LMU BioDB 2019 - User contributions [en]

Skinny Genes Deliverables

2019-12-05T23:19:46Z

Dramir36: /* Data/Files */ spaced out files

{{Skinny Genes}}

==Data/Files==
*[[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample-Data Relationship Table]]

*[[Media: Ymesfin_Barreto_ANOVA_no_duplicates_-_Copy.xlsx | ANOVA Results]]

Skinny Genes Deliverables

2019-12-05T23:19:29Z

Dramir36: /* Data/Files */ added ANOVA excel file

{{Skinny Genes}}

==Data/Files==
[[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample-Data Relationship Table]]
[[Media: Ymesfin_Barreto_ANOVA_no_duplicates_-_Copy.xlsx | ANOVA Results]]

Skinny Genes Deliverables

2019-12-05T23:18:12Z

Dramir36: /* Data/Files */ edited file name

{{Skinny Genes}}

==Data/Files==
[[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample-Data Relationship Table]]

Skinny Genes Deliverables

2019-12-05T23:17:37Z

Dramir36: inserted table relations

{{Skinny Genes}}

==Data/Files==
[[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample to Data Relationship Table]]

Skinny Genes Deliverables

2019-12-05T23:17:00Z

Dramir36: inputted title

{{Skinny Genes}}

==Data/Files==

Dramir36 Week 12/13

2019-11-26T08:14:54Z

Dramir36: completed journal

{{template: Dramir36}}

==Progress==

*Finished creating the ANOVA statistical analysis of the data.

*Currently trying to complete ID conversions of the remaining genes that have to be converted.

==Acknowledgments==

*Worked with [[User:ymesfin| Yeabsira Mesfin]] to complete ANOVA excel datasheet.

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

Template:Dramir36

2019-11-26T08:07:30Z

Dramir36: inserted individual week page

[[User:Dramir36]] [[template:Dramir36]] [[Skinny Genes]]

*'''Week 1'''

::[[Week 1]]

::[[Class Journal Week 1]]

*'''Week 2'''

::[[Week 2]]

::[[Class Journal Week 2]]

::[[Dramir36 Week 2]]

*'''Week 3'''

::[[Week 3]]

::[[Class Journal Week 3]]

::[[CDC28/YBR160W Week 3]]

*'''Week 4'''

::[[Week 4]]

::[[Class Journal Week 4]]

::[[Dramir36 Week 4]]

*'''Week 5'''

::[[Week 5]]

::[[Class Journal Week 5]]

::[[CRISPRlnc Group Journal]]

*'''Week 6'''

::[[Week 6]]

::[[Class Journal Week 6]]

::[[Dramir36 Week 6]]

*'''Week 7'''

::[[Week 7]]

::[[Class Journal Week 7]]

::[[Dramir36 Week 7]]

*'''Week 8'''

::[[Week 8]]

::[[Class Journal Week 8]]

::[[Dramir36 Week 8]]

*'''Week 9'''

::[[Week 9]]

::[[Class Journal Week 9]]

::[[Dramir36 Week 9]]

*'''Week 10'''

::[[Week 10]]

::[[Class Journal Week 10]]

::[[Dramir36 Week 10]]

*'''Week 11'''

::[[Week 11]]

::[[Dramir36 Week 11]]

*'''Week 12/13'''

::[[Week 12/13]]

::[[Dramir36 Week 12/13]]

*'''Week 14'''

*'''Week 15'''

[[Category:Journal Entry]]

Template:Dramir36

2019-11-26T08:04:32Z

Dramir36: linked week page

[[User:Dramir36]] [[template:Dramir36]] [[Skinny Genes]]

*'''Week 1'''

::[[Week 1]]

::[[Class Journal Week 1]]

*'''Week 2'''

::[[Week 2]]

::[[Class Journal Week 2]]

::[[Dramir36 Week 2]]

*'''Week 3'''

::[[Week 3]]

::[[Class Journal Week 3]]

::[[CDC28/YBR160W Week 3]]

*'''Week 4'''

::[[Week 4]]

::[[Class Journal Week 4]]

::[[Dramir36 Week 4]]

*'''Week 5'''

::[[Week 5]]

::[[Class Journal Week 5]]

::[[CRISPRlnc Group Journal]]

*'''Week 6'''

::[[Week 6]]

::[[Class Journal Week 6]]

::[[Dramir36 Week 6]]

*'''Week 7'''

::[[Week 7]]

::[[Class Journal Week 7]]

::[[Dramir36 Week 7]]

*'''Week 8'''

::[[Week 8]]

::[[Class Journal Week 8]]

::[[Dramir36 Week 8]]

*'''Week 9'''

::[[Week 9]]

::[[Class Journal Week 9]]

::[[Dramir36 Week 9]]

*'''Week 10'''

::[[Week 10]]

::[[Class Journal Week 10]]

::[[Dramir36 Week 10]]

*'''Week 11'''

::[[Week 11]]

::[[Dramir36 Week 11]]

*'''Week 12/13'''

::[[Week 12/13]]

*'''Week 14'''

*'''Week 15'''

[[Category:Journal Entry]]

Skinny Genes

2019-11-26T08:02:34Z

Dramir36: /* David's Reflection */ answered questions

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

'''Project Manager:''' Aby

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

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

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

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

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

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

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

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

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

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

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

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

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

====Christina's Reflection====
*Progress:
*#What worked?
*#What didn't work?
*#What will I do next to fix what didn't work?
====Mihir's Reflection====
*Progress:
** This week I worked on creating the format for encoding the entries into the database.

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

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

==Milestones==

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

Skinny Genes

2019-11-26T08:01:27Z

Dramir36: /* David's Reflection */ answered questions

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

'''Project Manager:''' Aby

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

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

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

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

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

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

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

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

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

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

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

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

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

====Christina's Reflection====
*Progress:
*#What worked?
*#What didn't work?
*#What will I do next to fix what didn't work?
====Mihir's Reflection====
*Progress:
** This week I worked on creating the format for encoding the entries into the database.

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

====David's Reflection====
*Progress:
*#What worked?
*#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====

File:Skinny Genes Editted Raw Data.xlsx

2019-11-21T23:11:26Z

Dramir36: Dramir36 uploaded a new version of File:Skinny Genes Editted Raw Data.xlsx

Skinny Genes

2019-11-20T00:03:14Z

Dramir36: /* Files */ correct edit

{{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==

Skinny Genes

2019-11-20T00:02:42Z

Dramir36: /* Files */ spaced link

{{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 Editted 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==

Skinny Genes

2019-11-20T00:02:25Z

Dramir36: /* Files */ added raw data file

{{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 Editted 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==

File:Skinny Genes Editted Raw Data.xlsx

2019-11-20T00:01:36Z

Dramir36:

Template:Skinny Genes

2019-11-19T23:10:31Z

Dramir36: edit Aby's role

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

[[Category: Group Projects]]

[[Category:Skinny Genes]]

[[Category:Group Projects]]

Dramir36 Week 11

2019-11-19T07:59:47Z

Dramir36: /* Conclusion */ added conclusion

==Purpose==
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==
*'''retrograde pathway:''' The mechanism of moving backward or against the usual direction of flow. [https://www.biology-online.org/dictionary/Retrograde Biology Dictionary (2019)]
*'''septin:''' A protein involved in cytokinesis and also functions in maintaining cell morphology [https://www.biology-online.org/dictionary/septin Biology Dictionary (2019)]
*'''β‐galactosidase:''' One of a class of enzymes which cuts the glycosidic bond between the sugar galactose and another sugar molecule (of a different type than galactose). [https://www.biology-online.org/dictionary/galactosidase Biology Dictionary (2019)]
*'''oxidoreductase:''' An enzyme that catalyzes the transfer of electrons from an electron donor (reductant) to an electron acceptor (oxidant) in a redox reaction [https://www.biology-online.org/dictionary/oxidoreductase Biology Dictionary (2019)]
*''' trehalose:''' A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates [https://www.biology-online.org/dictionary/Trehalose Biology Dictionary (2019)]
*'''supernatant:''' The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids. [https://www.biology-online.org/dictionary/Supernatant Biology Dictionary (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) [https://www.biology-online.org/dictionary/Biosynthesis Biology Dictionary (2019)]
*'''assimilation:''' The act of absorption or incorporation into the biological tissue. [https://www.biology-online.org/dictionary/Assimilate Biology Dictionary (2019)]
*'''isoform:''' Any of the proteins with the same function and similar amino acid sequence, encoded by different genes (or by RNA transcript). [https://www.biology-online.org/dictionary/Isoform Biology Dictionary (2019)]
*'''attenuate:''' Tapering gradually. [https://www.biology-online.org/dictionary/Attenuate Biology Dictionary (2019)]

==Outline of Journal Article==
## '''What is the main result presented in this paper?''' The main result is that there was a massive alteration in the expression profile shortly after potassium was removed from the medium. The lack of potassium drastically alters the sulfur metabolism, triggers an oxidative stress response, and activates the mitochondrial retrograde pathway. Another main finding was that after a short time without potassium, there were genes that became repressed, including genes that are involved in ribosome synthesis, translation, and the cell cycle.
## '''What is the importance or significance of this work?''' This research project is important because it shows how when Saccharomyces cerevisiae has a short-term potassium deprivation, there are impacts in the mRNA level of over one thousand genes.
## '''What were the limitations in previous studies that led them to perform this work?''' There wasn’t much insight of possible cellular functions that require potassium and the short-term effects on the gene expression profile when there is a deprivation from sudden depletion of potassium in the environment.
## '''How did they treat the yeast cells (what experiment were they doing?)''' Media that contains only traces of potassium and ammonium as nitrogen source, simulated an absence of potassium in the environment. Once the yeast has been incubated at different time points of a potassium-absent environment, RNA purification, cDNA synthesis and DNA microarray was conducted. RT-PCR assays were also conducted to see how the mutants and wild-type reacted to an increase or no increase of KCl.
## '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?''' Wild-type S. cerevisiae had four main strains that were used in the work. The main strain is BY4741. The other three strains were BY4741 without trk1, without trk2, and without both trk1 and trk2. All of the strains used in the work are haploid.
## '''What media did they grow them in? What temperature? What type of incubator? For how long?''' Recently developed YNB-based growth media was used to treat the yeast cells at 28 degrees Celsius for 10, 20, 40, 60, and 120 min by rapid filtration from four biological replicates. The control contained sufficient potassium, whereas the other media contained only traces of potassium and ammonium. The DH5ɑ cells were grown at 37 degrees Celsius in Luria-Bertani (LB) broth. There was no information given about the incubator that was used.
## '''What controls did they use?''' The control used was the wild-type strain BY4741 in media that contained 50 ml of KCl.
## '''How many replicates did they perform per treatment or timepoint?''' There were four biological replicates performed per timepoint.
## '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?''' The total RNA was extracted by using the Ribo Pure-Yeast kit (Ambion) following the manufacture’s instructions. RNA quality was assessed by electrophoresis in denaturing 0.8% agarose gels and quantified by measuring the A260 in a BioPhotometer (Eppendorf).
## '''What mathematical/statistical method did they use to analyze the data?''' A given gene was considered to be induced when the minus/ plus potassium signal ratio was equal or higher than 2.0-fold, whereas it was considered to be repressed when this signal was equal or less than 0.50-fold. The GEPAS server (v3.1) was used to pre-process the data.
## '''Are the data publicly available for download? From which web site?''' The Society for Applied Microbiology website offers the data, which is publicly available, and is located in the article’s “Supporting Information” section.
##'''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: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 1: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 2: 2A: Potassium starvation decreases sulfuric amino acid metabolism. 2B: Graph depicting relative concentrations of mRNA for genes associated with Met/Cys metabolism. 2C: The concentration of Met/Cys amino acids decreases with potassium treatment Fig. 3: 3A: Oxidative stress response genes are induced by potassium deprivation. 3B: ROS formation causes oxidation when switch to K+-free medium. 3C: Potassium starvation- decline in GSH and increase in GSSG. Fig. 4: 4A: Methylglyoxal increases with trehalose Metabolism. 4B: Genes involved in trehalose synthesis show an increase in expression. 4C: Genes in MG detoxification enhanced without potassium. Fig. 5: 5A: Potassium starvation leads to a strong increase in expression of CIT2 & DLD3 genes central to the retrograde response. 5B: Mitochondrial morphology was normal, and not the cause of the retrograde response. 5C: Potassium starvation leads to an accumulation of ammonium in the cell, and may be one cause of the retrograde response. 5D: Cells without Trk1 do not show significant ammonium accumulation. Fig. 6: 6A: Expression of genes controlling cyclins exhibit a varied response to K+ starvation. Fig. 7: 7A: Lack of potassium in yeast destabilizes the septin ring. 7B: CDC11-GFP localization is affected during K+ starvation. 7C: CDC11 protein levels are constant during starvation. 7D: CDC11 not properly localized in cells grown 60 min
## '''How does this work compare with previous studies?''' This work demonstrates that lack of potassium actually causes a fast and persistent increase in intracellular ammonium concentration.
## '''What are the important implications of this work?''' There is a significant amount of change in cells occur even during the retention of more than necessary potassium.
## '''What future directions should the authors take?''' The authors could separate the methods into their own research projects to prevent intervention or confusion with implementing new methods into the same project.
## '''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 only problem that I found with reading the results and the article in general is that, the authors inserted new techniques or analysis without much explanation, or the insertion of a new analysis method was not placed in the right spot of the article.

==Annotated Bibliography==
===1st Reference===
#''' The complete bibliographic reference in the APA style'''
#: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
# '''The link to the abstract from PubMed.'''
#:https://www.ncbi.nlm.nih.gov/pubmed/15784684?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral (if not available, write N/A).'''
#:N/A
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#:https://jcs.biologists.org/content/118/8/1617.article-info
#''' The link to the full PDF version of the article from the publisher web site.'''
#:https://jcs.biologists.org/content/joces/118/8/1617.full.pdf
# '''Who owns the rights to the article?'''
#: The Company of Biologists Limited 2005
#''' How is the article available to you?'''
#: Not open access and not open after a certain amount of time, but LMU Library allows access through a subscription.
# '''Is the article available online-only or both in print and online?'''
#: The article is available in both print and online view.
# '''Who is the publisher of the journal?'''
#:The Company of Biologists Ltd in Cambridge, which is a not-for-profit publishing organization. This organization is their own scientific society, and is not a member of the OAPA.
#''' How Long has the journal been in operation?'''
#: Since January of 1853
# '''Are the articles in this journal peer-reviewed?'''
#: Articles are peer-reviewed.
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
#: [https://jcs.biologists.org/content/edboard Editorial Board]
# '''What is the journal impact factor?'''
#: 4.517 (2018)
# '''Is the article a review or primary research article?'''
#: Primary research article
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
#: The data is not available.

