oxidative: Capable of oxidizing other substances. Of, pertaining to, or produced by oxidation. (Biology Online, 2019)

Glutathione: (Science: biochemistry) The tripeptide _ glutamylcysteinylglycine. It contains an unusual peptide Linkage between the _ carboxyl group of the glutamate side chain and the amine group of cysteine. (Biology Online, 2019)

Substrate: A substratum or an underlying stratum. (Biology Online, 2019)

Transduction: there are a group of viruses called bacteriophages. These bacteriophages inject their viral dna into the host cell of bacteria. The viral dna then becomes incorporated into the chromosome of the bacterium. Thus the viral dna forms part of the bacterial chromosome and will be copied to all daughter cells. Though this viral dna will become active again at low frequency's. (Biology Online, 2019)

==Outline==

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

The main result found in the article was how the Saccharomyces cerevisiae short-term potassium deprivation causes a lack of potassium which affects and changes sulfur metabolism. This leads to an oxidative stress response and activates the retrograde pathway. It is stated that the catalyst could possibly be ammonium accumulation that happens through the Trk1 potassium transporter. Other results include: a halt in gene expression required for ribosome biogenesis and translation, a decrease in the expression of diverse components used in the progression of cell cycle and blockage in septins assembly. Essentially, a shortage of potassium in the environment triggers an acute transcriptional response, which opens up new finds and more areas to be explored.

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

The significance of this work is the new discoveries and pathways involving potassium and its role in cellular life.

===What were the limitations in previous studies that led them to perform this work?===
There were no previous studies that directly correlate to this work. However, there are multiple studies that are able to supplement the work.

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

The yeast cells were put into a YBN growth medium that lacked normal amounts of potassium and ammonium (potassium starvation). The cells were recorded and monitored in time intervals of 0, 10, 20, 30, 40, 60 and 120 minutes.

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

'''Strains:'''

*YNR055.1

*YPC722, YPC723, YPC724,

*BY4741, BY4741 rtg2, BY4741 rtg3, BY4741 fzo1

*BYT1, BYT2, BYT12

*W303-1A

*DBY746

(*The information regarding the if they were haploid or diploid wa not given)

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

*Grown in translucent potassium-free YNB media
*Temperature: 28 Celsius
*Incubator: N/A
*The times used were 0, 10, 20, 40, 60 and 120 minutes

===What controls did they use?===
Controls: wild-type strain BY4741, 50mM KCI added

===How many replicates did they perform per treatment or timepoint?===
4 Replicates per timepoint

===What method did they use to prepare the RNA, label it and hybridize it to the microarray? ===
RNA extraction using the Ribo Pure™-Yeast kit

===What mathematical/statistical method did they use to analyze the data?===
They used GEPAS v3.1

===Are the data publicly available for download? From which web site?===
The data could be found at [https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x Society for Applied Microbiology]

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

'''Table 1''' shows the transcriptional changes between 10, 20, 40, 60, and 120 minutes. It measures the amount of genes that are induced and repressed at each timepoint.

'''Table 2''' shows a list of strains that were used.

'''Figure 1''' shows that the majority of genes were induced/repressed between 60-120 minutes after being transferred to a potassium free media. '''X''' = Timepoint '''Y''' = Genes

'''Figure 2''' '''(A)''' shows the how potassium starvation decreases sulfuric amino acid metabolism. This is seen in the model that depicts the how Met/Cys are metabolized. '''B''' is a graph that shows mRna concentration from the microarray '''X''' = mRna change '''Y''' = Genes. '''C''' shows the concentration of Met and Cys after the procedure. '''X''' = Timepoint '''Y''' = Genes (Met/Cys)

'''Figure 3''' shows the oxidative stress response in genes due to potassium deprivation. '''A''' shows the multiple genes reacting to potassium deprivation and is measured by the levels of oxidative stress. '''B''' shows images of the genes responding to the procedure. '''Y''' = Time intervals. '''C''' shows the change in Glutanione level due to potassium starvation.

'''Figure 4''' shows the effects of methylglyoxal production and treholse production from potassium starvation. '''A''' shows how the production of each is made. '''B''' shows the changes in expression '''X''' = Timepoint '''Y''' = Changes in expression (-fold). '''C''' shows the levels of methyglyoxal when affected by potassium starvation. '''X''' = Timepoint '''Y''' = Methyglyoxal Levels.

'''Figure 5''' shows the a correlation between the expression of CIT2 and DLD3 genes and potassium starvation. '''A''' shows the changes in expression for genes and an image of the changes in CIT2, DLD3 and ACT1. '''B''' shows the changes in mitochondrial change before and after the procedure and images of WT and fzo1. '''C''' & '''D''' shows the graph depicting the relative concentration of intracellular ammonium after treatment.

'''Figure 6''' shows expression of genes controlling cyclins express various responses to potassium starvation. '''A''' shows a graph demonstrating the change in expression levels of retrograde after potassium starvation. '''X''' = Timepoint '''Y''' = log2 change in expression levels. '''B''' are images depicting relative abundance of cyclin mRNA & '''C''' are images depicting relative abundance of cyclin protein

'''Figure 7''' shows that potassium starvation decreases septin ring formation. '''A''' shows a graph that represents the change in expression levels of septin ring fomration genes after potassium starvation. '''B''' are images depicting the localization of Cdc11-GFP during treatment. '''C''' are images depicting relative abundance of Cdc11 protein. '''D''' are images depicting the localization of Cdc11 protein

===How does this work compare with previous studies?===
No other previous works.

===What are the important implications of this work?===
The important implications of this work are understanding the results from potassium starvation and how it opens up a new study regarding cations starvation or the relationship of cations and cellular life.

===What future directions should the authors take?===
The authors should try to understand how potassium affects other cations or how potassium affects other objects aside from yeast.

===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?===
The author's data supported their conclusion and could be seen when they used analyzing the figures and tables. However, the paper was extremely dense and required more research in order to understand the procedure and results.

==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? Yeast (283103), potassium (259156), potassium and yeast (3055)
*#** 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 (66)
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? Yeast (3090000), potassium (4370000), potassium and yeast (1290000)
*#** 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 (41600)
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get? Yeast (272999), potassium (271094), potassium and yeast (2162)
*#** 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 (60)
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful included: Text availability, most recent, filtering out the older articles. It narrowed down my search to under 100 articles.
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful functions include: time intervals of when the articles were released/updated, date. The result changed from 21600 to 2100.
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful functions included: Times cited, Usage count, date after (year). Results went from 60 to 11
*#* 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?