===2nd Reference===
#''' The complete bibliographic reference in the APA style '''
#: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI https://doi.org/10.1534/genetics.111.128314
# '''The link to the abstract from PubMed.'''
#: https://www.ncbi.nlm.nih.gov/pubmed/22219508?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral.'''
#: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249366/
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#: https://www.genetics.org/content/190/1/51
#''' The link to the full PDF version of the article from the publisher web site.'''
#: https://www.genetics.org/content/genetics/190/1/51.full.pdf
# '''Who owns the rights to the article?'''
#: 2012 by the Genetics Society of America
#''' How is the article available to you?'''
#: Open Access
# '''Is the article available online-only or both in print and online?'''
#: Available in both print and online versions
# '''Who is the publisher of the journal? '''
#: Genetics located in Bethesda, Maryland, is a for-profit scientific society which is not part of the OAPA.
#''' How Long has the journal been in operation? (e.g., browse the archive for the earliest article published)'''
#: Journal began in January of 1916
# '''Are the articles in this journal peer-reviewed?'''
#: Articles are peer-reviewed
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
#: [https://www.genetics.org/content/editorial-board-section Editorial Board]
# '''What is the journal impact factor?'''
#: 3.564 (2018)
# '''Is the article a review or primary research article?'''
#: Review article
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
#: No data available

===PubMed, GoogleScholar, and Web of Science===
# '''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 and septin. 489 results
#**''' Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#**: Using "yeast and septin and cell cycle" really helped focus the search on yeast cell research, while also focusing on articles that mention septin and cell cycle research together. The results were narrowed to 41.
#* '''Google Scholar'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#**: "Morphogenesis and the cell cycle" 342,000 results
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#: "Yeast morphogenesis cell cycle" to specify that I am interested in yeast cell research. This narrowed down the results to 127,000.
#* '''Web of Science'''
#**''' What original keyword(s) did you use? How many results did you get?'''
#**: "Yeast and lack of potassium" 154 results
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#**: I added the term "environment" into my search so that articles that mention treating yeast cells in a potassium-absent environment are shown. The results were narrowed to 11.
# '''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?'''
#**: I focused the search to the tex words containing "yeast and septin and cell cycle" which lowered down the results to 29.
#* '''Google Scholar'''
#**''' Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#**: I used all the articles that contained the words "yeast and morphogenesis and cell cycle" which lowered down the results to 119,000.
#* '''Web of Science'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#**: I removed article categories that are not related to science research, but the results came out to stay at 11.
#* '''Perform a prospective search on your article in the Web of Science and answer the following:'''
#**''' How many articles does this article cite?'''
#**: This article has 31 cites
#**''' How many articles cite this article?'''
#**: 63 articles cite this article

===Reflect===
# '''What impact does the choice of keywords have on your results?'''
#: I realized that placing certain keywords first has a big affect on the number of results and the articles that appear first.
#''' What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?'''
#: PubMed can be very useful when acquiring information about articles but doesn't do a good job at making the full article easily accessible. Google Scholar can be very useful for initial article searches, but isn't very good at specific searches and gives way too many results. Web of Science is very good at giving specific article results but does not provide the full article after clicking the article from the search page.

==Conclusion==
:Two articles were looked into for further information for each. Three databases were used to search specific topics that were related to the main research article of our group, and each database gave different results, as each had their own special uses. Using different keywords or placing the keywords in a different order while searching, will give different results.

==Data/Files==
[[Media:Dramir36_The_short-term_response_of_yeast_to_potassium_starvation.pdf| The short-term response of yeast to potassium starvation]]

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x
*Biology Online. (2019). Biology Dictionary. https://www.biology-online.org/dictionary/Main_Page

==Acknowledgments==

Dramir36 Week 11

2019-11-19T07:56:15Z

Dramir36: /* Reflect */ answered questions

==Purpose==
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==
*'''retrograde pathway:''' The mechanism of moving backward or against the usual direction of flow. [https://www.biology-online.org/dictionary/Retrograde Biology Dictionary (2019)]
*'''septin:''' A protein involved in cytokinesis and also functions in maintaining cell morphology [https://www.biology-online.org/dictionary/septin Biology Dictionary (2019)]
*'''β‐galactosidase:''' One of a class of enzymes which cuts the glycosidic bond between the sugar galactose and another sugar molecule (of a different type than galactose). [https://www.biology-online.org/dictionary/galactosidase Biology Dictionary (2019)]
*'''oxidoreductase:''' An enzyme that catalyzes the transfer of electrons from an electron donor (reductant) to an electron acceptor (oxidant) in a redox reaction [https://www.biology-online.org/dictionary/oxidoreductase Biology Dictionary (2019)]
*''' trehalose:''' A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates [https://www.biology-online.org/dictionary/Trehalose Biology Dictionary (2019)]
*'''supernatant:''' The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids. [https://www.biology-online.org/dictionary/Supernatant Biology Dictionary (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) [https://www.biology-online.org/dictionary/Biosynthesis Biology Dictionary (2019)]
*'''assimilation:''' The act of absorption or incorporation into the biological tissue. [https://www.biology-online.org/dictionary/Assimilate Biology Dictionary (2019)]
*'''isoform:''' Any of the proteins with the same function and similar amino acid sequence, encoded by different genes (or by RNA transcript). [https://www.biology-online.org/dictionary/Isoform Biology Dictionary (2019)]
*'''attenuate:''' Tapering gradually. [https://www.biology-online.org/dictionary/Attenuate Biology Dictionary (2019)]

==Outline of Journal Article==
## '''What is the main result presented in this paper?''' The main result is that there was a massive alteration in the expression profile shortly after potassium was removed from the medium. The lack of potassium drastically alters the sulfur metabolism, triggers an oxidative stress response, and activates the mitochondrial retrograde pathway. Another main finding was that after a short time without potassium, there were genes that became repressed, including genes that are involved in ribosome synthesis, translation, and the cell cycle.
## '''What is the importance or significance of this work?''' This research project is important because it shows how when Saccharomyces cerevisiae has a short-term potassium deprivation, there are impacts in the mRNA level of over one thousand genes.
## '''What were the limitations in previous studies that led them to perform this work?''' There wasn’t much insight of possible cellular functions that require potassium and the short-term effects on the gene expression profile when there is a deprivation from sudden depletion of potassium in the environment.
## '''How did they treat the yeast cells (what experiment were they doing?)''' Media that contains only traces of potassium and ammonium as nitrogen source, simulated an absence of potassium in the environment. Once the yeast has been incubated at different time points of a potassium-absent environment, RNA purification, cDNA synthesis and DNA microarray was conducted. RT-PCR assays were also conducted to see how the mutants and wild-type reacted to an increase or no increase of KCl.
## '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?''' Wild-type S. cerevisiae had four main strains that were used in the work. The main strain is BY4741. The other three strains were BY4741 without trk1, without trk2, and without both trk1 and trk2. All of the strains used in the work are haploid.
## '''What media did they grow them in? What temperature? What type of incubator? For how long?''' Recently developed YNB-based growth media was used to treat the yeast cells at 28 degrees Celsius for 10, 20, 40, 60, and 120 min by rapid filtration from four biological replicates. The control contained sufficient potassium, whereas the other media contained only traces of potassium and ammonium. The DH5ɑ cells were grown at 37 degrees Celsius in Luria-Bertani (LB) broth. There was no information given about the incubator that was used.
## '''What controls did they use?''' The control used was the wild-type strain BY4741 in media that contained 50 ml of KCl.
## '''How many replicates did they perform per treatment or timepoint?''' There were four biological replicates performed per timepoint.
## '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?''' The total RNA was extracted by using the Ribo Pure-Yeast kit (Ambion) following the manufacture’s instructions. RNA quality was assessed by electrophoresis in denaturing 0.8% agarose gels and quantified by measuring the A260 in a BioPhotometer (Eppendorf).
## '''What mathematical/statistical method did they use to analyze the data?''' A given gene was considered to be induced when the minus/ plus potassium signal ratio was equal or higher than 2.0-fold, whereas it was considered to be repressed when this signal was equal or less than 0.50-fold. The GEPAS server (v3.1) was used to pre-process the data.
## '''Are the data publicly available for download? From which web site?''' The Society for Applied Microbiology website offers the data, which is publicly available, and is located in the article’s “Supporting Information” section.
##'''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: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 1: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 2: 2A: Potassium starvation decreases sulfuric amino acid metabolism. 2B: Graph depicting relative concentrations of mRNA for genes associated with Met/Cys metabolism. 2C: The concentration of Met/Cys amino acids decreases with potassium treatment Fig. 3: 3A: Oxidative stress response genes are induced by potassium deprivation. 3B: ROS formation causes oxidation when switch to K+-free medium. 3C: Potassium starvation- decline in GSH and increase in GSSG. Fig. 4: 4A: Methylglyoxal increases with trehalose Metabolism. 4B: Genes involved in trehalose synthesis show an increase in expression. 4C: Genes in MG detoxification enhanced without potassium. Fig. 5: 5A: Potassium starvation leads to a strong increase in expression of CIT2 & DLD3 genes central to the retrograde response. 5B: Mitochondrial morphology was normal, and not the cause of the retrograde response. 5C: Potassium starvation leads to an accumulation of ammonium in the cell, and may be one cause of the retrograde response. 5D: Cells without Trk1 do not show significant ammonium accumulation. Fig. 6: 6A: Expression of genes controlling cyclins exhibit a varied response to K+ starvation. Fig. 7: 7A: Lack of potassium in yeast destabilizes the septin ring. 7B: CDC11-GFP localization is affected during K+ starvation. 7C: CDC11 protein levels are constant during starvation. 7D: CDC11 not properly localized in cells grown 60 min
## '''How does this work compare with previous studies?''' This work demonstrates that lack of potassium actually causes a fast and persistent increase in intracellular ammonium concentration.
## '''What are the important implications of this work?''' There is a significant amount of change in cells occur even during the retention of more than necessary potassium.
## '''What future directions should the authors take?''' The authors could separate the methods into their own research projects to prevent intervention or confusion with implementing new methods into the same project.
## '''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 only problem that I found with reading the results and the article in general is that, the authors inserted new techniques or analysis without much explanation, or the insertion of a new analysis method was not placed in the right spot of the article.

==Annotated Bibliography==
===1st Reference===
#''' The complete bibliographic reference in the APA style'''
#: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
# '''The link to the abstract from PubMed.'''
#:https://www.ncbi.nlm.nih.gov/pubmed/15784684?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral (if not available, write N/A).'''
#:N/A
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#:https://jcs.biologists.org/content/118/8/1617.article-info
#''' The link to the full PDF version of the article from the publisher web site.'''
#:https://jcs.biologists.org/content/joces/118/8/1617.full.pdf
# '''Who owns the rights to the article?'''
#: The Company of Biologists Limited 2005
#''' How is the article available to you?'''
#: Not open access and not open after a certain amount of time, but LMU Library allows access through a subscription.
# '''Is the article available online-only or both in print and online?'''
#: The article is available in both print and online view.
# '''Who is the publisher of the journal?'''
#:The Company of Biologists Ltd in Cambridge, which is a not-for-profit publishing organization. This organization is their own scientific society, and is not a member of the OAPA.
#''' How Long has the journal been in operation?'''
#: Since January of 1853
# '''Are the articles in this journal peer-reviewed?'''
#: Articles are peer-reviewed.
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
#: [https://jcs.biologists.org/content/edboard Editorial Board]
# '''What is the journal impact factor?'''
#: 4.517 (2018)
# '''Is the article a review or primary research article?'''
#: Primary research article
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
#: The data is not available.

===2nd Reference===
#''' The complete bibliographic reference in the APA style '''
#: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI https://doi.org/10.1534/genetics.111.128314
# '''The link to the abstract from PubMed.'''
#: https://www.ncbi.nlm.nih.gov/pubmed/22219508?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral.'''
#: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249366/
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#: https://www.genetics.org/content/190/1/51
#''' The link to the full PDF version of the article from the publisher web site.'''
#: https://www.genetics.org/content/genetics/190/1/51.full.pdf
# '''Who owns the rights to the article?'''
#: 2012 by the Genetics Society of America
#''' How is the article available to you?'''
#: Open Access
# '''Is the article available online-only or both in print and online?'''
#: Available in both print and online versions
# '''Who is the publisher of the journal? '''
#: Genetics located in Bethesda, Maryland, is a for-profit scientific society which is not part of the OAPA.
#''' How Long has the journal been in operation? (e.g., browse the archive for the earliest article published)'''
#: Journal began in January of 1916
# '''Are the articles in this journal peer-reviewed?'''
#: Articles are peer-reviewed
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
#: [https://www.genetics.org/content/editorial-board-section Editorial Board]
# '''What is the journal impact factor?'''
#: 3.564 (2018)
# '''Is the article a review or primary research article?'''
#: Review article
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
#: No data available

===PubMed, GoogleScholar, and Web of Science===
# '''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 and septin. 489 results
#**''' Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#**: Using "yeast and septin and cell cycle" really helped focus the search on yeast cell research, while also focusing on articles that mention septin and cell cycle research together. The results were narrowed to 41.
#* '''Google Scholar'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#**: "Morphogenesis and the cell cycle" 342,000 results
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#: "Yeast morphogenesis cell cycle" to specify that I am interested in yeast cell research. This narrowed down the results to 127,000.
#* '''Web of Science'''
#**''' What original keyword(s) did you use? How many results did you get?'''
#**: "Yeast and lack of potassium" 154 results
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#**: I added the term "environment" into my search so that articles that mention treating yeast cells in a potassium-absent environment are shown. The results were narrowed to 11.
# '''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?'''
#**: I focused the search to the tex words containing "yeast and septin and cell cycle" which lowered down the results to 29.
#* '''Google Scholar'''
#**''' Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#**: I used all the articles that contained the words "yeast and morphogenesis and cell cycle" which lowered down the results to 119,000.
#* '''Web of Science'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#**: I removed article categories that are not related to science research, but the results came out to stay at 11.
#* '''Perform a prospective search on your article in the Web of Science and answer the following:'''
#**''' How many articles does this article cite?'''
#**: This article has 31 cites
#**''' How many articles cite this article?'''
#**: 63 articles cite this article

===Reflect===
# '''What impact does the choice of keywords have on your results?'''
#: I realized that placing certain keywords first has a big affect on the number of results and the articles that appear first.
#''' What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?'''
#: PubMed can be very useful when acquiring information about articles but doesn't do a good job at making the full article easily accessible. Google Scholar can be very useful for initial article searches, but isn't very good at specific searches and gives way too many results. Web of Science is very good at giving specific article results but does not provide the full article after clicking the article from the search page.

==Conclusion==

==Data/Files==
[[Media:Dramir36_The_short-term_response_of_yeast_to_potassium_starvation.pdf| The short-term response of yeast to potassium starvation]]

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x
*Biology Online. (2019). Biology Dictionary. https://www.biology-online.org/dictionary/Main_Page

==Acknowledgments==

Dramir36 Week 11

2019-11-19T07:49:20Z

Dramir36: /* PubMed, GoogleScholar, and Web of Science */ answered questions

==Purpose==
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==
*'''retrograde pathway:''' The mechanism of moving backward or against the usual direction of flow. [https://www.biology-online.org/dictionary/Retrograde Biology Dictionary (2019)]
*'''septin:''' A protein involved in cytokinesis and also functions in maintaining cell morphology [https://www.biology-online.org/dictionary/septin Biology Dictionary (2019)]
*'''β‐galactosidase:''' One of a class of enzymes which cuts the glycosidic bond between the sugar galactose and another sugar molecule (of a different type than galactose). [https://www.biology-online.org/dictionary/galactosidase Biology Dictionary (2019)]
*'''oxidoreductase:''' An enzyme that catalyzes the transfer of electrons from an electron donor (reductant) to an electron acceptor (oxidant) in a redox reaction [https://www.biology-online.org/dictionary/oxidoreductase Biology Dictionary (2019)]
*''' trehalose:''' A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates [https://www.biology-online.org/dictionary/Trehalose Biology Dictionary (2019)]
*'''supernatant:''' The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids. [https://www.biology-online.org/dictionary/Supernatant Biology Dictionary (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) [https://www.biology-online.org/dictionary/Biosynthesis Biology Dictionary (2019)]
*'''assimilation:''' The act of absorption or incorporation into the biological tissue. [https://www.biology-online.org/dictionary/Assimilate Biology Dictionary (2019)]
*'''isoform:''' Any of the proteins with the same function and similar amino acid sequence, encoded by different genes (or by RNA transcript). [https://www.biology-online.org/dictionary/Isoform Biology Dictionary (2019)]
*'''attenuate:''' Tapering gradually. [https://www.biology-online.org/dictionary/Attenuate Biology Dictionary (2019)]

==Outline of Journal Article==
## '''What is the main result presented in this paper?''' The main result is that there was a massive alteration in the expression profile shortly after potassium was removed from the medium. The lack of potassium drastically alters the sulfur metabolism, triggers an oxidative stress response, and activates the mitochondrial retrograde pathway. Another main finding was that after a short time without potassium, there were genes that became repressed, including genes that are involved in ribosome synthesis, translation, and the cell cycle.
## '''What is the importance or significance of this work?''' This research project is important because it shows how when Saccharomyces cerevisiae has a short-term potassium deprivation, there are impacts in the mRNA level of over one thousand genes.
## '''What were the limitations in previous studies that led them to perform this work?''' There wasn’t much insight of possible cellular functions that require potassium and the short-term effects on the gene expression profile when there is a deprivation from sudden depletion of potassium in the environment.
## '''How did they treat the yeast cells (what experiment were they doing?)''' Media that contains only traces of potassium and ammonium as nitrogen source, simulated an absence of potassium in the environment. Once the yeast has been incubated at different time points of a potassium-absent environment, RNA purification, cDNA synthesis and DNA microarray was conducted. RT-PCR assays were also conducted to see how the mutants and wild-type reacted to an increase or no increase of KCl.
## '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?''' Wild-type S. cerevisiae had four main strains that were used in the work. The main strain is BY4741. The other three strains were BY4741 without trk1, without trk2, and without both trk1 and trk2. All of the strains used in the work are haploid.
## '''What media did they grow them in? What temperature? What type of incubator? For how long?''' Recently developed YNB-based growth media was used to treat the yeast cells at 28 degrees Celsius for 10, 20, 40, 60, and 120 min by rapid filtration from four biological replicates. The control contained sufficient potassium, whereas the other media contained only traces of potassium and ammonium. The DH5ɑ cells were grown at 37 degrees Celsius in Luria-Bertani (LB) broth. There was no information given about the incubator that was used.
## '''What controls did they use?''' The control used was the wild-type strain BY4741 in media that contained 50 ml of KCl.
## '''How many replicates did they perform per treatment or timepoint?''' There were four biological replicates performed per timepoint.
## '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?''' The total RNA was extracted by using the Ribo Pure-Yeast kit (Ambion) following the manufacture’s instructions. RNA quality was assessed by electrophoresis in denaturing 0.8% agarose gels and quantified by measuring the A260 in a BioPhotometer (Eppendorf).
## '''What mathematical/statistical method did they use to analyze the data?''' A given gene was considered to be induced when the minus/ plus potassium signal ratio was equal or higher than 2.0-fold, whereas it was considered to be repressed when this signal was equal or less than 0.50-fold. The GEPAS server (v3.1) was used to pre-process the data.
## '''Are the data publicly available for download? From which web site?''' The Society for Applied Microbiology website offers the data, which is publicly available, and is located in the article’s “Supporting Information” section.
##'''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: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 1: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 2: 2A: Potassium starvation decreases sulfuric amino acid metabolism. 2B: Graph depicting relative concentrations of mRNA for genes associated with Met/Cys metabolism. 2C: The concentration of Met/Cys amino acids decreases with potassium treatment Fig. 3: 3A: Oxidative stress response genes are induced by potassium deprivation. 3B: ROS formation causes oxidation when switch to K+-free medium. 3C: Potassium starvation- decline in GSH and increase in GSSG. Fig. 4: 4A: Methylglyoxal increases with trehalose Metabolism. 4B: Genes involved in trehalose synthesis show an increase in expression. 4C: Genes in MG detoxification enhanced without potassium. Fig. 5: 5A: Potassium starvation leads to a strong increase in expression of CIT2 & DLD3 genes central to the retrograde response. 5B: Mitochondrial morphology was normal, and not the cause of the retrograde response. 5C: Potassium starvation leads to an accumulation of ammonium in the cell, and may be one cause of the retrograde response. 5D: Cells without Trk1 do not show significant ammonium accumulation. Fig. 6: 6A: Expression of genes controlling cyclins exhibit a varied response to K+ starvation. Fig. 7: 7A: Lack of potassium in yeast destabilizes the septin ring. 7B: CDC11-GFP localization is affected during K+ starvation. 7C: CDC11 protein levels are constant during starvation. 7D: CDC11 not properly localized in cells grown 60 min
## '''How does this work compare with previous studies?''' This work demonstrates that lack of potassium actually causes a fast and persistent increase in intracellular ammonium concentration.
## '''What are the important implications of this work?''' There is a significant amount of change in cells occur even during the retention of more than necessary potassium.
## '''What future directions should the authors take?''' The authors could separate the methods into their own research projects to prevent intervention or confusion with implementing new methods into the same project.
## '''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 only problem that I found with reading the results and the article in general is that, the authors inserted new techniques or analysis without much explanation, or the insertion of a new analysis method was not placed in the right spot of the article.

==Annotated Bibliography==
===1st Reference===
#''' The complete bibliographic reference in the APA style'''
#: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
# '''The link to the abstract from PubMed.'''
#:https://www.ncbi.nlm.nih.gov/pubmed/15784684?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral (if not available, write N/A).'''
#:N/A
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#:https://jcs.biologists.org/content/118/8/1617.article-info
#''' The link to the full PDF version of the article from the publisher web site.'''
#:https://jcs.biologists.org/content/joces/118/8/1617.full.pdf
# '''Who owns the rights to the article?'''
#: The Company of Biologists Limited 2005
#''' How is the article available to you?'''
#: Not open access and not open after a certain amount of time, but LMU Library allows access through a subscription.
# '''Is the article available online-only or both in print and online?'''
#: The article is available in both print and online view.
# '''Who is the publisher of the journal?'''
#:The Company of Biologists Ltd in Cambridge, which is a not-for-profit publishing organization. This organization is their own scientific society, and is not a member of the OAPA.
#''' How Long has the journal been in operation?'''
#: Since January of 1853
# '''Are the articles in this journal peer-reviewed?'''
#: Articles are peer-reviewed.
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
#: [https://jcs.biologists.org/content/edboard Editorial Board]
# '''What is the journal impact factor?'''
#: 4.517 (2018)
# '''Is the article a review or primary research article?'''
#: Primary research article
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
#: The data is not available.

===2nd Reference===
#''' The complete bibliographic reference in the APA style '''
#: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI https://doi.org/10.1534/genetics.111.128314
# '''The link to the abstract from PubMed.'''
#: https://www.ncbi.nlm.nih.gov/pubmed/22219508?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral.'''
#: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249366/
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#: https://www.genetics.org/content/190/1/51
#''' The link to the full PDF version of the article from the publisher web site.'''
#: https://www.genetics.org/content/genetics/190/1/51.full.pdf
# '''Who owns the rights to the article?'''
#: 2012 by the Genetics Society of America
#''' How is the article available to you?'''
#: Open Access
# '''Is the article available online-only or both in print and online?'''
#: Available in both print and online versions
# '''Who is the publisher of the journal? '''
#: Genetics located in Bethesda, Maryland, is a for-profit scientific society which is not part of the OAPA.
#''' How Long has the journal been in operation? (e.g., browse the archive for the earliest article published)'''
#: Journal began in January of 1916
# '''Are the articles in this journal peer-reviewed?'''
#: Articles are peer-reviewed
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
#: [https://www.genetics.org/content/editorial-board-section Editorial Board]
# '''What is the journal impact factor?'''
#: 3.564 (2018)
# '''Is the article a review or primary research article?'''
#: Review article
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
#: No data available

===PubMed, GoogleScholar, and Web of Science===
# '''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 and septin. 489 results
#**''' Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#**: Using "yeast and septin and cell cycle" really helped focus the search on yeast cell research, while also focusing on articles that mention septin and cell cycle research together. The results were narrowed to 41.
#* '''Google Scholar'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#**: "Morphogenesis and the cell cycle" 342,000 results
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#: "Yeast morphogenesis cell cycle" to specify that I am interested in yeast cell research. This narrowed down the results to 127,000.
#* '''Web of Science'''
#**''' What original keyword(s) did you use? How many results did you get?'''
#**: "Yeast and lack of potassium" 154 results
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#**: I added the term "environment" into my search so that articles that mention treating yeast cells in a potassium-absent environment are shown. The results were narrowed to 11.
# '''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?'''
#**: I focused the search to the tex words containing "yeast and septin and cell cycle" which lowered down the results to 29.
#* '''Google Scholar'''
#**''' Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#**: I used all the articles that contained the words "yeast and morphogenesis and cell cycle" which lowered down the results to 119,000.
#* '''Web of Science'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#**: I removed article categories that are not related to science research, but the results came out to stay at 11.
#* '''Perform a prospective search on your article in the Web of Science and answer the following:'''
#**''' How many articles does this article cite?'''
#**: This article has 31 cites
#**''' How many articles cite this article?'''
#**: 63 articles cite this article

===Reflect===
# '''What impact does the choice of keywords have on your results?'''
#''' What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?'''

==Conclusion==

==Data/Files==
[[Media:Dramir36_The_short-term_response_of_yeast_to_potassium_starvation.pdf| The short-term response of yeast to potassium starvation]]

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x
*Biology Online. (2019). Biology Dictionary. https://www.biology-online.org/dictionary/Main_Page

==Acknowledgments==

Dramir36 Week 11

2019-11-19T06:20:52Z

Dramir36: /* 2nd Reference */ added location

==Purpose==
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==
*'''retrograde pathway:''' The mechanism of moving backward or against the usual direction of flow. [https://www.biology-online.org/dictionary/Retrograde Biology Dictionary (2019)]
*'''septin:''' A protein involved in cytokinesis and also functions in maintaining cell morphology [https://www.biology-online.org/dictionary/septin Biology Dictionary (2019)]
*'''β‐galactosidase:''' One of a class of enzymes which cuts the glycosidic bond between the sugar galactose and another sugar molecule (of a different type than galactose). [https://www.biology-online.org/dictionary/galactosidase Biology Dictionary (2019)]
*'''oxidoreductase:''' An enzyme that catalyzes the transfer of electrons from an electron donor (reductant) to an electron acceptor (oxidant) in a redox reaction [https://www.biology-online.org/dictionary/oxidoreductase Biology Dictionary (2019)]
*''' trehalose:''' A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates [https://www.biology-online.org/dictionary/Trehalose Biology Dictionary (2019)]
*'''supernatant:''' The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids. [https://www.biology-online.org/dictionary/Supernatant Biology Dictionary (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) [https://www.biology-online.org/dictionary/Biosynthesis Biology Dictionary (2019)]
*'''assimilation:''' The act of absorption or incorporation into the biological tissue. [https://www.biology-online.org/dictionary/Assimilate Biology Dictionary (2019)]
*'''isoform:''' Any of the proteins with the same function and similar amino acid sequence, encoded by different genes (or by RNA transcript). [https://www.biology-online.org/dictionary/Isoform Biology Dictionary (2019)]
*'''attenuate:''' Tapering gradually. [https://www.biology-online.org/dictionary/Attenuate Biology Dictionary (2019)]

==Outline of Journal Article==
## '''What is the main result presented in this paper?''' The main result is that there was a massive alteration in the expression profile shortly after potassium was removed from the medium. The lack of potassium drastically alters the sulfur metabolism, triggers an oxidative stress response, and activates the mitochondrial retrograde pathway. Another main finding was that after a short time without potassium, there were genes that became repressed, including genes that are involved in ribosome synthesis, translation, and the cell cycle.
## '''What is the importance or significance of this work?''' This research project is important because it shows how when Saccharomyces cerevisiae has a short-term potassium deprivation, there are impacts in the mRNA level of over one thousand genes.
## '''What were the limitations in previous studies that led them to perform this work?''' There wasn’t much insight of possible cellular functions that require potassium and the short-term effects on the gene expression profile when there is a deprivation from sudden depletion of potassium in the environment.
## '''How did they treat the yeast cells (what experiment were they doing?)''' Media that contains only traces of potassium and ammonium as nitrogen source, simulated an absence of potassium in the environment. Once the yeast has been incubated at different time points of a potassium-absent environment, RNA purification, cDNA synthesis and DNA microarray was conducted. RT-PCR assays were also conducted to see how the mutants and wild-type reacted to an increase or no increase of KCl.
## '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?''' Wild-type S. cerevisiae had four main strains that were used in the work. The main strain is BY4741. The other three strains were BY4741 without trk1, without trk2, and without both trk1 and trk2. All of the strains used in the work are haploid.
## '''What media did they grow them in? What temperature? What type of incubator? For how long?''' Recently developed YNB-based growth media was used to treat the yeast cells at 28 degrees Celsius for 10, 20, 40, 60, and 120 min by rapid filtration from four biological replicates. The control contained sufficient potassium, whereas the other media contained only traces of potassium and ammonium. The DH5ɑ cells were grown at 37 degrees Celsius in Luria-Bertani (LB) broth. There was no information given about the incubator that was used.
## '''What controls did they use?''' The control used was the wild-type strain BY4741 in media that contained 50 ml of KCl.
## '''How many replicates did they perform per treatment or timepoint?''' There were four biological replicates performed per timepoint.
## '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?''' The total RNA was extracted by using the Ribo Pure-Yeast kit (Ambion) following the manufacture’s instructions. RNA quality was assessed by electrophoresis in denaturing 0.8% agarose gels and quantified by measuring the A260 in a BioPhotometer (Eppendorf).
## '''What mathematical/statistical method did they use to analyze the data?''' A given gene was considered to be induced when the minus/ plus potassium signal ratio was equal or higher than 2.0-fold, whereas it was considered to be repressed when this signal was equal or less than 0.50-fold. The GEPAS server (v3.1) was used to pre-process the data.
## '''Are the data publicly available for download? From which web site?''' The Society for Applied Microbiology website offers the data, which is publicly available, and is located in the article’s “Supporting Information” section.
##'''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: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 1: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 2: 2A: Potassium starvation decreases sulfuric amino acid metabolism. 2B: Graph depicting relative concentrations of mRNA for genes associated with Met/Cys metabolism. 2C: The concentration of Met/Cys amino acids decreases with potassium treatment Fig. 3: 3A: Oxidative stress response genes are induced by potassium deprivation. 3B: ROS formation causes oxidation when switch to K+-free medium. 3C: Potassium starvation- decline in GSH and increase in GSSG. Fig. 4: 4A: Methylglyoxal increases with trehalose Metabolism. 4B: Genes involved in trehalose synthesis show an increase in expression. 4C: Genes in MG detoxification enhanced without potassium. Fig. 5: 5A: Potassium starvation leads to a strong increase in expression of CIT2 & DLD3 genes central to the retrograde response. 5B: Mitochondrial morphology was normal, and not the cause of the retrograde response. 5C: Potassium starvation leads to an accumulation of ammonium in the cell, and may be one cause of the retrograde response. 5D: Cells without Trk1 do not show significant ammonium accumulation. Fig. 6: 6A: Expression of genes controlling cyclins exhibit a varied response to K+ starvation. Fig. 7: 7A: Lack of potassium in yeast destabilizes the septin ring. 7B: CDC11-GFP localization is affected during K+ starvation. 7C: CDC11 protein levels are constant during starvation. 7D: CDC11 not properly localized in cells grown 60 min
## '''How does this work compare with previous studies?''' This work demonstrates that lack of potassium actually causes a fast and persistent increase in intracellular ammonium concentration.
## '''What are the important implications of this work?''' There is a significant amount of change in cells occur even during the retention of more than necessary potassium.
## '''What future directions should the authors take?''' The authors could separate the methods into their own research projects to prevent intervention or confusion with implementing new methods into the same project.
## '''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 only problem that I found with reading the results and the article in general is that, the authors inserted new techniques or analysis without much explanation, or the insertion of a new analysis method was not placed in the right spot of the article.

==Annotated Bibliography==
===1st Reference===
#''' The complete bibliographic reference in the APA style'''
#: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
# '''The link to the abstract from PubMed.'''
#:https://www.ncbi.nlm.nih.gov/pubmed/15784684?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral (if not available, write N/A).'''
#:N/A
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#:https://jcs.biologists.org/content/118/8/1617.article-info
#''' The link to the full PDF version of the article from the publisher web site.'''
#:https://jcs.biologists.org/content/joces/118/8/1617.full.pdf
# '''Who owns the rights to the article?'''
#: The Company of Biologists Limited 2005
#''' How is the article available to you?'''
#: Not open access and not open after a certain amount of time, but LMU Library allows access through a subscription.
# '''Is the article available online-only or both in print and online?'''
#: The article is available in both print and online view.
# '''Who is the publisher of the journal?'''
#:The Company of Biologists Ltd in Cambridge, which is a not-for-profit publishing organization. This organization is their own scientific society, and is not a member of the OAPA.
#''' How Long has the journal been in operation?'''
#: Since January of 1853
# '''Are the articles in this journal peer-reviewed?'''
#: Articles are peer-reviewed.
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
#: [https://jcs.biologists.org/content/edboard Editorial Board]
# '''What is the journal impact factor?'''
#: 4.517 (2018)
# '''Is the article a review or primary research article?'''
#: Primary research article
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
#: The data is not available.