# 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)

# 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'''
# https://www.ncbi.nlm.nih.gov/pubmed/17048990
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609136/
# https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0040351
# https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.0040351&type=printable
# Copyright: � 2006 Hess et al
# Article is open to the public
# Availibility: Online
# Publisher: POS Biology
# Earliest Publish Date: 2003
# Peer-reviewed: Yes
# https://journals.plos.org/plosbiology/s/editorial-board
# Impact Factor: 8.386 (2018)
# Primary Research article
# https://ndownloader.figshare.com/files/471538

==Data/Files==

[[Media:Jonar_Cowan_Team_Skinny_Genes.pdf | Skinny Genes Presentation]]

==Conclusion==

==Acknowledgements==

This week we were put into teams. The team I was assigned to was Team [[Skinny_Genes|Skinny Genes]]. The other members are [[User:Msamdars|Mihir Samdars]], [[User:Ymesfin|Aby Mesfin]], [[User:Dramir36 |David Ramirez]], [[User:Cdomin12|Christina Dominguez]]. We worked in and out of class together Monday and Wednesday.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

==References==
# LMU BioDB 2019. (2019). Week 11. Retrieved November 7, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
# MediaWiki (2019). Category: Help. Retrieved November 11, 2019, from https://www.mediawiki.org/wiki/Category:Help
# Lagarias, J.C., Duanmu, D., Casero, D., Dent, R.M., Gallaher, S., Yang, W., Rockwell, N.C., Martin, S.S., Pellegrini, M., Niyogi, K.K., Merchant, S.S., Grossman, A.R. (2013). "Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival". Proceedings of the National Academy of Sciences of the United States of America. 110 (9): 3621–3626. doi:10.1073/pnas.1222375110.
# Douglas, L. M., Alvarez, F. J., McCreary, C., & Konopka, J. B. (2005). "Septin function in yeast model systems and pathogenic fungi". Eukaryotic Cell. 4 (9): 1503–12.
# Biology Online. (2019). Retrieved November 7, 2019 from https://biology-online.org
# Smith, A. (2000). Oxford Dictionary of Biochemistry and Molecular Biology: Revised Edition. Oxford University Press.
# Lackie, J. M. (Ed.). (2007). The dictionary of cell & molecular biology. Academic Press. Retrieved November 11, 2019 from http://ebookcentral.proquest.com/lib/lmu/detail.action?docID=311420.
# Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group. AmiGO: online access to ontology and annotation data. Bioinformatics. Jan 2009;25(2):288-289. Retrieved November 11, 2019 from http://amigo.geneontology.org/amigo/
# Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., ... & Fisk, D. G. (2011). Saccharomyces Genome Database: the genomics resource of budding yeast. ''Nucleic Acids Research'', 40(D1), D700-D705.

{{jcowan4}}
(*Participation: Table 2, Introduction (Background Information), Question 1, Question 3)

Jcowan4 Journal Week 11

2019-11-19T04:34:27Z

Jcowan4: /* Annotated Bibliography */ answered

==Biological Terms==

Intracellular: Occurring or being (situated) inside a cell or cells. (Biology Online, 2019)

Transcriptomic: The study of all RNA molecules in a cell. RNA is copied from pieces of DNA and contains information to make proteins and perform other important functions in the cell. Transcriptomics is used to learn more about how genes are turned on in different types of cells and how this may help cause certain diseases, such as cancer.

Extracellular: Occurring or being (situated) outside the cell or cells. (Biology Online, 2019)

Methionine: (Science: biochemistry) Contains the SCH3 group that can act as a methyl donor (see s adenosyl methionine). Common in proteins but at low frequency. The met x linkage is subject to specific cleavage by cyanogen bromide. (Biology Online, 2019)

Biosynthesis: The production of a complex chemical compound from simpler precursors in a living organism, usually involving enzymes (to catalyze the reaction) and energy source (such as ATP). (Biology Online, 2019)

B-galactosidase: A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.

Homocysteine: The chemical reactions and pathways resulting in the formation of homocysteine, 2-amino-4-sulfanylbutanoic acid.

Oxidative: Capable of oxidizing other substances. Of, pertaining to, or produced by oxidation. (Biology Online, 2019)

Glutathione: (Science: biochemistry) The tripeptide _ glutamylcysteinylglycine. It contains an unusual peptide Linkage between the _ carboxyl group of the glutamate side chain and the amine group of cysteine. (Biology Online, 2019)

Substrate: A substratum or an underlying stratum. (Biology Online, 2019)

Transduction: there are a group of viruses called bacteriophages. These bacteriophages inject their viral dna into the host cell of bacteria. The viral dna then becomes incorporated into the chromosome of the bacterium. Thus the viral dna forms part of the bacterial chromosome and will be copied to all daughter cells. Though this viral dna will become active again at low frequency's. (Biology Online, 2019)

==Outline==

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

The main result found in the article was how the Saccharomyces cerevisiae short-term potassium deprivation causes a lack of potassium which affects and changes sulfur metabolism. This leads to an oxidative stress response and activates the retrograde pathway. It is stated that the catalyst could possibly be ammonium accumulation that happens through the Trk1 potassium transporter. Other results include: a halt in gene expression required for ribosome biogenesis and translation, a decrease in the expression of diverse components used in the progression of cell cycle and blockage in septins assembly. Essentially, a shortage of potassium in the environment triggers an acute transcriptional response, which opens up new finds and more areas to be explored.

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

The significance of this work is the new discoveries and pathways involving potassium and its role in cellular life.

===What were the limitations in previous studies that led them to perform this work?===
There were no previous studies that directly correlate to this work. However, there are multiple studies that are able to supplement the work.

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

The yeast cells were put into a YBN growth medium that lacked normal amounts of potassium and ammonium (potassium starvation). The cells were recorded and monitored in time intervals of 0, 10, 20, 30, 40, 60 and 120 minutes.

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

'''Strains:'''

*YNR055.1

*YPC722, YPC723, YPC724,

*BY4741, BY4741 rtg2, BY4741 rtg3, BY4741 fzo1

*BYT1, BYT2, BYT12

*W303-1A

*DBY746

(*The information regarding the if they were haploid or diploid wa not given)

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

*Grown in translucent potassium-free YNB media
*Temperature: 28 Celsius
*Incubator: N/A
*The times used were 0, 10, 20, 40, 60 and 120 minutes

===What controls did they use?===
Controls: wild-type strain BY4741, 50mM KCI added

===How many replicates did they perform per treatment or timepoint?===
4 Replicates per timepoint

===What method did they use to prepare the RNA, label it and hybridize it to the microarray? ===
RNA extraction using the Ribo Pure™-Yeast kit

===What mathematical/statistical method did they use to analyze the data?===
They used GEPAS v3.1

===Are the data publicly available for download? From which web site?===
The data could be found at [https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x Society for Applied Microbiology]

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

'''Table 1''' shows the transcriptional changes between 10, 20, 40, 60, and 120 minutes. It measures the amount of genes that are induced and repressed at each timepoint.

'''Table 2''' shows a list of strains that were used.

'''Figure 1''' shows that the majority of genes were induced/repressed between 60-120 minutes after being transferred to a potassium free media. '''X''' = Timepoint '''Y''' = Genes

'''Figure 2''' '''(A)''' shows the how potassium starvation decreases sulfuric amino acid metabolism. This is seen in the model that depicts the how Met/Cys are metabolized. '''B''' is a graph that shows mRna concentration from the microarray '''X''' = mRna change '''Y''' = Genes. '''C''' shows the concentration of Met and Cys after the procedure. '''X''' = Timepoint '''Y''' = Genes (Met/Cys)

'''Figure 3''' shows the oxidative stress response in genes due to potassium deprivation. '''A''' shows the multiple genes reacting to potassium deprivation and is measured by the levels of oxidative stress. '''B''' shows images of the genes responding to the procedure. '''Y''' = Time intervals. '''C''' shows the change in Glutanione level due to potassium starvation.

'''Figure 4''' shows the effects of methylglyoxal production and treholse production from potassium starvation. '''A''' shows how the production of each is made. '''B''' shows the changes in expression '''X''' = Timepoint '''Y''' = Changes in expression (-fold). '''C''' shows the levels of methyglyoxal when affected by potassium starvation. '''X''' = Timepoint '''Y''' = Methyglyoxal Levels.