===2nd Reference===
#''' The complete bibliographic reference in the APA style '''
#: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI https://doi.org/10.1534/genetics.111.128314
# '''The link to the abstract from PubMed.'''
#: https://www.ncbi.nlm.nih.gov/pubmed/22219508?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral.'''
#: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249366/
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#: https://www.genetics.org/content/190/1/51
#''' The link to the full PDF version of the article from the publisher web site.'''
#: https://www.genetics.org/content/genetics/190/1/51.full.pdf
# '''Who owns the rights to the article?'''
#: 2012 by the Genetics Society of America
#''' How is the article available to you?'''
#: Open Access
# '''Is the article available online-only or both in print and online?'''
#: Available in both print and online versions
# '''Who is the publisher of the journal? '''
#: Genetics located in Bethesda, Maryland, is a for-profit scientific society which is not part of the OAPA.
#''' How Long has the journal been in operation? (e.g., browse the archive for the earliest article published)'''
#: Journal began in January of 1916
# '''Are the articles in this journal peer-reviewed?'''
#: Articles are peer-reviewed
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
#: [https://www.genetics.org/content/editorial-board-section Editorial Board]
# '''What is the journal impact factor?'''
#: 3.564 (2018)
# '''Is the article a review or primary research article?'''
#: Review article
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
#: No data available

===PubMed, GoogleScholar, and Web of Science===
# '''Use a keyword search for the first three databases/tools and answer the following: '''
#* '''PubMed'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#**''' Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#* '''Google Scholar'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#* '''Web of Science'''
#**''' What original keyword(s) did you use? How many results did you get?'''
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
# '''Use the advanced search functions for each of these three databases/tools and answer the following: '''
#*''' PubMed'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Google Scholar'''
#**''' Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Web of Science'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Perform a prospective search on your article in the Web of Science and answer the following:'''
#**''' How many articles does this article cite?'''
#**''' How many articles cite this article?'''

===Reflect===
# '''What impact does the choice of keywords have on your results?'''
#''' What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?'''

==Conclusion==

==Data/Files==
[[Media:Dramir36_The_short-term_response_of_yeast_to_potassium_starvation.pdf| The short-term response of yeast to potassium starvation]]

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x
*Biology Online. (2019). Biology Dictionary. https://www.biology-online.org/dictionary/Main_Page

==Acknowledgments==

Dramir36 Week 11

2019-11-19T06:19:44Z

Dramir36: /* 1st Reference */ changed date of journal start

==Purpose==
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==
*'''retrograde pathway:''' The mechanism of moving backward or against the usual direction of flow. [https://www.biology-online.org/dictionary/Retrograde Biology Dictionary (2019)]
*'''septin:''' A protein involved in cytokinesis and also functions in maintaining cell morphology [https://www.biology-online.org/dictionary/septin Biology Dictionary (2019)]
*'''β‐galactosidase:''' One of a class of enzymes which cuts the glycosidic bond between the sugar galactose and another sugar molecule (of a different type than galactose). [https://www.biology-online.org/dictionary/galactosidase Biology Dictionary (2019)]
*'''oxidoreductase:''' An enzyme that catalyzes the transfer of electrons from an electron donor (reductant) to an electron acceptor (oxidant) in a redox reaction [https://www.biology-online.org/dictionary/oxidoreductase Biology Dictionary (2019)]
*''' trehalose:''' A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates [https://www.biology-online.org/dictionary/Trehalose Biology Dictionary (2019)]
*'''supernatant:''' The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids. [https://www.biology-online.org/dictionary/Supernatant Biology Dictionary (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) [https://www.biology-online.org/dictionary/Biosynthesis Biology Dictionary (2019)]
*'''assimilation:''' The act of absorption or incorporation into the biological tissue. [https://www.biology-online.org/dictionary/Assimilate Biology Dictionary (2019)]
*'''isoform:''' Any of the proteins with the same function and similar amino acid sequence, encoded by different genes (or by RNA transcript). [https://www.biology-online.org/dictionary/Isoform Biology Dictionary (2019)]
*'''attenuate:''' Tapering gradually. [https://www.biology-online.org/dictionary/Attenuate Biology Dictionary (2019)]

==Outline of Journal Article==
## '''What is the main result presented in this paper?''' The main result is that there was a massive alteration in the expression profile shortly after potassium was removed from the medium. The lack of potassium drastically alters the sulfur metabolism, triggers an oxidative stress response, and activates the mitochondrial retrograde pathway. Another main finding was that after a short time without potassium, there were genes that became repressed, including genes that are involved in ribosome synthesis, translation, and the cell cycle.
## '''What is the importance or significance of this work?''' This research project is important because it shows how when Saccharomyces cerevisiae has a short-term potassium deprivation, there are impacts in the mRNA level of over one thousand genes.
## '''What were the limitations in previous studies that led them to perform this work?''' There wasn’t much insight of possible cellular functions that require potassium and the short-term effects on the gene expression profile when there is a deprivation from sudden depletion of potassium in the environment.
## '''How did they treat the yeast cells (what experiment were they doing?)''' Media that contains only traces of potassium and ammonium as nitrogen source, simulated an absence of potassium in the environment. Once the yeast has been incubated at different time points of a potassium-absent environment, RNA purification, cDNA synthesis and DNA microarray was conducted. RT-PCR assays were also conducted to see how the mutants and wild-type reacted to an increase or no increase of KCl.
## '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?''' Wild-type S. cerevisiae had four main strains that were used in the work. The main strain is BY4741. The other three strains were BY4741 without trk1, without trk2, and without both trk1 and trk2. All of the strains used in the work are haploid.
## '''What media did they grow them in? What temperature? What type of incubator? For how long?''' Recently developed YNB-based growth media was used to treat the yeast cells at 28 degrees Celsius for 10, 20, 40, 60, and 120 min by rapid filtration from four biological replicates. The control contained sufficient potassium, whereas the other media contained only traces of potassium and ammonium. The DH5ɑ cells were grown at 37 degrees Celsius in Luria-Bertani (LB) broth. There was no information given about the incubator that was used.
## '''What controls did they use?''' The control used was the wild-type strain BY4741 in media that contained 50 ml of KCl.
## '''How many replicates did they perform per treatment or timepoint?''' There were four biological replicates performed per timepoint.
## '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?''' The total RNA was extracted by using the Ribo Pure-Yeast kit (Ambion) following the manufacture’s instructions. RNA quality was assessed by electrophoresis in denaturing 0.8% agarose gels and quantified by measuring the A260 in a BioPhotometer (Eppendorf).
## '''What mathematical/statistical method did they use to analyze the data?''' A given gene was considered to be induced when the minus/ plus potassium signal ratio was equal or higher than 2.0-fold, whereas it was considered to be repressed when this signal was equal or less than 0.50-fold. The GEPAS server (v3.1) was used to pre-process the data.
## '''Are the data publicly available for download? From which web site?''' The Society for Applied Microbiology website offers the data, which is publicly available, and is located in the article’s “Supporting Information” section.
##'''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: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 1: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 2: 2A: Potassium starvation decreases sulfuric amino acid metabolism. 2B: Graph depicting relative concentrations of mRNA for genes associated with Met/Cys metabolism. 2C: The concentration of Met/Cys amino acids decreases with potassium treatment Fig. 3: 3A: Oxidative stress response genes are induced by potassium deprivation. 3B: ROS formation causes oxidation when switch to K+-free medium. 3C: Potassium starvation- decline in GSH and increase in GSSG. Fig. 4: 4A: Methylglyoxal increases with trehalose Metabolism. 4B: Genes involved in trehalose synthesis show an increase in expression. 4C: Genes in MG detoxification enhanced without potassium. Fig. 5: 5A: Potassium starvation leads to a strong increase in expression of CIT2 & DLD3 genes central to the retrograde response. 5B: Mitochondrial morphology was normal, and not the cause of the retrograde response. 5C: Potassium starvation leads to an accumulation of ammonium in the cell, and may be one cause of the retrograde response. 5D: Cells without Trk1 do not show significant ammonium accumulation. Fig. 6: 6A: Expression of genes controlling cyclins exhibit a varied response to K+ starvation. Fig. 7: 7A: Lack of potassium in yeast destabilizes the septin ring. 7B: CDC11-GFP localization is affected during K+ starvation. 7C: CDC11 protein levels are constant during starvation. 7D: CDC11 not properly localized in cells grown 60 min
## '''How does this work compare with previous studies?''' This work demonstrates that lack of potassium actually causes a fast and persistent increase in intracellular ammonium concentration.
## '''What are the important implications of this work?''' There is a significant amount of change in cells occur even during the retention of more than necessary potassium.
## '''What future directions should the authors take?''' The authors could separate the methods into their own research projects to prevent intervention or confusion with implementing new methods into the same project.
## '''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 only problem that I found with reading the results and the article in general is that, the authors inserted new techniques or analysis without much explanation, or the insertion of a new analysis method was not placed in the right spot of the article.

==Annotated Bibliography==
===1st Reference===
#''' The complete bibliographic reference in the APA style'''
#: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
# '''The link to the abstract from PubMed.'''
#:https://www.ncbi.nlm.nih.gov/pubmed/15784684?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral (if not available, write N/A).'''
#:N/A
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#:https://jcs.biologists.org/content/118/8/1617.article-info
#''' The link to the full PDF version of the article from the publisher web site.'''
#:https://jcs.biologists.org/content/joces/118/8/1617.full.pdf
# '''Who owns the rights to the article?'''
#: The Company of Biologists Limited 2005
#''' How is the article available to you?'''
#: Not open access and not open after a certain amount of time, but LMU Library allows access through a subscription.
# '''Is the article available online-only or both in print and online?'''
#: The article is available in both print and online view.
# '''Who is the publisher of the journal?'''
#:The Company of Biologists Ltd in Cambridge, which is a not-for-profit publishing organization. This organization is their own scientific society, and is not a member of the OAPA.
#''' How Long has the journal been in operation?'''
#: Since January of 1853
# '''Are the articles in this journal peer-reviewed?'''
#: Articles are peer-reviewed.
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
#: [https://jcs.biologists.org/content/edboard Editorial Board]
# '''What is the journal impact factor?'''
#: 4.517 (2018)
# '''Is the article a review or primary research article?'''
#: Primary research article
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
#: The data is not available.

===2nd Reference===
#''' The complete bibliographic reference in the APA style '''
#: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI https://doi.org/10.1534/genetics.111.128314
# '''The link to the abstract from PubMed.'''
#: https://www.ncbi.nlm.nih.gov/pubmed/22219508?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral.'''
#: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249366/
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#: https://www.genetics.org/content/190/1/51
#''' The link to the full PDF version of the article from the publisher web site.'''
#: https://www.genetics.org/content/genetics/190/1/51.full.pdf
# '''Who owns the rights to the article?'''
#: 2012 by the Genetics Society of America
#''' How is the article available to you?'''
#: Open Access
# '''Is the article available online-only or both in print and online?'''
#: Available in both print and online versions
# '''Who is the publisher of the journal? '''
#: Genetics located in Bethesda, is a for-profit scientific society which is not part of the OAPA.
#''' How Long has the journal been in operation? (e.g., browse the archive for the earliest article published)'''
#: Journal began in January of 1916
# '''Are the articles in this journal peer-reviewed?'''
#: Articles are peer-reviewed
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
#: [https://www.genetics.org/content/editorial-board-section Editorial Board]
# '''What is the journal impact factor?'''
#: 3.564 (2018)
# '''Is the article a review or primary research article?'''
#: Review article
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
#: No data available

===PubMed, GoogleScholar, and Web of Science===
# '''Use a keyword search for the first three databases/tools and answer the following: '''
#* '''PubMed'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#**''' Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#* '''Google Scholar'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#* '''Web of Science'''
#**''' What original keyword(s) did you use? How many results did you get?'''
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
# '''Use the advanced search functions for each of these three databases/tools and answer the following: '''
#*''' PubMed'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Google Scholar'''
#**''' Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Web of Science'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Perform a prospective search on your article in the Web of Science and answer the following:'''
#**''' How many articles does this article cite?'''
#**''' How many articles cite this article?'''

===Reflect===
# '''What impact does the choice of keywords have on your results?'''
#''' What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?'''

==Conclusion==

==Data/Files==
[[Media:Dramir36_The_short-term_response_of_yeast_to_potassium_starvation.pdf| The short-term response of yeast to potassium starvation]]

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x
*Biology Online. (2019). Biology Dictionary. https://www.biology-online.org/dictionary/Main_Page

==Acknowledgments==

Dramir36 Week 11

2019-11-19T06:17:56Z

Dramir36: /* 1st Reference */ added impact factor

==Purpose==
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==
*'''retrograde pathway:''' The mechanism of moving backward or against the usual direction of flow. [https://www.biology-online.org/dictionary/Retrograde Biology Dictionary (2019)]
*'''septin:''' A protein involved in cytokinesis and also functions in maintaining cell morphology [https://www.biology-online.org/dictionary/septin Biology Dictionary (2019)]
*'''β‐galactosidase:''' One of a class of enzymes which cuts the glycosidic bond between the sugar galactose and another sugar molecule (of a different type than galactose). [https://www.biology-online.org/dictionary/galactosidase Biology Dictionary (2019)]
*'''oxidoreductase:''' An enzyme that catalyzes the transfer of electrons from an electron donor (reductant) to an electron acceptor (oxidant) in a redox reaction [https://www.biology-online.org/dictionary/oxidoreductase Biology Dictionary (2019)]
*''' trehalose:''' A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates [https://www.biology-online.org/dictionary/Trehalose Biology Dictionary (2019)]
*'''supernatant:''' The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids. [https://www.biology-online.org/dictionary/Supernatant Biology Dictionary (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) [https://www.biology-online.org/dictionary/Biosynthesis Biology Dictionary (2019)]
*'''assimilation:''' The act of absorption or incorporation into the biological tissue. [https://www.biology-online.org/dictionary/Assimilate Biology Dictionary (2019)]
*'''isoform:''' Any of the proteins with the same function and similar amino acid sequence, encoded by different genes (or by RNA transcript). [https://www.biology-online.org/dictionary/Isoform Biology Dictionary (2019)]
*'''attenuate:''' Tapering gradually. [https://www.biology-online.org/dictionary/Attenuate Biology Dictionary (2019)]