'''Figure 5''' shows the a correlation between the expression of CIT2 and DLD3 genes and potassium starvation. '''A''' shows the changes in expression for genes and an image of the changes in CIT2, DLD3 and ACT1. '''B''' shows the changes in mitochondrial change before and after the procedure and images of WT and fzo1. '''C''' & '''D''' shows the graph depicting the relative concentration of intracellular ammonium after treatment.

'''Figure 6''' shows expression of genes controlling cyclins express various responses to potassium starvation. '''A''' shows a graph demonstrating the change in expression levels of retrograde after potassium starvation. '''X''' = Timepoint '''Y''' = log2 change in expression levels. '''B''' are images depicting relative abundance of cyclin mRNA & '''C''' are images depicting relative abundance of cyclin protein

'''Figure 7''' shows that potassium starvation decreases septin ring formation. '''A''' shows a graph that represents the change in expression levels of septin ring fomration genes after potassium starvation. '''B''' are images depicting the localization of Cdc11-GFP during treatment. '''C''' are images depicting relative abundance of Cdc11 protein. '''D''' are images depicting the localization of Cdc11 protein

===How does this work compare with previous studies?===
No other previous works.

===What are the important implications of this work?===
The important implications of this work are understanding the results from potassium starvation and how it opens up a new study regarding cations starvation or the relationship of cations and cellular life.

===What future directions should the authors take?===
The authors should try to understand how potassium affects other cations or how potassium affects other objects aside from yeast.

===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?===
The author's data supported their conclusion and could be seen when they used analyzing the figures and tables. However, the paper was extremely dense and required more research in order to understand the procedure and results.

==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? Yeast (283103), potassium (259156), potassium and yeast (3055)
*#** 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 (66)
*#* Google Scholar
*#** What original keyword(s) did you use? How many results did you get? Yeast (3090000), potassium (4370000), potassium and yeast (1290000)
*#** 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 (41600)
*#* Web of Science
*#** What original keyword(s) did you use? How many results did you get? Yeast (272999), potassium (271094), potassium and yeast (2162)
*#** 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 (60)
*# Use the advanced search functions for each of these three databases/tools and answer the following:
*#* PubMed
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful included: Text availability, most recent, filtering out the older articles. It narrowed down my search to under 100 articles.
*#* Google Scholar
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful functions include: time intervals of when the articles were released/updated, date. The result changed from 21600 to 2100.
*#* Web of Science
*#** Which advanced search functions were most useful to narrow down the search? How many results did you get? The most useful functions included: Times cited, Usage count, date after (year). Results went from 60 to 11
*#* 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?

# 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)

==Data/Files==

[[Media:Jonar_Cowan_Team_Skinny_Genes.pdf | Skinny Genes Presentation]]

==Conclusion==

==Acknowledgements==

This week we were put into teams. The team I was assigned to was Team [[Skinny_Genes|Skinny Genes]]. The other members are [[User:Msamdars|Mihir Samdars]], [[User:Ymesfin|Aby Mesfin]], [[User:Dramir36 |David Ramirez]], [[User:Cdomin12|Christina Dominguez]]. We worked in and out of class together Monday and Wednesday.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

==References==
# LMU BioDB 2019. (2019). Week 11. Retrieved November 7, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
# MediaWiki (2019). Category: Help. Retrieved November 11, 2019, from https://www.mediawiki.org/wiki/Category:Help
# Lagarias, J.C., Duanmu, D., Casero, D., Dent, R.M., Gallaher, S., Yang, W., Rockwell, N.C., Martin, S.S., Pellegrini, M., Niyogi, K.K., Merchant, S.S., Grossman, A.R. (2013). "Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival". Proceedings of the National Academy of Sciences of the United States of America. 110 (9): 3621–3626. doi:10.1073/pnas.1222375110.
# Douglas, L. M., Alvarez, F. J., McCreary, C., & Konopka, J. B. (2005). "Septin function in yeast model systems and pathogenic fungi". Eukaryotic Cell. 4 (9): 1503–12.
# Biology Online. (2019). Retrieved November 7, 2019 from https://biology-online.org
# Smith, A. (2000). Oxford Dictionary of Biochemistry and Molecular Biology: Revised Edition. Oxford University Press.
# Lackie, J. M. (Ed.). (2007). The dictionary of cell & molecular biology. Academic Press. Retrieved November 11, 2019 from http://ebookcentral.proquest.com/lib/lmu/detail.action?docID=311420.
# Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group. AmiGO: online access to ontology and annotation data. Bioinformatics. Jan 2009;25(2):288-289. Retrieved November 11, 2019 from http://amigo.geneontology.org/amigo/
# Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., ... & Fisk, D. G. (2011). Saccharomyces Genome Database: the genomics resource of budding yeast. ''Nucleic Acids Research'', 40(D1), D700-D705.

{{jcowan4}}
(*Participation: Table 2, Introduction (Background Information), Question 1, Question 3)

Skinny Genes

2019-11-19T03:29:56Z

Jcowan4: /* Annotated Bibliography */ added my articles and citations

{{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
#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

==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)

Skinny Genes

2019-11-14T07:59:22Z

Jcowan4: /* Jonar's Reflection */ signature

{{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

==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)

Jcowan4 Journal Week 11

2019-11-14T07:58:51Z

Jcowan4: /* Data/Files */ added presentation

==Biological Terms==

Intracellular: Occurring or being (situated) inside a cell or cells. (Biology Online, 2019)

Transcriptomic: The study of all RNA molecules in a cell. RNA is copied from pieces of DNA and contains information to make proteins and perform other important functions in the cell. Transcriptomics is used to learn more about how genes are turned on in different types of cells and how this may help cause certain diseases, such as cancer.

Extracellular: Occurring or being (situated) outside the cell or cells. (Biology Online, 2019)

Methionine: (Science: biochemistry) Contains the SCH3 group that can act as a methyl donor (see s adenosyl methionine). Common in proteins but at low frequency. The met x linkage is subject to specific cleavage by cyanogen bromide. (Biology Online, 2019)

Biosynthesis: The production of a complex chemical compound from simpler precursors in a living organism, usually involving enzymes (to catalyze the reaction) and energy source (such as ATP). (Biology Online, 2019)

B-galactosidase: A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.

Homocysteine: The chemical reactions and pathways resulting in the formation of homocysteine, 2-amino-4-sulfanylbutanoic acid.

Oxidative: Capable of oxidizing other substances. Of, pertaining to, or produced by oxidation. (Biology Online, 2019)

Glutathione: (Science: biochemistry) The tripeptide _ glutamylcysteinylglycine. It contains an unusual peptide Linkage between the _ carboxyl group of the glutamate side chain and the amine group of cysteine. (Biology Online, 2019)

Substrate: A substratum or an underlying stratum. (Biology Online, 2019)

Transduction: there are a group of viruses called bacteriophages. These bacteriophages inject their viral dna into the host cell of bacteria. The viral dna then becomes incorporated into the chromosome of the bacterium. Thus the viral dna forms part of the bacterial chromosome and will be copied to all daughter cells. Though this viral dna will become active again at low frequency's. (Biology Online, 2019)

==Outline==

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

The main result found in the article was how the Saccharomyces cerevisiae short-term potassium deprivation causes a lack of potassium which affects and changes sulfur metabolism. This leads to an oxidative stress response and activates the retrograde pathway. It is stated that the catalyst could possibly be ammonium accumulation that happens through the Trk1 potassium transporter. Other results include: a halt in gene expression required for ribosome biogenesis and translation, a decrease in the expression of diverse components used in the progression of cell cycle and blockage in septins assembly. Essentially, a shortage of potassium in the environment triggers an acute transcriptional response, which opens up new finds and more areas to be explored.