==Outline of Journal Article==
## '''What is the main result presented in this paper?''' The main result is that there was a massive alteration in the expression profile shortly after potassium was removed from the medium. The lack of potassium drastically alters the sulfur metabolism, triggers an oxidative stress response, and activates the mitochondrial retrograde pathway. Another main finding was that after a short time without potassium, there were genes that became repressed, including genes that are involved in ribosome synthesis, translation, and the cell cycle.
## '''What is the importance or significance of this work?''' This research project is important because it shows how when Saccharomyces cerevisiae has a short-term potassium deprivation, there are impacts in the mRNA level of over one thousand genes.
## '''What were the limitations in previous studies that led them to perform this work?''' There wasn’t much insight of possible cellular functions that require potassium and the short-term effects on the gene expression profile when there is a deprivation from sudden depletion of potassium in the environment.
## '''How did they treat the yeast cells (what experiment were they doing?)''' Media that contains only traces of potassium and ammonium as nitrogen source, simulated an absence of potassium in the environment. Once the yeast has been incubated at different time points of a potassium-absent environment, RNA purification, cDNA synthesis and DNA microarray was conducted. RT-PCR assays were also conducted to see how the mutants and wild-type reacted to an increase or no increase of KCl.
## '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?''' Wild-type S. cerevisiae had four main strains that were used in the work. The main strain is BY4741. The other three strains were BY4741 without trk1, without trk2, and without both trk1 and trk2. All of the strains used in the work are haploid.
## '''What media did they grow them in? What temperature? What type of incubator? For how long?''' Recently developed YNB-based growth media was used to treat the yeast cells at 28 degrees Celsius for 10, 20, 40, 60, and 120 min by rapid filtration from four biological replicates. The control contained sufficient potassium, whereas the other media contained only traces of potassium and ammonium. The DH5ɑ cells were grown at 37 degrees Celsius in Luria-Bertani (LB) broth. There was no information given about the incubator that was used.
## '''What controls did they use?''' The control used was the wild-type strain BY4741 in media that contained 50 ml of KCl.
## '''How many replicates did they perform per treatment or timepoint?''' There were four biological replicates performed per timepoint.
## '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?''' The total RNA was extracted by using the Ribo Pure-Yeast kit (Ambion) following the manufacture’s instructions. RNA quality was assessed by electrophoresis in denaturing 0.8% agarose gels and quantified by measuring the A260 in a BioPhotometer (Eppendorf).
## '''What mathematical/statistical method did they use to analyze the data?''' A given gene was considered to be induced when the minus/ plus potassium signal ratio was equal or higher than 2.0-fold, whereas it was considered to be repressed when this signal was equal or less than 0.50-fold. The GEPAS server (v3.1) was used to pre-process the data.
## '''Are the data publicly available for download? From which web site?''' The Society for Applied Microbiology website offers the data, which is publicly available, and is located in the article’s “Supporting Information” section.
##'''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: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 1: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 2: 2A: Potassium starvation decreases sulfuric amino acid metabolism. 2B: Graph depicting relative concentrations of mRNA for genes associated with Met/Cys metabolism. 2C: The concentration of Met/Cys amino acids decreases with potassium treatment Fig. 3: 3A: Oxidative stress response genes are induced by potassium deprivation. 3B: ROS formation causes oxidation when switch to K+-free medium. 3C: Potassium starvation- decline in GSH and increase in GSSG. Fig. 4: 4A: Methylglyoxal increases with trehalose Metabolism. 4B: Genes involved in trehalose synthesis show an increase in expression. 4C: Genes in MG detoxification enhanced without potassium. Fig. 5: 5A: Potassium starvation leads to a strong increase in expression of CIT2 & DLD3 genes central to the retrograde response. 5B: Mitochondrial morphology was normal, and not the cause of the retrograde response. 5C: Potassium starvation leads to an accumulation of ammonium in the cell, and may be one cause of the retrograde response. 5D: Cells without Trk1 do not show significant ammonium accumulation. Fig. 6: 6A: Expression of genes controlling cyclins exhibit a varied response to K+ starvation. Fig. 7: 7A: Lack of potassium in yeast destabilizes the septin ring. 7B: CDC11-GFP localization is affected during K+ starvation. 7C: CDC11 protein levels are constant during starvation. 7D: CDC11 not properly localized in cells grown 60 min
## '''How does this work compare with previous studies?''' This work demonstrates that lack of potassium actually causes a fast and persistent increase in intracellular ammonium concentration.
## '''What are the important implications of this work?''' There is a significant amount of change in cells occur even during the retention of more than necessary potassium.
## '''What future directions should the authors take?''' The authors could separate the methods into their own research projects to prevent intervention or confusion with implementing new methods into the same project.
## '''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 only problem that I found with reading the results and the article in general is that, the authors inserted new techniques or analysis without much explanation, or the insertion of a new analysis method was not placed in the right spot of the article.

==Annotated Bibliography==
===1st Reference===
#''' The complete bibliographic reference in the APA style'''
#: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
# '''The link to the abstract from PubMed.'''
#:https://www.ncbi.nlm.nih.gov/pubmed/15784684?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral (if not available, write N/A).'''
#:N/A
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#:https://jcs.biologists.org/content/118/8/1617.article-info
#''' The link to the full PDF version of the article from the publisher web site.'''
#:https://jcs.biologists.org/content/joces/118/8/1617.full.pdf
# '''Who owns the rights to the article?'''
#: The Company of Biologists Limited 2005
#''' How is the article available to you?'''
#: Not open access and not open after a certain amount of time, but LMU Library allows access through a subscription.
# '''Is the article available online-only or both in print and online?'''
#: The article is available in both print and online view.
# '''Who is the publisher of the journal?'''
#:The Company of Biologists Ltd in Cambridge, which is a not-for-profit publishing organization. This organization is their own scientific society, and is not a member of the OAPA.
#''' How Long has the journal been in operation?'''
#: Since March 22, 2005
# '''Are the articles in this journal peer-reviewed?'''
#: Articles are peer-reviewed.
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
#: [https://jcs.biologists.org/content/edboard Editorial Board]
# '''What is the journal impact factor?'''
#: 4.517 (2018)
# '''Is the article a review or primary research article?'''
#: Primary research article
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
#: The data is not available.

===2nd Reference===
#''' The complete bibliographic reference in the APA style '''
#: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI https://doi.org/10.1534/genetics.111.128314
# '''The link to the abstract from PubMed.'''
#: https://www.ncbi.nlm.nih.gov/pubmed/22219508?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral.'''
#: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249366/
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#: https://www.genetics.org/content/190/1/51
#''' The link to the full PDF version of the article from the publisher web site.'''
#: https://www.genetics.org/content/genetics/190/1/51.full.pdf
# '''Who owns the rights to the article?'''
#: 2012 by the Genetics Society of America
#''' How is the article available to you?'''
#: Open Access
# '''Is the article available online-only or both in print and online?'''
#: Available in both print and online versions
# '''Who is the publisher of the journal? '''
#: Genetics located in Bethesda, is a for-profit scientific society which is not part of the OAPA.
#''' How Long has the journal been in operation? (e.g., browse the archive for the earliest article published)'''
#: Journal began in January of 1916
# '''Are the articles in this journal peer-reviewed?'''
#: Articles are peer-reviewed
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
#: [https://www.genetics.org/content/editorial-board-section Editorial Board]
# '''What is the journal impact factor?'''
#: 3.564 (2018)
# '''Is the article a review or primary research article?'''
#: Review article
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
#: No data available

===PubMed, GoogleScholar, and Web of Science===
# '''Use a keyword search for the first three databases/tools and answer the following: '''
#* '''PubMed'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#**''' Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#* '''Google Scholar'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#* '''Web of Science'''
#**''' What original keyword(s) did you use? How many results did you get?'''
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
# '''Use the advanced search functions for each of these three databases/tools and answer the following: '''
#*''' PubMed'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Google Scholar'''
#**''' Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Web of Science'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Perform a prospective search on your article in the Web of Science and answer the following:'''
#**''' How many articles does this article cite?'''
#**''' How many articles cite this article?'''

===Reflect===
# '''What impact does the choice of keywords have on your results?'''
#''' What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?'''

==Conclusion==

==Data/Files==
[[Media:Dramir36_The_short-term_response_of_yeast_to_potassium_starvation.pdf| The short-term response of yeast to potassium starvation]]

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x
*Biology Online. (2019). Biology Dictionary. https://www.biology-online.org/dictionary/Main_Page

==Acknowledgments==

Dramir36 Week 11

2019-11-19T06:17:21Z

Dramir36: /* 2nd Reference */ answered 2nd reference questions

==Purpose==
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==
*'''retrograde pathway:''' The mechanism of moving backward or against the usual direction of flow. [https://www.biology-online.org/dictionary/Retrograde Biology Dictionary (2019)]
*'''septin:''' A protein involved in cytokinesis and also functions in maintaining cell morphology [https://www.biology-online.org/dictionary/septin Biology Dictionary (2019)]
*'''β‐galactosidase:''' One of a class of enzymes which cuts the glycosidic bond between the sugar galactose and another sugar molecule (of a different type than galactose). [https://www.biology-online.org/dictionary/galactosidase Biology Dictionary (2019)]
*'''oxidoreductase:''' An enzyme that catalyzes the transfer of electrons from an electron donor (reductant) to an electron acceptor (oxidant) in a redox reaction [https://www.biology-online.org/dictionary/oxidoreductase Biology Dictionary (2019)]
*''' trehalose:''' A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates [https://www.biology-online.org/dictionary/Trehalose Biology Dictionary (2019)]
*'''supernatant:''' The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids. [https://www.biology-online.org/dictionary/Supernatant Biology Dictionary (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) [https://www.biology-online.org/dictionary/Biosynthesis Biology Dictionary (2019)]
*'''assimilation:''' The act of absorption or incorporation into the biological tissue. [https://www.biology-online.org/dictionary/Assimilate Biology Dictionary (2019)]
*'''isoform:''' Any of the proteins with the same function and similar amino acid sequence, encoded by different genes (or by RNA transcript). [https://www.biology-online.org/dictionary/Isoform Biology Dictionary (2019)]
*'''attenuate:''' Tapering gradually. [https://www.biology-online.org/dictionary/Attenuate Biology Dictionary (2019)]

==Outline of Journal Article==
## '''What is the main result presented in this paper?''' The main result is that there was a massive alteration in the expression profile shortly after potassium was removed from the medium. The lack of potassium drastically alters the sulfur metabolism, triggers an oxidative stress response, and activates the mitochondrial retrograde pathway. Another main finding was that after a short time without potassium, there were genes that became repressed, including genes that are involved in ribosome synthesis, translation, and the cell cycle.
## '''What is the importance or significance of this work?''' This research project is important because it shows how when Saccharomyces cerevisiae has a short-term potassium deprivation, there are impacts in the mRNA level of over one thousand genes.
## '''What were the limitations in previous studies that led them to perform this work?''' There wasn’t much insight of possible cellular functions that require potassium and the short-term effects on the gene expression profile when there is a deprivation from sudden depletion of potassium in the environment.
## '''How did they treat the yeast cells (what experiment were they doing?)''' Media that contains only traces of potassium and ammonium as nitrogen source, simulated an absence of potassium in the environment. Once the yeast has been incubated at different time points of a potassium-absent environment, RNA purification, cDNA synthesis and DNA microarray was conducted. RT-PCR assays were also conducted to see how the mutants and wild-type reacted to an increase or no increase of KCl.
## '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?''' Wild-type S. cerevisiae had four main strains that were used in the work. The main strain is BY4741. The other three strains were BY4741 without trk1, without trk2, and without both trk1 and trk2. All of the strains used in the work are haploid.
## '''What media did they grow them in? What temperature? What type of incubator? For how long?''' Recently developed YNB-based growth media was used to treat the yeast cells at 28 degrees Celsius for 10, 20, 40, 60, and 120 min by rapid filtration from four biological replicates. The control contained sufficient potassium, whereas the other media contained only traces of potassium and ammonium. The DH5ɑ cells were grown at 37 degrees Celsius in Luria-Bertani (LB) broth. There was no information given about the incubator that was used.
## '''What controls did they use?''' The control used was the wild-type strain BY4741 in media that contained 50 ml of KCl.
## '''How many replicates did they perform per treatment or timepoint?''' There were four biological replicates performed per timepoint.
## '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?''' The total RNA was extracted by using the Ribo Pure-Yeast kit (Ambion) following the manufacture’s instructions. RNA quality was assessed by electrophoresis in denaturing 0.8% agarose gels and quantified by measuring the A260 in a BioPhotometer (Eppendorf).
## '''What mathematical/statistical method did they use to analyze the data?''' A given gene was considered to be induced when the minus/ plus potassium signal ratio was equal or higher than 2.0-fold, whereas it was considered to be repressed when this signal was equal or less than 0.50-fold. The GEPAS server (v3.1) was used to pre-process the data.
## '''Are the data publicly available for download? From which web site?''' The Society for Applied Microbiology website offers the data, which is publicly available, and is located in the article’s “Supporting Information” section.
##'''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: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 1: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 2: 2A: Potassium starvation decreases sulfuric amino acid metabolism. 2B: Graph depicting relative concentrations of mRNA for genes associated with Met/Cys metabolism. 2C: The concentration of Met/Cys amino acids decreases with potassium treatment Fig. 3: 3A: Oxidative stress response genes are induced by potassium deprivation. 3B: ROS formation causes oxidation when switch to K+-free medium. 3C: Potassium starvation- decline in GSH and increase in GSSG. Fig. 4: 4A: Methylglyoxal increases with trehalose Metabolism. 4B: Genes involved in trehalose synthesis show an increase in expression. 4C: Genes in MG detoxification enhanced without potassium. Fig. 5: 5A: Potassium starvation leads to a strong increase in expression of CIT2 & DLD3 genes central to the retrograde response. 5B: Mitochondrial morphology was normal, and not the cause of the retrograde response. 5C: Potassium starvation leads to an accumulation of ammonium in the cell, and may be one cause of the retrograde response. 5D: Cells without Trk1 do not show significant ammonium accumulation. Fig. 6: 6A: Expression of genes controlling cyclins exhibit a varied response to K+ starvation. Fig. 7: 7A: Lack of potassium in yeast destabilizes the septin ring. 7B: CDC11-GFP localization is affected during K+ starvation. 7C: CDC11 protein levels are constant during starvation. 7D: CDC11 not properly localized in cells grown 60 min
## '''How does this work compare with previous studies?''' This work demonstrates that lack of potassium actually causes a fast and persistent increase in intracellular ammonium concentration.
## '''What are the important implications of this work?''' There is a significant amount of change in cells occur even during the retention of more than necessary potassium.
## '''What future directions should the authors take?''' The authors could separate the methods into their own research projects to prevent intervention or confusion with implementing new methods into the same project.
## '''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 only problem that I found with reading the results and the article in general is that, the authors inserted new techniques or analysis without much explanation, or the insertion of a new analysis method was not placed in the right spot of the article.

==Annotated Bibliography==
===1st Reference===
#''' The complete bibliographic reference in the APA style'''
#: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
# '''The link to the abstract from PubMed.'''
#:https://www.ncbi.nlm.nih.gov/pubmed/15784684?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral (if not available, write N/A).'''
#:N/A
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#:https://jcs.biologists.org/content/118/8/1617.article-info
#''' The link to the full PDF version of the article from the publisher web site.'''
#:https://jcs.biologists.org/content/joces/118/8/1617.full.pdf
# '''Who owns the rights to the article?'''
#: The Company of Biologists Limited 2005
#''' How is the article available to you?'''
#: Not open access and not open after a certain amount of time, but LMU Library allows access through a subscription.
# '''Is the article available online-only or both in print and online?'''
#: The article is available in both print and online view.
# '''Who is the publisher of the journal?'''
#:The Company of Biologists Ltd in Cambridge, which is a not-for-profit publishing organization. This organization is their own scientific society, and is not a member of the OAPA.
#''' How Long has the journal been in operation?'''
#: Since March 22, 2005
# '''Are the articles in this journal peer-reviewed?'''
#: Articles are peer-reviewed.
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
#: [https://jcs.biologists.org/content/edboard Editorial Board]
# '''What is the journal impact factor?'''
#: No impact factor available
# '''Is the article a review or primary research article?'''
#: Primary research article
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
#: The data is not available.
===2nd Reference===
#''' The complete bibliographic reference in the APA style '''
#: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI https://doi.org/10.1534/genetics.111.128314
# '''The link to the abstract from PubMed.'''
#: https://www.ncbi.nlm.nih.gov/pubmed/22219508?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral.'''
#: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249366/
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#: https://www.genetics.org/content/190/1/51
#''' The link to the full PDF version of the article from the publisher web site.'''
#: https://www.genetics.org/content/genetics/190/1/51.full.pdf
# '''Who owns the rights to the article?'''
#: 2012 by the Genetics Society of America
#''' How is the article available to you?'''
#: Open Access
# '''Is the article available online-only or both in print and online?'''
#: Available in both print and online versions
# '''Who is the publisher of the journal? '''
#: Genetics located in Bethesda, is a for-profit scientific society which is not part of the OAPA.
#''' How Long has the journal been in operation? (e.g., browse the archive for the earliest article published)'''
#: Journal began in January of 1916
# '''Are the articles in this journal peer-reviewed?'''
#: Articles are peer-reviewed
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
#: [https://www.genetics.org/content/editorial-board-section Editorial Board]
# '''What is the journal impact factor?'''
#: 3.564 (2018)
# '''Is the article a review or primary research article?'''
#: Review article
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
#: No data available

===PubMed, GoogleScholar, and Web of Science===
# '''Use a keyword search for the first three databases/tools and answer the following: '''
#* '''PubMed'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#**''' Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#* '''Google Scholar'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#* '''Web of Science'''
#**''' What original keyword(s) did you use? How many results did you get?'''
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
# '''Use the advanced search functions for each of these three databases/tools and answer the following: '''
#*''' PubMed'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Google Scholar'''
#**''' Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Web of Science'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Perform a prospective search on your article in the Web of Science and answer the following:'''
#**''' How many articles does this article cite?'''
#**''' How many articles cite this article?'''

===Reflect===
# '''What impact does the choice of keywords have on your results?'''
#''' What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?'''

==Conclusion==

==Data/Files==
[[Media:Dramir36_The_short-term_response_of_yeast_to_potassium_starvation.pdf| The short-term response of yeast to potassium starvation]]

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x
*Biology Online. (2019). Biology Dictionary. https://www.biology-online.org/dictionary/Main_Page

==Acknowledgments==

Dramir36 Week 11

2019-11-19T05:35:00Z

Dramir36: /* Annotated Bibliography */ answered 1st reference

==Purpose==
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==
*'''retrograde pathway:''' The mechanism of moving backward or against the usual direction of flow. [https://www.biology-online.org/dictionary/Retrograde Biology Dictionary (2019)]
*'''septin:''' A protein involved in cytokinesis and also functions in maintaining cell morphology [https://www.biology-online.org/dictionary/septin Biology Dictionary (2019)]
*'''β‐galactosidase:''' One of a class of enzymes which cuts the glycosidic bond between the sugar galactose and another sugar molecule (of a different type than galactose). [https://www.biology-online.org/dictionary/galactosidase Biology Dictionary (2019)]
*'''oxidoreductase:''' An enzyme that catalyzes the transfer of electrons from an electron donor (reductant) to an electron acceptor (oxidant) in a redox reaction [https://www.biology-online.org/dictionary/oxidoreductase Biology Dictionary (2019)]
*''' trehalose:''' A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates [https://www.biology-online.org/dictionary/Trehalose Biology Dictionary (2019)]
*'''supernatant:''' The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids. [https://www.biology-online.org/dictionary/Supernatant Biology Dictionary (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) [https://www.biology-online.org/dictionary/Biosynthesis Biology Dictionary (2019)]
*'''assimilation:''' The act of absorption or incorporation into the biological tissue. [https://www.biology-online.org/dictionary/Assimilate Biology Dictionary (2019)]
*'''isoform:''' Any of the proteins with the same function and similar amino acid sequence, encoded by different genes (or by RNA transcript). [https://www.biology-online.org/dictionary/Isoform Biology Dictionary (2019)]
*'''attenuate:''' Tapering gradually. [https://www.biology-online.org/dictionary/Attenuate Biology Dictionary (2019)]

==Outline of Journal Article==
## '''What is the main result presented in this paper?''' The main result is that there was a massive alteration in the expression profile shortly after potassium was removed from the medium. The lack of potassium drastically alters the sulfur metabolism, triggers an oxidative stress response, and activates the mitochondrial retrograde pathway. Another main finding was that after a short time without potassium, there were genes that became repressed, including genes that are involved in ribosome synthesis, translation, and the cell cycle.
## '''What is the importance or significance of this work?''' This research project is important because it shows how when Saccharomyces cerevisiae has a short-term potassium deprivation, there are impacts in the mRNA level of over one thousand genes.
## '''What were the limitations in previous studies that led them to perform this work?''' There wasn’t much insight of possible cellular functions that require potassium and the short-term effects on the gene expression profile when there is a deprivation from sudden depletion of potassium in the environment.
## '''How did they treat the yeast cells (what experiment were they doing?)''' Media that contains only traces of potassium and ammonium as nitrogen source, simulated an absence of potassium in the environment. Once the yeast has been incubated at different time points of a potassium-absent environment, RNA purification, cDNA synthesis and DNA microarray was conducted. RT-PCR assays were also conducted to see how the mutants and wild-type reacted to an increase or no increase of KCl.
## '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?''' Wild-type S. cerevisiae had four main strains that were used in the work. The main strain is BY4741. The other three strains were BY4741 without trk1, without trk2, and without both trk1 and trk2. All of the strains used in the work are haploid.
## '''What media did they grow them in? What temperature? What type of incubator? For how long?''' Recently developed YNB-based growth media was used to treat the yeast cells at 28 degrees Celsius for 10, 20, 40, 60, and 120 min by rapid filtration from four biological replicates. The control contained sufficient potassium, whereas the other media contained only traces of potassium and ammonium. The DH5ɑ cells were grown at 37 degrees Celsius in Luria-Bertani (LB) broth. There was no information given about the incubator that was used.
## '''What controls did they use?''' The control used was the wild-type strain BY4741 in media that contained 50 ml of KCl.
## '''How many replicates did they perform per treatment or timepoint?''' There were four biological replicates performed per timepoint.
## '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?''' The total RNA was extracted by using the Ribo Pure-Yeast kit (Ambion) following the manufacture’s instructions. RNA quality was assessed by electrophoresis in denaturing 0.8% agarose gels and quantified by measuring the A260 in a BioPhotometer (Eppendorf).
## '''What mathematical/statistical method did they use to analyze the data?''' A given gene was considered to be induced when the minus/ plus potassium signal ratio was equal or higher than 2.0-fold, whereas it was considered to be repressed when this signal was equal or less than 0.50-fold. The GEPAS server (v3.1) was used to pre-process the data.
## '''Are the data publicly available for download? From which web site?''' The Society for Applied Microbiology website offers the data, which is publicly available, and is located in the article’s “Supporting Information” section.
##'''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: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 1: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 2: 2A: Potassium starvation decreases sulfuric amino acid metabolism. 2B: Graph depicting relative concentrations of mRNA for genes associated with Met/Cys metabolism. 2C: The concentration of Met/Cys amino acids decreases with potassium treatment Fig. 3: 3A: Oxidative stress response genes are induced by potassium deprivation. 3B: ROS formation causes oxidation when switch to K+-free medium. 3C: Potassium starvation- decline in GSH and increase in GSSG. Fig. 4: 4A: Methylglyoxal increases with trehalose Metabolism. 4B: Genes involved in trehalose synthesis show an increase in expression. 4C: Genes in MG detoxification enhanced without potassium. Fig. 5: 5A: Potassium starvation leads to a strong increase in expression of CIT2 & DLD3 genes central to the retrograde response. 5B: Mitochondrial morphology was normal, and not the cause of the retrograde response. 5C: Potassium starvation leads to an accumulation of ammonium in the cell, and may be one cause of the retrograde response. 5D: Cells without Trk1 do not show significant ammonium accumulation. Fig. 6: 6A: Expression of genes controlling cyclins exhibit a varied response to K+ starvation. Fig. 7: 7A: Lack of potassium in yeast destabilizes the septin ring. 7B: CDC11-GFP localization is affected during K+ starvation. 7C: CDC11 protein levels are constant during starvation. 7D: CDC11 not properly localized in cells grown 60 min
## '''How does this work compare with previous studies?''' This work demonstrates that lack of potassium actually causes a fast and persistent increase in intracellular ammonium concentration.
## '''What are the important implications of this work?''' There is a significant amount of change in cells occur even during the retention of more than necessary potassium.
## '''What future directions should the authors take?''' The authors could separate the methods into their own research projects to prevent intervention or confusion with implementing new methods into the same project.
## '''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 only problem that I found with reading the results and the article in general is that, the authors inserted new techniques or analysis without much explanation, or the insertion of a new analysis method was not placed in the right spot of the article.

==Annotated Bibliography==
===1st Reference===
#''' The complete bibliographic reference in the APA style'''
#: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
# '''The link to the abstract from PubMed.'''
#:https://www.ncbi.nlm.nih.gov/pubmed/15784684?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral (if not available, write N/A).'''
#:N/A
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#:https://jcs.biologists.org/content/118/8/1617.article-info
#''' The link to the full PDF version of the article from the publisher web site.'''
#:https://jcs.biologists.org/content/joces/118/8/1617.full.pdf
# '''Who owns the rights to the article?'''
#: The Company of Biologists Limited 2005
#''' How is the article available to you?'''
#: Not open access and not open after a certain amount of time, but LMU Library allows access through a subscription.
# '''Is the article available online-only or both in print and online?'''
#: The article is available in both print and online view.
# '''Who is the publisher of the journal?'''
#:The Company of Biologists Ltd in Cambridge, which is a not-for-profit publishing organization. This organization is their own scientific society, and is not a member of the OAPA.
#''' How Long has the journal been in operation?'''
#: Since March 22, 2005
# '''Are the articles in this journal peer-reviewed?'''
#: Articles are peer-reviewed.
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
#: [https://jcs.biologists.org/content/edboard Editorial Board]
# '''What is the journal impact factor?'''
#: No impact factor available
# '''Is the article a review or primary research article?'''
#: Primary research article
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''
#: The data is not available.
===2nd Reference===
#''' The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.'''
# '''The link to the abstract from PubMed.'''
# '''The link to the full text of the article in PubMedCentral (if not available, write N/A).'''
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#''' The link to the full PDF version of the article from the publisher web site.'''
# '''Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.'''
#''' How is the article available to you?'''
#*''' Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.'''
#* '''If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.'''
#* '''Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.'''
#* '''Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.'''
# '''Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
# '''Who is the publisher of the journal? '''
#* '''Is the publisher for-profit or non-profit?'''
#* '''Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)'''
#* '''Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?'''
#* '''What country is the journal published in?'''
#''' How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)'''
# '''Are the articles in this journal peer-reviewed?'''
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
# '''What is the journal impact factor? (Look to see if it is provided on the journal home page.)'''
# '''Is the article a review or primary research article?'''
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''

===PubMed, GoogleScholar, and Web of Science===
# '''Use a keyword search for the first three databases/tools and answer the following: '''
#* '''PubMed'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#**''' Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#* '''Google Scholar'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#* '''Web of Science'''
#**''' What original keyword(s) did you use? How many results did you get?'''
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
# '''Use the advanced search functions for each of these three databases/tools and answer the following: '''
#*''' PubMed'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Google Scholar'''
#**''' Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Web of Science'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Perform a prospective search on your article in the Web of Science and answer the following:'''
#**''' How many articles does this article cite?'''
#**''' How many articles cite this article?'''

===Reflect===
# '''What impact does the choice of keywords have on your results?'''
#''' What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?'''

==Conclusion==

==Data/Files==
[[Media:Dramir36_The_short-term_response_of_yeast_to_potassium_starvation.pdf| The short-term response of yeast to potassium starvation]]

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x
*Biology Online. (2019). Biology Dictionary. https://www.biology-online.org/dictionary/Main_Page

==Acknowledgments==

Dramir36 Week 11

2019-11-19T03:59:05Z

Dramir36: /* Annotated Bibliography */ answered some questions

==Purpose==
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==
*'''retrograde pathway:''' The mechanism of moving backward or against the usual direction of flow. [https://www.biology-online.org/dictionary/Retrograde Biology Dictionary (2019)]
*'''septin:''' A protein involved in cytokinesis and also functions in maintaining cell morphology [https://www.biology-online.org/dictionary/septin Biology Dictionary (2019)]
*'''β‐galactosidase:''' One of a class of enzymes which cuts the glycosidic bond between the sugar galactose and another sugar molecule (of a different type than galactose). [https://www.biology-online.org/dictionary/galactosidase Biology Dictionary (2019)]
*'''oxidoreductase:''' An enzyme that catalyzes the transfer of electrons from an electron donor (reductant) to an electron acceptor (oxidant) in a redox reaction [https://www.biology-online.org/dictionary/oxidoreductase Biology Dictionary (2019)]
*''' trehalose:''' A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates [https://www.biology-online.org/dictionary/Trehalose Biology Dictionary (2019)]
*'''supernatant:''' The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids. [https://www.biology-online.org/dictionary/Supernatant Biology Dictionary (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) [https://www.biology-online.org/dictionary/Biosynthesis Biology Dictionary (2019)]
*'''assimilation:''' The act of absorption or incorporation into the biological tissue. [https://www.biology-online.org/dictionary/Assimilate Biology Dictionary (2019)]
*'''isoform:''' Any of the proteins with the same function and similar amino acid sequence, encoded by different genes (or by RNA transcript). [https://www.biology-online.org/dictionary/Isoform Biology Dictionary (2019)]
*'''attenuate:''' Tapering gradually. [https://www.biology-online.org/dictionary/Attenuate Biology Dictionary (2019)]

==Outline of Journal Article==
## '''What is the main result presented in this paper?''' The main result is that there was a massive alteration in the expression profile shortly after potassium was removed from the medium. The lack of potassium drastically alters the sulfur metabolism, triggers an oxidative stress response, and activates the mitochondrial retrograde pathway. Another main finding was that after a short time without potassium, there were genes that became repressed, including genes that are involved in ribosome synthesis, translation, and the cell cycle.
## '''What is the importance or significance of this work?''' This research project is important because it shows how when Saccharomyces cerevisiae has a short-term potassium deprivation, there are impacts in the mRNA level of over one thousand genes.
## '''What were the limitations in previous studies that led them to perform this work?''' There wasn’t much insight of possible cellular functions that require potassium and the short-term effects on the gene expression profile when there is a deprivation from sudden depletion of potassium in the environment.
## '''How did they treat the yeast cells (what experiment were they doing?)''' Media that contains only traces of potassium and ammonium as nitrogen source, simulated an absence of potassium in the environment. Once the yeast has been incubated at different time points of a potassium-absent environment, RNA purification, cDNA synthesis and DNA microarray was conducted. RT-PCR assays were also conducted to see how the mutants and wild-type reacted to an increase or no increase of KCl.
## '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?''' Wild-type S. cerevisiae had four main strains that were used in the work. The main strain is BY4741. The other three strains were BY4741 without trk1, without trk2, and without both trk1 and trk2. All of the strains used in the work are haploid.
## '''What media did they grow them in? What temperature? What type of incubator? For how long?''' Recently developed YNB-based growth media was used to treat the yeast cells at 28 degrees Celsius for 10, 20, 40, 60, and 120 min by rapid filtration from four biological replicates. The control contained sufficient potassium, whereas the other media contained only traces of potassium and ammonium. The DH5ɑ cells were grown at 37 degrees Celsius in Luria-Bertani (LB) broth. There was no information given about the incubator that was used.
## '''What controls did they use?''' The control used was the wild-type strain BY4741 in media that contained 50 ml of KCl.
## '''How many replicates did they perform per treatment or timepoint?''' There were four biological replicates performed per timepoint.
## '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?''' The total RNA was extracted by using the Ribo Pure-Yeast kit (Ambion) following the manufacture’s instructions. RNA quality was assessed by electrophoresis in denaturing 0.8% agarose gels and quantified by measuring the A260 in a BioPhotometer (Eppendorf).
## '''What mathematical/statistical method did they use to analyze the data?''' A given gene was considered to be induced when the minus/ plus potassium signal ratio was equal or higher than 2.0-fold, whereas it was considered to be repressed when this signal was equal or less than 0.50-fold. The GEPAS server (v3.1) was used to pre-process the data.
## '''Are the data publicly available for download? From which web site?''' The Society for Applied Microbiology website offers the data, which is publicly available, and is located in the article’s “Supporting Information” section.
##'''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: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 1: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 2: 2A: Potassium starvation decreases sulfuric amino acid metabolism. 2B: Graph depicting relative concentrations of mRNA for genes associated with Met/Cys metabolism. 2C: The concentration of Met/Cys amino acids decreases with potassium treatment Fig. 3: 3A: Oxidative stress response genes are induced by potassium deprivation. 3B: ROS formation causes oxidation when switch to K+-free medium. 3C: Potassium starvation- decline in GSH and increase in GSSG. Fig. 4: 4A: Methylglyoxal increases with trehalose Metabolism. 4B: Genes involved in trehalose synthesis show an increase in expression. 4C: Genes in MG detoxification enhanced without potassium. Fig. 5: 5A: Potassium starvation leads to a strong increase in expression of CIT2 & DLD3 genes central to the retrograde response. 5B: Mitochondrial morphology was normal, and not the cause of the retrograde response. 5C: Potassium starvation leads to an accumulation of ammonium in the cell, and may be one cause of the retrograde response. 5D: Cells without Trk1 do not show significant ammonium accumulation. Fig. 6: 6A: Expression of genes controlling cyclins exhibit a varied response to K+ starvation. Fig. 7: 7A: Lack of potassium in yeast destabilizes the septin ring. 7B: CDC11-GFP localization is affected during K+ starvation. 7C: CDC11 protein levels are constant during starvation. 7D: CDC11 not properly localized in cells grown 60 min
## '''How does this work compare with previous studies?''' This work demonstrates that lack of potassium actually causes a fast and persistent increase in intracellular ammonium concentration.
## '''What are the important implications of this work?''' There is a significant amount of change in cells occur even during the retention of more than necessary potassium.
## '''What future directions should the authors take?''' The authors could separate the methods into their own research projects to prevent intervention or confusion with implementing new methods into the same project.
## '''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 only problem that I found with reading the results and the article in general is that, the authors inserted new techniques or analysis without much explanation, or the insertion of a new analysis method was not placed in the right spot of the article.