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

The significance of this work is the new discoveries and pathways involving potassium and its role in cellular life.

===What were the limitations in previous studies that led them to perform this work?===
There were no previous studies that directly correlate to this work. However, there are multiple studies that are able to supplement the work.

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

The yeast cells were put into a YBN growth medium that lacked normal amounts of potassium and ammonium (potassium starvation). The cells were recorded and monitored in time intervals of 0, 10, 20, 30, 40, 60 and 120 minutes.

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

'''Strains:'''

*YNR055.1

*YPC722, YPC723, YPC724,

*BY4741, BY4741 rtg2, BY4741 rtg3, BY4741 fzo1

*BYT1, BYT2, BYT12

*W303-1A

*DBY746

(*The information regarding the if they were haploid or diploid wa not given)

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

*Grown in translucent potassium-free YNB media
*Temperature: 28 Celsius
*Incubator: N/A
*The times used were 0, 10, 20, 40, 60 and 120 minutes

===What controls did they use?===
Controls: wild-type strain BY4741, 50mM KCI added

===How many replicates did they perform per treatment or timepoint?===
4 Replicates per timepoint

===What method did they use to prepare the RNA, label it and hybridize it to the microarray? ===
RNA extraction using the Ribo Pure™-Yeast kit

===What mathematical/statistical method did they use to analyze the data?===
They used GEPAS v3.1

===Are the data publicly available for download? From which web site?===
The data could be found at [https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x Society for Applied Microbiology]

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

'''Table 1''' shows the transcriptional changes between 10, 20, 40, 60, and 120 minutes. It measures the amount of genes that are induced and repressed at each timepoint.

'''Table 2''' shows a list of strains that were used.

'''Figure 1''' shows that the majority of genes were induced/repressed between 60-120 minutes after being transferred to a potassium free media. '''X''' = Timepoint '''Y''' = Genes

'''Figure 2''' '''(A)''' shows the how potassium starvation decreases sulfuric amino acid metabolism. This is seen in the model that depicts the how Met/Cys are metabolized. '''B''' is a graph that shows mRna concentration from the microarray '''X''' = mRna change '''Y''' = Genes. '''C''' shows the concentration of Met and Cys after the procedure. '''X''' = Timepoint '''Y''' = Genes (Met/Cys)

'''Figure 3''' shows the oxidative stress response in genes due to potassium deprivation. '''A''' shows the multiple genes reacting to potassium deprivation and is measured by the levels of oxidative stress. '''B''' shows images of the genes responding to the procedure. '''Y''' = Time intervals. '''C''' shows the change in Glutanione level due to potassium starvation.

'''Figure 4''' shows the effects of methylglyoxal production and treholse production from potassium starvation. '''A''' shows how the production of each is made. '''B''' shows the changes in expression '''X''' = Timepoint '''Y''' = Changes in expression (-fold). '''C''' shows the levels of methyglyoxal when affected by potassium starvation. '''X''' = Timepoint '''Y''' = Methyglyoxal Levels.

'''Figure 5''' shows the a correlation between the expression of CIT2 and DLD3 genes and potassium starvation. '''A''' shows the changes in expression for genes and an image of the changes in CIT2, DLD3 and ACT1. '''B''' shows the changes in mitochondrial change before and after the procedure and images of WT and fzo1. '''C''' & '''D''' shows the graph depicting the relative concentration of intracellular ammonium after treatment.

'''Figure 6''' shows expression of genes controlling cyclins express various responses to potassium starvation. '''A''' shows a graph demonstrating the change in expression levels of retrograde after potassium starvation. '''X''' = Timepoint '''Y''' = log2 change in expression levels. '''B''' are images depicting relative abundance of cyclin mRNA & '''C''' are images depicting relative abundance of cyclin protein

'''Figure 7''' shows that potassium starvation decreases septin ring formation. '''A''' shows a graph that represents the change in expression levels of septin ring fomration genes after potassium starvation. '''B''' are images depicting the localization of Cdc11-GFP during treatment. '''C''' are images depicting relative abundance of Cdc11 protein. '''D''' are images depicting the localization of Cdc11 protein

===How does this work compare with previous studies?===
No other previous works.

===What are the important implications of this work?===
The important implications of this work are understanding the results from potassium starvation and how it opens up a new study regarding cations starvation or the relationship of cations and cellular life.

===What future directions should the authors take?===
The authors should try to understand how potassium affects other cations or how potassium affects other objects aside from yeast.

===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?===
The author's data supported their conclusion and could be seen when they used analyzing the figures and tables. However, the paper was extremely dense and required more research in order to understand the procedure and results.

==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?

==Data/Files==

[[Media:Jonar_Cowan_Team_Skinny_Genes.pdf | Skinny Genes Presentation]]

==Conclusion==

==Acknowledgements==

This week we were put into teams. The team I was assigned to was Team [[Skinny_Genes|Skinny Genes]]. The other members are [[User:Msamdars|Mihir Samdars]], [[User:Ymesfin|Aby Mesfin]], [[User:Dramir36 |David Ramirez]], [[User:Cdomin12|Christina Dominguez]]. We worked in and out of class together Monday and Wednesday.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

==References==
# LMU BioDB 2019. (2019). Week 11. Retrieved November 7, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
# MediaWiki (2019). Category: Help. Retrieved November 11, 2019, from https://www.mediawiki.org/wiki/Category:Help
# Lagarias, J.C., Duanmu, D., Casero, D., Dent, R.M., Gallaher, S., Yang, W., Rockwell, N.C., Martin, S.S., Pellegrini, M., Niyogi, K.K., Merchant, S.S., Grossman, A.R. (2013). "Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival". Proceedings of the National Academy of Sciences of the United States of America. 110 (9): 3621–3626. doi:10.1073/pnas.1222375110.
# Douglas, L. M., Alvarez, F. J., McCreary, C., & Konopka, J. B. (2005). "Septin function in yeast model systems and pathogenic fungi". Eukaryotic Cell. 4 (9): 1503–12.
# Biology Online. (2019). Retrieved November 7, 2019 from https://biology-online.org
# Smith, A. (2000). Oxford Dictionary of Biochemistry and Molecular Biology: Revised Edition. Oxford University Press.
# Lackie, J. M. (Ed.). (2007). The dictionary of cell & molecular biology. Academic Press. Retrieved November 11, 2019 from http://ebookcentral.proquest.com/lib/lmu/detail.action?docID=311420.
# Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group. AmiGO: online access to ontology and annotation data. Bioinformatics. Jan 2009;25(2):288-289. Retrieved November 11, 2019 from http://amigo.geneontology.org/amigo/
# Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., ... & Fisk, D. G. (2011). Saccharomyces Genome Database: the genomics resource of budding yeast. ''Nucleic Acids Research'', 40(D1), D700-D705.

{{jcowan4}}
(*Participation: Table 2, Introduction (Background Information), Question 1, Question 3)

File:Jonar Cowan Team Skinny Genes.pdf

2019-11-14T07:57:03Z

Jcowan4: Team Presentation for Skinny Genes

== Summary ==
Team Presentation for Skinny Genes

Jcowan4 Journal Week 11

2019-11-14T06:14:06Z

Jcowan4: /* Biological Terms */ added definition

==Biological Terms==

Intracellular: Occurring or being (situated) inside a cell or cells. (Biology Online, 2019)

Transcriptomic: The study of all RNA molecules in a cell. RNA is copied from pieces of DNA and contains information to make proteins and perform other important functions in the cell. Transcriptomics is used to learn more about how genes are turned on in different types of cells and how this may help cause certain diseases, such as cancer.