==Annotated Bibliography==
===1st Reference===
#''' The complete bibliographic reference in the APA style'''
#: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
# '''The link to the abstract from PubMed.'''
#:https://www.ncbi.nlm.nih.gov/pubmed/15784684?dopt=Abstract
# '''The link to the full text of the article in PubMedCentral (if not available, write N/A).'''
#:N/A
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#:https://jcs.biologists.org/content/118/8/1617.article-info
#''' The link to the full PDF version of the article from the publisher web site.'''
#:https://jcs.biologists.org/content/joces/118/8/1617.full.pdf
# '''Who owns the rights to the article?'''
#: The Company of Biologists Limited 2005
#''' How is the article available to you?'''
#: Not open access and not open after a certain amount of time, but LMU Library allows access through a subscription.
# '''Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
# '''Who is the publisher of the journal? '''
#* '''Is the publisher for-profit or non-profit?'''
#* '''Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)'''
#* '''Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?'''
#* '''What country is the journal published in?'''
#''' How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)'''
# '''Are the articles in this journal peer-reviewed?'''
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
# '''What is the journal impact factor? (Look to see if it is provided on the journal home page.)'''
# '''Is the article a review or primary research article?'''
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''

===2nd Reference===
#''' The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.'''
# '''The link to the abstract from PubMed.'''
# '''The link to the full text of the article in PubMedCentral (if not available, write N/A).'''
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#''' The link to the full PDF version of the article from the publisher web site.'''
# '''Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.'''
#''' How is the article available to you?'''
#*''' Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.'''
#* '''If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.'''
#* '''Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.'''
#* '''Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.'''
# '''Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
# '''Who is the publisher of the journal? '''
#* '''Is the publisher for-profit or non-profit?'''
#* '''Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)'''
#* '''Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?'''
#* '''What country is the journal published in?'''
#''' How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)'''
# '''Are the articles in this journal peer-reviewed?'''
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
# '''What is the journal impact factor? (Look to see if it is provided on the journal home page.)'''
# '''Is the article a review or primary research article?'''
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''

===PubMed, GoogleScholar, and Web of Science===
# '''Use a keyword search for the first three databases/tools and answer the following: '''
#* '''PubMed'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#**''' Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#* '''Google Scholar'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#* '''Web of Science'''
#**''' What original keyword(s) did you use? How many results did you get?'''
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
# '''Use the advanced search functions for each of these three databases/tools and answer the following: '''
#*''' PubMed'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Google Scholar'''
#**''' Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Web of Science'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Perform a prospective search on your article in the Web of Science and answer the following:'''
#**''' How many articles does this article cite?'''
#**''' How many articles cite this article?'''

===Reflect===
# '''What impact does the choice of keywords have on your results?'''
#''' What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?'''

==Conclusion==

==Data/Files==
[[Media:Dramir36_The_short-term_response_of_yeast_to_potassium_starvation.pdf| The short-term response of yeast to potassium starvation]]

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x
*Biology Online. (2019). Biology Dictionary. https://www.biology-online.org/dictionary/Main_Page

==Acknowledgments==

Skinny Genes

2019-11-19T03:27:25Z

Dramir36: /* Annotated Bibliography */ added David's references

{{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

==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)

Dramir36 Week 11

2019-11-19T03:13:49Z

Dramir36: /* Annotated Bibliography */ added reference titles and edits

==Purpose==
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==
*'''retrograde pathway:''' The mechanism of moving backward or against the usual direction of flow. [https://www.biology-online.org/dictionary/Retrograde Biology Dictionary (2019)]
*'''septin:''' A protein involved in cytokinesis and also functions in maintaining cell morphology [https://www.biology-online.org/dictionary/septin Biology Dictionary (2019)]
*'''β‐galactosidase:''' One of a class of enzymes which cuts the glycosidic bond between the sugar galactose and another sugar molecule (of a different type than galactose). [https://www.biology-online.org/dictionary/galactosidase Biology Dictionary (2019)]
*'''oxidoreductase:''' An enzyme that catalyzes the transfer of electrons from an electron donor (reductant) to an electron acceptor (oxidant) in a redox reaction [https://www.biology-online.org/dictionary/oxidoreductase Biology Dictionary (2019)]
*''' trehalose:''' A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates [https://www.biology-online.org/dictionary/Trehalose Biology Dictionary (2019)]
*'''supernatant:''' The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids. [https://www.biology-online.org/dictionary/Supernatant Biology Dictionary (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) [https://www.biology-online.org/dictionary/Biosynthesis Biology Dictionary (2019)]
*'''assimilation:''' The act of absorption or incorporation into the biological tissue. [https://www.biology-online.org/dictionary/Assimilate Biology Dictionary (2019)]
*'''isoform:''' Any of the proteins with the same function and similar amino acid sequence, encoded by different genes (or by RNA transcript). [https://www.biology-online.org/dictionary/Isoform Biology Dictionary (2019)]
*'''attenuate:''' Tapering gradually. [https://www.biology-online.org/dictionary/Attenuate Biology Dictionary (2019)]

==Outline of Journal Article==
## '''What is the main result presented in this paper?''' The main result is that there was a massive alteration in the expression profile shortly after potassium was removed from the medium. The lack of potassium drastically alters the sulfur metabolism, triggers an oxidative stress response, and activates the mitochondrial retrograde pathway. Another main finding was that after a short time without potassium, there were genes that became repressed, including genes that are involved in ribosome synthesis, translation, and the cell cycle.
## '''What is the importance or significance of this work?''' This research project is important because it shows how when Saccharomyces cerevisiae has a short-term potassium deprivation, there are impacts in the mRNA level of over one thousand genes.
## '''What were the limitations in previous studies that led them to perform this work?''' There wasn’t much insight of possible cellular functions that require potassium and the short-term effects on the gene expression profile when there is a deprivation from sudden depletion of potassium in the environment.
## '''How did they treat the yeast cells (what experiment were they doing?)''' Media that contains only traces of potassium and ammonium as nitrogen source, simulated an absence of potassium in the environment. Once the yeast has been incubated at different time points of a potassium-absent environment, RNA purification, cDNA synthesis and DNA microarray was conducted. RT-PCR assays were also conducted to see how the mutants and wild-type reacted to an increase or no increase of KCl.
## '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?''' Wild-type S. cerevisiae had four main strains that were used in the work. The main strain is BY4741. The other three strains were BY4741 without trk1, without trk2, and without both trk1 and trk2. All of the strains used in the work are haploid.
## '''What media did they grow them in? What temperature? What type of incubator? For how long?''' Recently developed YNB-based growth media was used to treat the yeast cells at 28 degrees Celsius for 10, 20, 40, 60, and 120 min by rapid filtration from four biological replicates. The control contained sufficient potassium, whereas the other media contained only traces of potassium and ammonium. The DH5ɑ cells were grown at 37 degrees Celsius in Luria-Bertani (LB) broth. There was no information given about the incubator that was used.
## '''What controls did they use?''' The control used was the wild-type strain BY4741 in media that contained 50 ml of KCl.
## '''How many replicates did they perform per treatment or timepoint?''' There were four biological replicates performed per timepoint.
## '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?''' The total RNA was extracted by using the Ribo Pure-Yeast kit (Ambion) following the manufacture’s instructions. RNA quality was assessed by electrophoresis in denaturing 0.8% agarose gels and quantified by measuring the A260 in a BioPhotometer (Eppendorf).
## '''What mathematical/statistical method did they use to analyze the data?''' A given gene was considered to be induced when the minus/ plus potassium signal ratio was equal or higher than 2.0-fold, whereas it was considered to be repressed when this signal was equal or less than 0.50-fold. The GEPAS server (v3.1) was used to pre-process the data.
## '''Are the data publicly available for download? From which web site?''' The Society for Applied Microbiology website offers the data, which is publicly available, and is located in the article’s “Supporting Information” section.
##'''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: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 1: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 2: 2A: Potassium starvation decreases sulfuric amino acid metabolism. 2B: Graph depicting relative concentrations of mRNA for genes associated with Met/Cys metabolism. 2C: The concentration of Met/Cys amino acids decreases with potassium treatment Fig. 3: 3A: Oxidative stress response genes are induced by potassium deprivation. 3B: ROS formation causes oxidation when switch to K+-free medium. 3C: Potassium starvation- decline in GSH and increase in GSSG. Fig. 4: 4A: Methylglyoxal increases with trehalose Metabolism. 4B: Genes involved in trehalose synthesis show an increase in expression. 4C: Genes in MG detoxification enhanced without potassium. Fig. 5: 5A: Potassium starvation leads to a strong increase in expression of CIT2 & DLD3 genes central to the retrograde response. 5B: Mitochondrial morphology was normal, and not the cause of the retrograde response. 5C: Potassium starvation leads to an accumulation of ammonium in the cell, and may be one cause of the retrograde response. 5D: Cells without Trk1 do not show significant ammonium accumulation. Fig. 6: 6A: Expression of genes controlling cyclins exhibit a varied response to K+ starvation. Fig. 7: 7A: Lack of potassium in yeast destabilizes the septin ring. 7B: CDC11-GFP localization is affected during K+ starvation. 7C: CDC11 protein levels are constant during starvation. 7D: CDC11 not properly localized in cells grown 60 min
## '''How does this work compare with previous studies?''' This work demonstrates that lack of potassium actually causes a fast and persistent increase in intracellular ammonium concentration.
## '''What are the important implications of this work?''' There is a significant amount of change in cells occur even during the retention of more than necessary potassium.
## '''What future directions should the authors take?''' The authors could separate the methods into their own research projects to prevent intervention or confusion with implementing new methods into the same project.
## '''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 only problem that I found with reading the results and the article in general is that, the authors inserted new techniques or analysis without much explanation, or the insertion of a new analysis method was not placed in the right spot of the article.

==Annotated Bibliography==
===1st Reference===
#''' The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.'''
# '''The link to the abstract from PubMed.'''
# '''The link to the full text of the article in PubMedCentral (if not available, write N/A).'''
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#''' The link to the full PDF version of the article from the publisher web site.'''
# '''Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.'''
#''' How is the article available to you?'''
#*''' Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.'''
#* '''If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.'''
#* '''Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.'''
#* '''Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.'''
# '''Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
# '''Who is the publisher of the journal? '''
#* '''Is the publisher for-profit or non-profit?'''
#* '''Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)'''
#* '''Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?'''
#* '''What country is the journal published in?'''
#''' How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)'''
# '''Are the articles in this journal peer-reviewed?'''
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
# '''What is the journal impact factor? (Look to see if it is provided on the journal home page.)'''
# '''Is the article a review or primary research article?'''
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''

===2nd Reference===
#''' The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.'''
# '''The link to the abstract from PubMed.'''
# '''The link to the full text of the article in PubMedCentral (if not available, write N/A).'''
#''' The link to the full text of the article (HTML format) from the publisher web site.'''
#''' The link to the full PDF version of the article from the publisher web site.'''
# '''Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.'''
#''' How is the article available to you?'''
#*''' Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.'''
#* '''If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.'''
#* '''Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.'''
#* '''Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.'''
# '''Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
# '''Who is the publisher of the journal? '''
#* '''Is the publisher for-profit or non-profit?'''
#* '''Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)'''
#* '''Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?'''
#* '''What country is the journal published in?'''
#''' How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)'''
# '''Are the articles in this journal peer-reviewed?'''
#'''Provide a link to the scientific advisory board/editorial board of the journal.'''
# '''What is the journal impact factor? (Look to see if it is provided on the journal home page.)'''
# '''Is the article a review or primary research article?'''
# '''Are the data associated with this article available? If so, provide a link to the dataset.'''

===PubMed, GoogleScholar, and Web of Science===
# '''Use a keyword search for the first three databases/tools and answer the following: '''
#* '''PubMed'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#**''' Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#* '''Google Scholar'''
#** '''What original keyword(s) did you use? How many results did you get?'''
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
#* '''Web of Science'''
#**''' What original keyword(s) did you use? How many results did you get?'''
#** '''Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?'''
# '''Use the advanced search functions for each of these three databases/tools and answer the following: '''
#*''' PubMed'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Google Scholar'''
#**''' Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Web of Science'''
#** '''Which advanced search functions were most useful to narrow down the search? How many results did you get?'''
#* '''Perform a prospective search on your article in the Web of Science and answer the following:'''
#**''' How many articles does this article cite?'''
#**''' How many articles cite this article?'''

===Reflect===
# '''What impact does the choice of keywords have on your results?'''
#''' What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?'''

==Conclusion==

==Data/Files==
[[Media:Dramir36_The_short-term_response_of_yeast_to_potassium_starvation.pdf| The short-term response of yeast to potassium starvation]]

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x
*Biology Online. (2019). Biology Dictionary. https://www.biology-online.org/dictionary/Main_Page

==Acknowledgments==

Dramir36 Week 11

2019-11-19T03:05:57Z

Dramir36: /* Annotated Bibliography */ bolded questions

==Purpose==
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==
*'''retrograde pathway:''' The mechanism of moving backward or against the usual direction of flow. [https://www.biology-online.org/dictionary/Retrograde Biology Dictionary (2019)]
*'''septin:''' A protein involved in cytokinesis and also functions in maintaining cell morphology [https://www.biology-online.org/dictionary/septin Biology Dictionary (2019)]
*'''β‐galactosidase:''' One of a class of enzymes which cuts the glycosidic bond between the sugar galactose and another sugar molecule (of a different type than galactose). [https://www.biology-online.org/dictionary/galactosidase Biology Dictionary (2019)]
*'''oxidoreductase:''' An enzyme that catalyzes the transfer of electrons from an electron donor (reductant) to an electron acceptor (oxidant) in a redox reaction [https://www.biology-online.org/dictionary/oxidoreductase Biology Dictionary (2019)]
*''' trehalose:''' A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates [https://www.biology-online.org/dictionary/Trehalose Biology Dictionary (2019)]
*'''supernatant:''' The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids. [https://www.biology-online.org/dictionary/Supernatant Biology Dictionary (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) [https://www.biology-online.org/dictionary/Biosynthesis Biology Dictionary (2019)]
*'''assimilation:''' The act of absorption or incorporation into the biological tissue. [https://www.biology-online.org/dictionary/Assimilate Biology Dictionary (2019)]
*'''isoform:''' Any of the proteins with the same function and similar amino acid sequence, encoded by different genes (or by RNA transcript). [https://www.biology-online.org/dictionary/Isoform Biology Dictionary (2019)]
*'''attenuate:''' Tapering gradually. [https://www.biology-online.org/dictionary/Attenuate Biology Dictionary (2019)]