Extracellular: Occurring or being (situated) outside the cell or cells. (Biology Online, 2019)

Methionine: (Science: biochemistry) Contains the SCH3 group that can act as a methyl donor (see s adenosyl methionine). Common in proteins but at low frequency. The met x linkage is subject to specific cleavage by cyanogen bromide. (Biology Online, 2019)

Biosynthesis: The production of a complex chemical compound from simpler precursors in a living organism, usually involving enzymes (to catalyze the reaction) and energy source (such as ATP). (Biology Online, 2019)

B-galactosidase: A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.

Homocysteine: The chemical reactions and pathways resulting in the formation of homocysteine, 2-amino-4-sulfanylbutanoic acid.

Oxidative: Capable of oxidizing other substances. Of, pertaining to, or produced by oxidation. (Biology Online, 2019)

Glutathione: (Science: biochemistry) The tripeptide _ glutamylcysteinylglycine. It contains an unusual peptide Linkage between the _ carboxyl group of the glutamate side chain and the amine group of cysteine. (Biology Online, 2019)

Substrate: A substratum or an underlying stratum. (Biology Online, 2019)

Transduction: there are a group of viruses called bacteriophages. These bacteriophages inject their viral dna into the host cell of bacteria. The viral dna then becomes incorporated into the chromosome of the bacterium. Thus the viral dna forms part of the bacterial chromosome and will be copied to all daughter cells. Though this viral dna will become active again at low frequency's. (Biology Online, 2019)

==Outline==

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

The main result found in the article was how the Saccharomyces cerevisiae short-term potassium deprivation causes a lack of potassium which affects and changes sulfur metabolism. This leads to an oxidative stress response and activates the retrograde pathway. It is stated that the catalyst could possibly be ammonium accumulation that happens through the Trk1 potassium transporter. Other results include: a halt in gene expression required for ribosome biogenesis and translation, a decrease in the expression of diverse components used in the progression of cell cycle and blockage in septins assembly. Essentially, a shortage of potassium in the environment triggers an acute transcriptional response, which opens up new finds and more areas to be explored.

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

The significance of this work is the new discoveries and pathways involving potassium and its role in cellular life.

===What were the limitations in previous studies that led them to perform this work?===
There were no previous studies that directly correlate to this work. However, there are multiple studies that are able to supplement the work.

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

The yeast cells were put into a YBN growth medium that lacked normal amounts of potassium and ammonium (potassium starvation). The cells were recorded and monitored in time intervals of 0, 10, 20, 30, 40, 60 and 120 minutes.

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

'''Strains:'''

*YNR055.1

*YPC722, YPC723, YPC724,

*BY4741, BY4741 rtg2, BY4741 rtg3, BY4741 fzo1

*BYT1, BYT2, BYT12

*W303-1A

*DBY746

(*The information regarding the if they were haploid or diploid wa not given)

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

*Grown in translucent potassium-free YNB media
*Temperature: 28 Celsius
*Incubator: N/A
*The times used were 0, 10, 20, 40, 60 and 120 minutes

===What controls did they use?===
Controls: wild-type strain BY4741, 50mM KCI added

===How many replicates did they perform per treatment or timepoint?===
4 Replicates per timepoint

===What method did they use to prepare the RNA, label it and hybridize it to the microarray? ===
RNA extraction using the Ribo Pure™-Yeast kit

===What mathematical/statistical method did they use to analyze the data?===
They used GEPAS v3.1

===Are the data publicly available for download? From which web site?===
The data could be found at [https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x Society for Applied Microbiology]

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

'''Table 1''' shows the transcriptional changes between 10, 20, 40, 60, and 120 minutes. It measures the amount of genes that are induced and repressed at each timepoint.

'''Table 2''' shows a list of strains that were used.

'''Figure 1''' shows that the majority of genes were induced/repressed between 60-120 minutes after being transferred to a potassium free media. '''X''' = Timepoint '''Y''' = Genes

'''Figure 2''' '''(A)''' shows the how potassium starvation decreases sulfuric amino acid metabolism. This is seen in the model that depicts the how Met/Cys are metabolized. '''B''' is a graph that shows mRna concentration from the microarray '''X''' = mRna change '''Y''' = Genes. '''C''' shows the concentration of Met and Cys after the procedure. '''X''' = Timepoint '''Y''' = Genes (Met/Cys)

'''Figure 3''' shows the oxidative stress response in genes due to potassium deprivation. '''A''' shows the multiple genes reacting to potassium deprivation and is measured by the levels of oxidative stress. '''B''' shows images of the genes responding to the procedure. '''Y''' = Time intervals. '''C''' shows the change in Glutanione level due to potassium starvation.

'''Figure 4''' shows the effects of methylglyoxal production and treholse production from potassium starvation. '''A''' shows how the production of each is made. '''B''' shows the changes in expression '''X''' = Timepoint '''Y''' = Changes in expression (-fold). '''C''' shows the levels of methyglyoxal when affected by potassium starvation. '''X''' = Timepoint '''Y''' = Methyglyoxal Levels.

'''Figure 5''' shows the a correlation between the expression of CIT2 and DLD3 genes and potassium starvation. '''A''' shows the changes in expression for genes and an image of the changes in CIT2, DLD3 and ACT1. '''B''' shows the changes in mitochondrial change before and after the procedure and images of WT and fzo1. '''C''' & '''D''' shows the graph depicting the relative concentration of intracellular ammonium after treatment.

'''Figure 6''' shows expression of genes controlling cyclins express various responses to potassium starvation. '''A''' shows a graph demonstrating the change in expression levels of retrograde after potassium starvation. '''X''' = Timepoint '''Y''' = log2 change in expression levels. '''B''' are images depicting relative abundance of cyclin mRNA & '''C''' are images depicting relative abundance of cyclin protein

'''Figure 7''' shows that potassium starvation decreases septin ring formation. '''A''' shows a graph that represents the change in expression levels of septin ring fomration genes after potassium starvation. '''B''' are images depicting the localization of Cdc11-GFP during treatment. '''C''' are images depicting relative abundance of Cdc11 protein. '''D''' are images depicting the localization of Cdc11 protein

===How does this work compare with previous studies?===
No other previous works.

===What are the important implications of this work?===
The important implications of this work are understanding the results from potassium starvation and how it opens up a new study regarding cations starvation or the relationship of cations and cellular life.

===What future directions should the authors take?===
The authors should try to understand how potassium affects other cations or how potassium affects other objects aside from yeast.

===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?===
The author's data supported their conclusion and could be seen when they used analyzing the figures and tables. However, the paper was extremely dense and required more research in order to understand the procedure and results.

==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?

==Data/Files==

==Conclusion==

==Acknowledgements==

This week we were put into teams. The team I was assigned to was Team [[Skinny_Genes|Skinny Genes]]. The other members are [[User:Msamdars|Mihir Samdars]], [[User:Ymesfin|Aby Mesfin]], [[User:Dramir36 |David Ramirez]], [[User:Cdomin12|Christina Dominguez]]. We worked in and out of class together Monday and Wednesday.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

==References==
# LMU BioDB 2019. (2019). Week 11. Retrieved November 7, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
# MediaWiki (2019). Category: Help. Retrieved November 11, 2019, from https://www.mediawiki.org/wiki/Category:Help
# Lagarias, J.C., Duanmu, D., Casero, D., Dent, R.M., Gallaher, S., Yang, W., Rockwell, N.C., Martin, S.S., Pellegrini, M., Niyogi, K.K., Merchant, S.S., Grossman, A.R. (2013). "Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival". Proceedings of the National Academy of Sciences of the United States of America. 110 (9): 3621–3626. doi:10.1073/pnas.1222375110.
# Douglas, L. M., Alvarez, F. J., McCreary, C., & Konopka, J. B. (2005). "Septin function in yeast model systems and pathogenic fungi". Eukaryotic Cell. 4 (9): 1503–12.
# Biology Online. (2019). Retrieved November 7, 2019 from https://biology-online.org
# Smith, A. (2000). Oxford Dictionary of Biochemistry and Molecular Biology: Revised Edition. Oxford University Press.
# Lackie, J. M. (Ed.). (2007). The dictionary of cell & molecular biology. Academic Press. Retrieved November 11, 2019 from http://ebookcentral.proquest.com/lib/lmu/detail.action?docID=311420.
# Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group. AmiGO: online access to ontology and annotation data. Bioinformatics. Jan 2009;25(2):288-289. Retrieved November 11, 2019 from http://amigo.geneontology.org/amigo/
# Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., ... & Fisk, D. G. (2011). Saccharomyces Genome Database: the genomics resource of budding yeast. ''Nucleic Acids Research'', 40(D1), D700-D705.

{{jcowan4}}
(*Participation: Table 2, Introduction (Background Information), Question 1, Question 3)

Jcowan4 Journal Week 11

2019-11-14T05:55:02Z

Jcowan4: /* References */ added references

==Biological Terms==

Intracellular

Transcriptomic

Extracellular

Methionine

Biosynthesis

B-galactosidase

Homocysteine

Oxidative

Glutathione

Substrate

Transduction

==Outline==

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

The main result found in the article was how the Saccharomyces cerevisiae short-term potassium deprivation causes a lack of potassium which affects and changes sulfur metabolism. This leads to an oxidative stress response and activates the retrograde pathway. It is stated that the catalyst could possibly be ammonium accumulation that happens through the Trk1 potassium transporter. Other results include: a halt in gene expression required for ribosome biogenesis and translation, a decrease in the expression of diverse components used in the progression of cell cycle and blockage in septins assembly. Essentially, a shortage of potassium in the environment triggers an acute transcriptional response, which opens up new finds and more areas to be explored.

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

The significance of this work is the new discoveries and pathways involving potassium and its role in cellular life.

===What were the limitations in previous studies that led them to perform this work?===
There were no previous studies that directly correlate to this work. However, there are multiple studies that are able to supplement the work.

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

The yeast cells were put into a YBN growth medium that lacked normal amounts of potassium and ammonium (potassium starvation). The cells were recorded and monitored in time intervals of 0, 10, 20, 30, 40, 60 and 120 minutes.

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

'''Strains:'''

*YNR055.1

*YPC722, YPC723, YPC724,

*BY4741, BY4741 rtg2, BY4741 rtg3, BY4741 fzo1

*BYT1, BYT2, BYT12

*W303-1A

*DBY746

(*The information regarding the if they were haploid or diploid wa not given)

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

*Grown in translucent potassium-free YNB media
*Temperature: 28 Celsius
*Incubator: N/A
*The times used were 0, 10, 20, 40, 60 and 120 minutes

===What controls did they use?===
Controls: wild-type strain BY4741, 50mM KCI added

===How many replicates did they perform per treatment or timepoint?===
4 Replicates per timepoint

===What method did they use to prepare the RNA, label it and hybridize it to the microarray? ===
RNA extraction using the Ribo Pure™-Yeast kit

===What mathematical/statistical method did they use to analyze the data?===
They used GEPAS v3.1

===Are the data publicly available for download? From which web site?===
The data could be found at [https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x Society for Applied Microbiology]

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

'''Table 1''' shows the transcriptional changes between 10, 20, 40, 60, and 120 minutes. It measures the amount of genes that are induced and repressed at each timepoint.

'''Table 2''' shows a list of strains that were used.

'''Figure 1''' shows that the majority of genes were induced/repressed between 60-120 minutes after being transferred to a potassium free media. '''X''' = Timepoint '''Y''' = Genes

'''Figure 2''' '''(A)''' shows the how potassium starvation decreases sulfuric amino acid metabolism. This is seen in the model that depicts the how Met/Cys are metabolized. '''B''' is a graph that shows mRna concentration from the microarray '''X''' = mRna change '''Y''' = Genes. '''C''' shows the concentration of Met and Cys after the procedure. '''X''' = Timepoint '''Y''' = Genes (Met/Cys)

'''Figure 3''' shows the oxidative stress response in genes due to potassium deprivation. '''A''' shows the multiple genes reacting to potassium deprivation and is measured by the levels of oxidative stress. '''B''' shows images of the genes responding to the procedure. '''Y''' = Time intervals. '''C''' shows the change in Glutanione level due to potassium starvation.

'''Figure 4''' shows the effects of methylglyoxal production and treholse production from potassium starvation. '''A''' shows how the production of each is made. '''B''' shows the changes in expression '''X''' = Timepoint '''Y''' = Changes in expression (-fold). '''C''' shows the levels of methyglyoxal when affected by potassium starvation. '''X''' = Timepoint '''Y''' = Methyglyoxal Levels.

'''Figure 5''' shows the a correlation between the expression of CIT2 and DLD3 genes and potassium starvation. '''A''' shows the changes in expression for genes and an image of the changes in CIT2, DLD3 and ACT1. '''B''' shows the changes in mitochondrial change before and after the procedure and images of WT and fzo1. '''C''' & '''D''' shows the graph depicting the relative concentration of intracellular ammonium after treatment.

'''Figure 6''' shows expression of genes controlling cyclins express various responses to potassium starvation. '''A''' shows a graph demonstrating the change in expression levels of retrograde after potassium starvation. '''X''' = Timepoint '''Y''' = log2 change in expression levels. '''B''' are images depicting relative abundance of cyclin mRNA & '''C''' are images depicting relative abundance of cyclin protein

'''Figure 7''' shows that potassium starvation decreases septin ring formation. '''A''' shows a graph that represents the change in expression levels of septin ring fomration genes after potassium starvation. '''B''' are images depicting the localization of Cdc11-GFP during treatment. '''C''' are images depicting relative abundance of Cdc11 protein. '''D''' are images depicting the localization of Cdc11 protein

===How does this work compare with previous studies?===
No other previous works.

===What are the important implications of this work?===
The important implications of this work are understanding the results from potassium starvation and how it opens up a new study regarding cations starvation or the relationship of cations and cellular life.

===What future directions should the authors take?===
The authors should try to understand how potassium affects other cations or how potassium affects other objects aside from yeast.

===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?===
The author's data supported their conclusion and could be seen when they used analyzing the figures and tables. However, the paper was extremely dense and required more research in order to understand the procedure and results.

==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?

==Data/Files==

==Conclusion==

==Acknowledgements==

This week we were put into teams. The team I was assigned to was Team [[Skinny_Genes|Skinny Genes]]. The other members are [[User:Msamdars|Mihir Samdars]], [[User:Ymesfin|Aby Mesfin]], [[User:Dramir36 |David Ramirez]], [[User:Cdomin12|Christina Dominguez]]. We worked in and out of class together Monday and Wednesday.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

==References==
# LMU BioDB 2019. (2019). Week 11. Retrieved November 7, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
# MediaWiki (2019). Category: Help. Retrieved November 11, 2019, from https://www.mediawiki.org/wiki/Category:Help
# Lagarias, J.C., Duanmu, D., Casero, D., Dent, R.M., Gallaher, S., Yang, W., Rockwell, N.C., Martin, S.S., Pellegrini, M., Niyogi, K.K., Merchant, S.S., Grossman, A.R. (2013). "Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival". Proceedings of the National Academy of Sciences of the United States of America. 110 (9): 3621–3626. doi:10.1073/pnas.1222375110.
# Douglas, L. M., Alvarez, F. J., McCreary, C., & Konopka, J. B. (2005). "Septin function in yeast model systems and pathogenic fungi". Eukaryotic Cell. 4 (9): 1503–12.
# Biology Online. (2019). Retrieved November 7, 2019 from https://biology-online.org
# Smith, A. (2000). Oxford Dictionary of Biochemistry and Molecular Biology: Revised Edition. Oxford University Press.
# Lackie, J. M. (Ed.). (2007). The dictionary of cell & molecular biology. Academic Press. Retrieved November 11, 2019 from http://ebookcentral.proquest.com/lib/lmu/detail.action?docID=311420.
# Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group. AmiGO: online access to ontology and annotation data. Bioinformatics. Jan 2009;25(2):288-289. Retrieved November 11, 2019 from http://amigo.geneontology.org/amigo/
# Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., ... & Fisk, D. G. (2011). Saccharomyces Genome Database: the genomics resource of budding yeast. ''Nucleic Acids Research'', 40(D1), D700-D705.

{{jcowan4}}
(*Participation: Table 2, Introduction (Background Information), Question 1, Question 3)

Skinny Genes

2019-11-14T05:54:03Z

Jcowan4: /* Jonar's Reflection */ answered

{{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: 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.

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

Jcowan4 Journal Week 11

2019-11-14T05:50:19Z

Jcowan4: /* Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. */ answering

==Biological Terms==

Intracellular

Transcriptomic

Extracellular

Methionine

Biosynthesis

B-galactosidase

Homocysteine

Oxidative

Glutathione

Substrate

Transduction

==Outline==

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

The main result found in the article was how the Saccharomyces cerevisiae short-term potassium deprivation causes a lack of potassium which affects and changes sulfur metabolism. This leads to an oxidative stress response and activates the retrograde pathway. It is stated that the catalyst could possibly be ammonium accumulation that happens through the Trk1 potassium transporter. Other results include: a halt in gene expression required for ribosome biogenesis and translation, a decrease in the expression of diverse components used in the progression of cell cycle and blockage in septins assembly. Essentially, a shortage of potassium in the environment triggers an acute transcriptional response, which opens up new finds and more areas to be explored.

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

The significance of this work is the new discoveries and pathways involving potassium and its role in cellular life.

===What were the limitations in previous studies that led them to perform this work?===
There were no previous studies that directly correlate to this work. However, there are multiple studies that are able to supplement the work.

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

The yeast cells were put into a YBN growth medium that lacked normal amounts of potassium and ammonium (potassium starvation). The cells were recorded and monitored in time intervals of 0, 10, 20, 30, 40, 60 and 120 minutes.

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

'''Strains:'''

*YNR055.1

*YPC722, YPC723, YPC724,

*BY4741, BY4741 rtg2, BY4741 rtg3, BY4741 fzo1

*BYT1, BYT2, BYT12

*W303-1A

*DBY746

(*The information regarding the if they were haploid or diploid wa not given)

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

*Grown in translucent potassium-free YNB media
*Temperature: 28 Celsius
*Incubator: N/A
*The times used were 0, 10, 20, 40, 60 and 120 minutes

===What controls did they use?===
Controls: wild-type strain BY4741, 50mM KCI added

===How many replicates did they perform per treatment or timepoint?===
4 Replicates per timepoint

===What method did they use to prepare the RNA, label it and hybridize it to the microarray? ===
RNA extraction using the Ribo Pure™-Yeast kit

===What mathematical/statistical method did they use to analyze the data?===
They used GEPAS v3.1

===Are the data publicly available for download? From which web site?===
The data could be found at [https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x Society for Applied Microbiology]

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

'''Table 1''' shows the transcriptional changes between 10, 20, 40, 60, and 120 minutes. It measures the amount of genes that are induced and repressed at each timepoint.

'''Table 2''' shows a list of strains that were used.

'''Figure 1''' shows that the majority of genes were induced/repressed between 60-120 minutes after being transferred to a potassium free media. '''X''' = Timepoint '''Y''' = Genes

'''Figure 2''' '''(A)''' shows the how potassium starvation decreases sulfuric amino acid metabolism. This is seen in the model that depicts the how Met/Cys are metabolized. '''B''' is a graph that shows mRna concentration from the microarray '''X''' = mRna change '''Y''' = Genes. '''C''' shows the concentration of Met and Cys after the procedure. '''X''' = Timepoint '''Y''' = Genes (Met/Cys)

'''Figure 3''' shows the oxidative stress response in genes due to potassium deprivation. '''A''' shows the multiple genes reacting to potassium deprivation and is measured by the levels of oxidative stress. '''B''' shows images of the genes responding to the procedure. '''Y''' = Time intervals. '''C''' shows the change in Glutanione level due to potassium starvation.

'''Figure 4''' shows the effects of methylglyoxal production and treholse production from potassium starvation. '''A''' shows how the production of each is made. '''B''' shows the changes in expression '''X''' = Timepoint '''Y''' = Changes in expression (-fold). '''C''' shows the levels of methyglyoxal when affected by potassium starvation. '''X''' = Timepoint '''Y''' = Methyglyoxal Levels.

'''Figure 5''' shows the a correlation between the expression of CIT2 and DLD3 genes and potassium starvation. '''A''' shows the changes in expression for genes and an image of the changes in CIT2, DLD3 and ACT1. '''B''' shows the changes in mitochondrial change before and after the procedure and images of WT and fzo1. '''C''' & '''D''' shows the graph depicting the relative concentration of intracellular ammonium after treatment.

'''Figure 6''' shows expression of genes controlling cyclins express various responses to potassium starvation. '''A''' shows a graph demonstrating the change in expression levels of retrograde after potassium starvation. '''X''' = Timepoint '''Y''' = log2 change in expression levels. '''B''' are images depicting relative abundance of cyclin mRNA & '''C''' are images depicting relative abundance of cyclin protein

'''Figure 7''' shows that potassium starvation decreases septin ring formation. '''A''' shows a graph that represents the change in expression levels of septin ring fomration genes after potassium starvation. '''B''' are images depicting the localization of Cdc11-GFP during treatment. '''C''' are images depicting relative abundance of Cdc11 protein. '''D''' are images depicting the localization of Cdc11 protein

===How does this work compare with previous studies?===
No other previous works.

===What are the important implications of this work?===
The important implications of this work are understanding the results from potassium starvation and how it opens up a new study regarding cations starvation or the relationship of cations and cellular life.

===What future directions should the authors take?===
The authors should try to understand how potassium affects other cations or how potassium affects other objects aside from yeast.

===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?===
The author's data supported their conclusion and could be seen when they used analyzing the figures and tables. However, the paper was extremely dense and required more research in order to understand the procedure and results.

==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?

==Data/Files==

==Conclusion==

==Acknowledgements==

This week we were put into teams. The team I was assigned to was Team [[Skinny_Genes|Skinny Genes]]. The other members are [[User:Msamdars|Mihir Samdars]], [[User:Ymesfin|Aby Mesfin]], [[User:Dramir36 |David Ramirez]], [[User:Cdomin12|Christina Dominguez]]. We worked in and out of class together Monday and Wednesday.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

==References==
{{jcowan4}}
(*Participation: Table 2, Introduction (Background Information), Question 1, Question 3)

Jcowan4 Journal Week 11

2019-11-14T03:44:00Z

Jcowan4: /* Briefly state the result shown in each of the figures and tables, not just the ones you are presenting. */ partially answered

==Biological Terms==

Intracellular

Transcriptomic

Extracellular

Methionine

Biosynthesis

B-galactosidase

Homocysteine

Oxidative

Glutathione

Substrate

Transduction

==Outline==

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

The main result found in the article was how the Saccharomyces cerevisiae short-term potassium deprivation causes a lack of potassium which affects and changes sulfur metabolism. This leads to an oxidative stress response and activates the retrograde pathway. It is stated that the catalyst could possibly be ammonium accumulation that happens through the Trk1 potassium transporter. Other results include: a halt in gene expression required for ribosome biogenesis and translation, a decrease in the expression of diverse components used in the progression of cell cycle and blockage in septins assembly. Essentially, a shortage of potassium in the environment triggers an acute transcriptional response, which opens up new finds and more areas to be explored.

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

The significance of this work is the new discoveries and pathways involving potassium and its role in cellular life.

===What were the limitations in previous studies that led them to perform this work?===
There were no previous studies that directly correlate to this work. However, there are multiple studies that are able to supplement the work.

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

The yeast cells were put into a YBN growth medium that lacked normal amounts of potassium and ammonium (potassium starvation). The cells were recorded and monitored in time intervals of 0, 10, 20, 30, 40, 60 and 120 minutes.

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

'''Strains:'''

*YNR055.1

*YPC722, YPC723, YPC724,

*BY4741, BY4741 rtg2, BY4741 rtg3, BY4741 fzo1

*BYT1, BYT2, BYT12

*W303-1A

*DBY746

(*The information regarding the if they were haploid or diploid wa not given)

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

*Grown in translucent potassium-free YNB media
*Temperature: 28 Celsius
*Incubator: N/A
*The times used were 0, 10, 20, 40, 60 and 120 minutes

===What controls did they use?===
Controls: wild-type strain BY4741, 50mM KCI added

===How many replicates did they perform per treatment or timepoint?===
4 Replicates per timepoint

===What method did they use to prepare the RNA, label it and hybridize it to the microarray? ===
RNA extraction using the Ribo Pure™-Yeast kit

===What mathematical/statistical method did they use to analyze the data?===
They used GEPAS v3.1

===Are the data publicly available for download? From which web site?===
The data could be found at [https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x Society for Applied Microbiology]

===Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.===
*'''What do the X and Y axes represent?'''

*'''How were the measurements made?'''

*'''What trends are shown by the plots and what conclusions can you draw from the data?'''

'''Table 1''' shows the transcriptional changes between 10, 20, 40, 60, and 120 minutes. It measures the amount of genes that are induced and repressed at each timepoint.

'''Table 2''' shows a list of strains that were used.

'''Figure 1''' shows that the majority of genes were induced/repressed between 60-120 minutes after being transferred to a potassium free media. '''X''' = Timepoint '''Y''' = Genes

'''Figure 2''' '''(A)''' shows the how potassium starvation decreases sulfuric amino acid metabolism. This is seen in the model that depicts the how Met/Cys are metabolized. '''B''' is a graph that shows mRna concentration from the microarray '''X''' = mRna change '''Y''' = Genes. '''C''' shows the concentration of Met and Cys after the procedure. '''X''' = Timepoint '''Y''' = Genes (Met/Cys)

'''Figure 3''' shows the oxidative stress response in genes due to potassium deprivation. '''A''' shows the multiple genes reacting to potassium deprivation and is measured by the levels of oxidative stress. '''B''' shows images of the genes responding to the procedure. '''Y''' = Time intervals. '''C''' shows the change in Glutanione level due to potassium starvation.

'''Figure 4''' shows the effects of methylglyoxal production and treholse production from potassium starvation. '''A''' shows how the production of each is made. '''B''' shows the changes in expression '''X''' = Timepoint '''Y''' = Changes in expression (-fold). '''C''' shows the levels of methyglyoxal when affected by potassium starvation. '''X''' = Timepoint '''Y''' = Methyglyoxal Levels.

'''Figure 5''' shows the a correlation between the expression of CIT2 and DLD3 genes and potassium starvation. '''A''' shows the changes in expression for genes and an image of the changes in CIT2, DLD3 and ACT1. '''B''' shows the changes in mitochondrial change before and after the procedure and images of WT and fzo1. '''C'''

'''Figure 6'''

'''Figure 7'''

===How does this work compare with previous studies?===
No other previous works.

===What are the important implications of this work?===
The important implications of this work are understanding the results from potassium starvation and how it opens up a new study regarding cations starvation or the relationship of cations and cellular life.

===What future directions should the authors take?===
The authors should try to understand how potassium affects other cations or how potassium affects other objects aside from yeast.

===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?===
The author's data supported their conclusion and could be seen when they used analyzing the figures and tables. However, the paper was extremely dense and required more research in order to understand the procedure and results.

==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?

==Data/Files==

==Conclusion==

==Acknowledgements==

This week we were put into teams. The team I was assigned to was Team [[Skinny_Genes|Skinny Genes]]. The other members are [[User:Msamdars|Mihir Samdars]], [[User:Ymesfin|Aby Mesfin]], [[User:Dramir36 |David Ramirez]], [[User:Cdomin12|Christina Dominguez]]. We worked in and out of class together Monday and Wednesday.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

==References==
{{jcowan4}}
(*Participation: Table 2, Introduction (Background Information), Question 1, Question 3)

Jcowan4 Journal Week 11

2019-11-14T02:39:33Z

Jcowan4: /* What future directions should the authors take? */ answered

Jcowan4 Journal Week 11

2019-11-14T02:34:54Z

Jcowan4: /* What are the important implications of this work? */ answered

Jcowan4 Journal Week 11

2019-11-14T02:31:48Z

Jcowan4: /* How does this work compare with previous studies? */ answered

Jcowan4 Journal Week 11

2019-11-14T02:30:58Z

Jcowan4: /* 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? */ answered

Jcowan4 Journal Week 11

2019-11-14T02:20:39Z

Jcowan4: /* Are the data publicly available for download? From which web site? */ answered

Jcowan4 Journal Week 11

2019-11-14T02:19:47Z

Jcowan4: /* What mathematical/statistical method did they use to analyze the data? */ answered

Jcowan4 Journal Week 11

2019-11-14T02:18:24Z

Jcowan4: /* How many replicates did they perform per treatment or timepoint? */ edited

Jcowan4 Journal Week 11

2019-11-14T02:18:09Z

Jcowan4: /* What method did they use to prepare the RNA, label it and hybridize it to the microarray? */ answered

Jcowan4 Journal Week 11

2019-11-14T02:15:11Z

Jcowan4: /* What were the limitations in previous studies that led them to perform this work? */ answered

Jcowan4 Journal Week 11

2019-11-14T01:58:35Z

Jcowan4: /* What strain(s) of yeast did they use? Were the strain(s) haploid or diploid? */ organized

Jcowan4 Journal Week 11

2019-11-14T01:57:44Z

Jcowan4: /* What strain(s) of yeast did they use? Were the strain(s) haploid or diploid? */ fixed format

Jcowan4 Journal Week 11

2019-11-14T01:55:49Z

Jcowan4: /* What strain(s) of yeast did they use? Were the strain(s) haploid or diploid? */ bolded strains