==Outline of Journal Article==
## '''What is the main result presented in this paper?''' The main result is that there was a massive alteration in the expression profile shortly after potassium was removed from the medium. The lack of potassium drastically alters the sulfur metabolism, triggers an oxidative stress response, and activates the mitochondrial retrograde pathway. Another main finding was that after a short time without potassium, there were genes that became repressed, including genes that are involved in ribosome synthesis, translation, and the cell cycle.
## '''What is the importance or significance of this work?''' This research project is important because it shows how when Saccharomyces cerevisiae has a short-term potassium deprivation, there are impacts in the mRNA level of over one thousand genes.
## '''What were the limitations in previous studies that led them to perform this work?''' There wasn’t much insight of possible cellular functions that require potassium and the short-term effects on the gene expression profile when there is a deprivation from sudden depletion of potassium in the environment.
## '''How did they treat the yeast cells (what experiment were they doing?)''' Media that contains only traces of potassium and ammonium as nitrogen source, simulated an absence of potassium in the environment. Once the yeast has been incubated at different time points of a potassium-absent environment, RNA purification, cDNA synthesis and DNA microarray was conducted. RT-PCR assays were also conducted to see how the mutants and wild-type reacted to an increase or no increase of KCl.
## '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?''' Wild-type S. cerevisiae had four main strains that were used in the work. The main strain is BY4741. The other three strains were BY4741 without trk1, without trk2, and without both trk1 and trk2. All of the strains used in the work are haploid.
## '''What media did they grow them in? What temperature? What type of incubator? For how long?''' Recently developed YNB-based growth media was used to treat the yeast cells at 28 degrees Celsius for 10, 20, 40, 60, and 120 min by rapid filtration from four biological replicates. The control contained sufficient potassium, whereas the other media contained only traces of potassium and ammonium. The DH5ɑ cells were grown at 37 degrees Celsius in Luria-Bertani (LB) broth. There was no information given about the incubator that was used.
## '''What controls did they use?''' The control used was the wild-type strain BY4741 in media that contained 50 ml of KCl.
## '''How many replicates did they perform per treatment or timepoint?''' There were four biological replicates performed per timepoint.
## '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?''' The total RNA was extracted by using the Ribo Pure-Yeast kit (Ambion) following the manufacture’s instructions. RNA quality was assessed by electrophoresis in denaturing 0.8% agarose gels and quantified by measuring the A260 in a BioPhotometer (Eppendorf).
## '''What mathematical/statistical method did they use to analyze the data?''' A given gene was considered to be induced when the minus/ plus potassium signal ratio was equal or higher than 2.0-fold, whereas it was considered to be repressed when this signal was equal or less than 0.50-fold. The GEPAS server (v3.1) was used to pre-process the data.
## '''Are the data publicly available for download? From which web site?''' The Society for Applied Microbiology website offers the data, which is publicly available, and is located in the article’s “Supporting Information” section.
##'''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: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 1: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 2: 2A: Potassium starvation decreases sulfuric amino acid metabolism. 2B: Graph depicting relative concentrations of mRNA for genes associated with Met/Cys metabolism. 2C: The concentration of Met/Cys amino acids decreases with potassium treatment Fig. 3: 3A: Oxidative stress response genes are induced by potassium deprivation. 3B: ROS formation causes oxidation when switch to K+-free medium. 3C: Potassium starvation- decline in GSH and increase in GSSG. Fig. 4: 4A: Methylglyoxal increases with trehalose Metabolism. 4B: Genes involved in trehalose synthesis show an increase in expression. 4C: Genes in MG detoxification enhanced without potassium. Fig. 5: 5A: Potassium starvation leads to a strong increase in expression of CIT2 & DLD3 genes central to the retrograde response. 5B: Mitochondrial morphology was normal, and not the cause of the retrograde response. 5C: Potassium starvation leads to an accumulation of ammonium in the cell, and may be one cause of the retrograde response. 5D: Cells without Trk1 do not show significant ammonium accumulation. Fig. 6: 6A: Expression of genes controlling cyclins exhibit a varied response to K+ starvation. Fig. 7: 7A: Lack of potassium in yeast destabilizes the septin ring. 7B: CDC11-GFP localization is affected during K+ starvation. 7C: CDC11 protein levels are constant during starvation. 7D: CDC11 not properly localized in cells grown 60 min
## '''How does this work compare with previous studies?''' This work demonstrates that lack of potassium actually causes a fast and persistent increase in intracellular ammonium concentration.
## '''What are the important implications of this work?''' There is a significant amount of change in cells occur even during the retention of more than necessary potassium.
## '''What future directions should the authors take?''' The authors could separate the methods into their own research projects to prevent intervention or confusion with implementing new methods into the same project.
## '''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 only problem that I found with reading the results and the article in general is that, the authors inserted new techniques or analysis without much explanation, or the insertion of a new analysis method was not placed in the right spot of the article.

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

==Conclusion==

==Data/Files==
[[Media:Dramir36_The_short-term_response_of_yeast_to_potassium_starvation.pdf| The short-term response of yeast to potassium starvation]]

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x
*Biology Online. (2019). Biology Dictionary. https://www.biology-online.org/dictionary/Main_Page

==Acknowledgments==

Dramir36 Week 11

2019-11-19T02:54:06Z

Dramir36: /* Annotated Bibliography */ edited questions

==Purpose==
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==
*'''retrograde pathway:''' The mechanism of moving backward or against the usual direction of flow. [https://www.biology-online.org/dictionary/Retrograde Biology Dictionary (2019)]
*'''septin:''' A protein involved in cytokinesis and also functions in maintaining cell morphology [https://www.biology-online.org/dictionary/septin Biology Dictionary (2019)]
*'''β‐galactosidase:''' One of a class of enzymes which cuts the glycosidic bond between the sugar galactose and another sugar molecule (of a different type than galactose). [https://www.biology-online.org/dictionary/galactosidase Biology Dictionary (2019)]
*'''oxidoreductase:''' An enzyme that catalyzes the transfer of electrons from an electron donor (reductant) to an electron acceptor (oxidant) in a redox reaction [https://www.biology-online.org/dictionary/oxidoreductase Biology Dictionary (2019)]
*''' trehalose:''' A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates [https://www.biology-online.org/dictionary/Trehalose Biology Dictionary (2019)]
*'''supernatant:''' The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids. [https://www.biology-online.org/dictionary/Supernatant Biology Dictionary (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) [https://www.biology-online.org/dictionary/Biosynthesis Biology Dictionary (2019)]
*'''assimilation:''' The act of absorption or incorporation into the biological tissue. [https://www.biology-online.org/dictionary/Assimilate Biology Dictionary (2019)]
*'''isoform:''' Any of the proteins with the same function and similar amino acid sequence, encoded by different genes (or by RNA transcript). [https://www.biology-online.org/dictionary/Isoform Biology Dictionary (2019)]
*'''attenuate:''' Tapering gradually. [https://www.biology-online.org/dictionary/Attenuate Biology Dictionary (2019)]

==Outline of Journal Article==
## '''What is the main result presented in this paper?''' The main result is that there was a massive alteration in the expression profile shortly after potassium was removed from the medium. The lack of potassium drastically alters the sulfur metabolism, triggers an oxidative stress response, and activates the mitochondrial retrograde pathway. Another main finding was that after a short time without potassium, there were genes that became repressed, including genes that are involved in ribosome synthesis, translation, and the cell cycle.
## '''What is the importance or significance of this work?''' This research project is important because it shows how when Saccharomyces cerevisiae has a short-term potassium deprivation, there are impacts in the mRNA level of over one thousand genes.
## '''What were the limitations in previous studies that led them to perform this work?''' There wasn’t much insight of possible cellular functions that require potassium and the short-term effects on the gene expression profile when there is a deprivation from sudden depletion of potassium in the environment.
## '''How did they treat the yeast cells (what experiment were they doing?)''' Media that contains only traces of potassium and ammonium as nitrogen source, simulated an absence of potassium in the environment. Once the yeast has been incubated at different time points of a potassium-absent environment, RNA purification, cDNA synthesis and DNA microarray was conducted. RT-PCR assays were also conducted to see how the mutants and wild-type reacted to an increase or no increase of KCl.
## '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?''' Wild-type S. cerevisiae had four main strains that were used in the work. The main strain is BY4741. The other three strains were BY4741 without trk1, without trk2, and without both trk1 and trk2. All of the strains used in the work are haploid.
## '''What media did they grow them in? What temperature? What type of incubator? For how long?''' Recently developed YNB-based growth media was used to treat the yeast cells at 28 degrees Celsius for 10, 20, 40, 60, and 120 min by rapid filtration from four biological replicates. The control contained sufficient potassium, whereas the other media contained only traces of potassium and ammonium. The DH5ɑ cells were grown at 37 degrees Celsius in Luria-Bertani (LB) broth. There was no information given about the incubator that was used.
## '''What controls did they use?''' The control used was the wild-type strain BY4741 in media that contained 50 ml of KCl.
## '''How many replicates did they perform per treatment or timepoint?''' There were four biological replicates performed per timepoint.
## '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?''' The total RNA was extracted by using the Ribo Pure-Yeast kit (Ambion) following the manufacture’s instructions. RNA quality was assessed by electrophoresis in denaturing 0.8% agarose gels and quantified by measuring the A260 in a BioPhotometer (Eppendorf).
## '''What mathematical/statistical method did they use to analyze the data?''' A given gene was considered to be induced when the minus/ plus potassium signal ratio was equal or higher than 2.0-fold, whereas it was considered to be repressed when this signal was equal or less than 0.50-fold. The GEPAS server (v3.1) was used to pre-process the data.
## '''Are the data publicly available for download? From which web site?''' The Society for Applied Microbiology website offers the data, which is publicly available, and is located in the article’s “Supporting Information” section.
##'''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: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 1: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 2: 2A: Potassium starvation decreases sulfuric amino acid metabolism. 2B: Graph depicting relative concentrations of mRNA for genes associated with Met/Cys metabolism. 2C: The concentration of Met/Cys amino acids decreases with potassium treatment Fig. 3: 3A: Oxidative stress response genes are induced by potassium deprivation. 3B: ROS formation causes oxidation when switch to K+-free medium. 3C: Potassium starvation- decline in GSH and increase in GSSG. Fig. 4: 4A: Methylglyoxal increases with trehalose Metabolism. 4B: Genes involved in trehalose synthesis show an increase in expression. 4C: Genes in MG detoxification enhanced without potassium. Fig. 5: 5A: Potassium starvation leads to a strong increase in expression of CIT2 & DLD3 genes central to the retrograde response. 5B: Mitochondrial morphology was normal, and not the cause of the retrograde response. 5C: Potassium starvation leads to an accumulation of ammonium in the cell, and may be one cause of the retrograde response. 5D: Cells without Trk1 do not show significant ammonium accumulation. Fig. 6: 6A: Expression of genes controlling cyclins exhibit a varied response to K+ starvation. Fig. 7: 7A: Lack of potassium in yeast destabilizes the septin ring. 7B: CDC11-GFP localization is affected during K+ starvation. 7C: CDC11 protein levels are constant during starvation. 7D: CDC11 not properly localized in cells grown 60 min
## '''How does this work compare with previous studies?''' This work demonstrates that lack of potassium actually causes a fast and persistent increase in intracellular ammonium concentration.
## '''What are the important implications of this work?''' There is a significant amount of change in cells occur even during the retention of more than necessary potassium.
## '''What future directions should the authors take?''' The authors could separate the methods into their own research projects to prevent intervention or confusion with implementing new methods into the same project.
## '''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 only problem that I found with reading the results and the article in general is that, the authors inserted new techniques or analysis without much explanation, or the insertion of a new analysis method was not placed in the right spot of the article.

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

==Conclusion==

==Data/Files==
[[Media:Dramir36_The_short-term_response_of_yeast_to_potassium_starvation.pdf| The short-term response of yeast to potassium starvation]]

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x
*Biology Online. (2019). Biology Dictionary. https://www.biology-online.org/dictionary/Main_Page

==Acknowledgments==

Dramir36 Week 11

2019-11-19T02:50:31Z

Dramir36: /* Annotated Bibliography */ added questions

==Purpose==
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==
*'''retrograde pathway:''' The mechanism of moving backward or against the usual direction of flow. [https://www.biology-online.org/dictionary/Retrograde Biology Dictionary (2019)]
*'''septin:''' A protein involved in cytokinesis and also functions in maintaining cell morphology [https://www.biology-online.org/dictionary/septin Biology Dictionary (2019)]
*'''β‐galactosidase:''' One of a class of enzymes which cuts the glycosidic bond between the sugar galactose and another sugar molecule (of a different type than galactose). [https://www.biology-online.org/dictionary/galactosidase Biology Dictionary (2019)]
*'''oxidoreductase:''' An enzyme that catalyzes the transfer of electrons from an electron donor (reductant) to an electron acceptor (oxidant) in a redox reaction [https://www.biology-online.org/dictionary/oxidoreductase Biology Dictionary (2019)]
*''' trehalose:''' A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates [https://www.biology-online.org/dictionary/Trehalose Biology Dictionary (2019)]
*'''supernatant:''' The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids. [https://www.biology-online.org/dictionary/Supernatant Biology Dictionary (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) [https://www.biology-online.org/dictionary/Biosynthesis Biology Dictionary (2019)]
*'''assimilation:''' The act of absorption or incorporation into the biological tissue. [https://www.biology-online.org/dictionary/Assimilate Biology Dictionary (2019)]
*'''isoform:''' Any of the proteins with the same function and similar amino acid sequence, encoded by different genes (or by RNA transcript). [https://www.biology-online.org/dictionary/Isoform Biology Dictionary (2019)]
*'''attenuate:''' Tapering gradually. [https://www.biology-online.org/dictionary/Attenuate Biology Dictionary (2019)]

==Outline of Journal Article==
## '''What is the main result presented in this paper?''' The main result is that there was a massive alteration in the expression profile shortly after potassium was removed from the medium. The lack of potassium drastically alters the sulfur metabolism, triggers an oxidative stress response, and activates the mitochondrial retrograde pathway. Another main finding was that after a short time without potassium, there were genes that became repressed, including genes that are involved in ribosome synthesis, translation, and the cell cycle.
## '''What is the importance or significance of this work?''' This research project is important because it shows how when Saccharomyces cerevisiae has a short-term potassium deprivation, there are impacts in the mRNA level of over one thousand genes.
## '''What were the limitations in previous studies that led them to perform this work?''' There wasn’t much insight of possible cellular functions that require potassium and the short-term effects on the gene expression profile when there is a deprivation from sudden depletion of potassium in the environment.
## '''How did they treat the yeast cells (what experiment were they doing?)''' Media that contains only traces of potassium and ammonium as nitrogen source, simulated an absence of potassium in the environment. Once the yeast has been incubated at different time points of a potassium-absent environment, RNA purification, cDNA synthesis and DNA microarray was conducted. RT-PCR assays were also conducted to see how the mutants and wild-type reacted to an increase or no increase of KCl.
## '''What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?''' Wild-type S. cerevisiae had four main strains that were used in the work. The main strain is BY4741. The other three strains were BY4741 without trk1, without trk2, and without both trk1 and trk2. All of the strains used in the work are haploid.
## '''What media did they grow them in? What temperature? What type of incubator? For how long?''' Recently developed YNB-based growth media was used to treat the yeast cells at 28 degrees Celsius for 10, 20, 40, 60, and 120 min by rapid filtration from four biological replicates. The control contained sufficient potassium, whereas the other media contained only traces of potassium and ammonium. The DH5ɑ cells were grown at 37 degrees Celsius in Luria-Bertani (LB) broth. There was no information given about the incubator that was used.
## '''What controls did they use?''' The control used was the wild-type strain BY4741 in media that contained 50 ml of KCl.
## '''How many replicates did they perform per treatment or timepoint?''' There were four biological replicates performed per timepoint.
## '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?''' The total RNA was extracted by using the Ribo Pure-Yeast kit (Ambion) following the manufacture’s instructions. RNA quality was assessed by electrophoresis in denaturing 0.8% agarose gels and quantified by measuring the A260 in a BioPhotometer (Eppendorf).
## '''What mathematical/statistical method did they use to analyze the data?''' A given gene was considered to be induced when the minus/ plus potassium signal ratio was equal or higher than 2.0-fold, whereas it was considered to be repressed when this signal was equal or less than 0.50-fold. The GEPAS server (v3.1) was used to pre-process the data.
## '''Are the data publicly available for download? From which web site?''' The Society for Applied Microbiology website offers the data, which is publicly available, and is located in the article’s “Supporting Information” section.
##'''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: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 1: The majority of the genes were induced and repressed 60-120 min after the cells were transferred to potassium free media. Fig. 2: 2A: Potassium starvation decreases sulfuric amino acid metabolism. 2B: Graph depicting relative concentrations of mRNA for genes associated with Met/Cys metabolism. 2C: The concentration of Met/Cys amino acids decreases with potassium treatment Fig. 3: 3A: Oxidative stress response genes are induced by potassium deprivation. 3B: ROS formation causes oxidation when switch to K+-free medium. 3C: Potassium starvation- decline in GSH and increase in GSSG. Fig. 4: 4A: Methylglyoxal increases with trehalose Metabolism. 4B: Genes involved in trehalose synthesis show an increase in expression. 4C: Genes in MG detoxification enhanced without potassium. Fig. 5: 5A: Potassium starvation leads to a strong increase in expression of CIT2 & DLD3 genes central to the retrograde response. 5B: Mitochondrial morphology was normal, and not the cause of the retrograde response. 5C: Potassium starvation leads to an accumulation of ammonium in the cell, and may be one cause of the retrograde response. 5D: Cells without Trk1 do not show significant ammonium accumulation. Fig. 6: 6A: Expression of genes controlling cyclins exhibit a varied response to K+ starvation. Fig. 7: 7A: Lack of potassium in yeast destabilizes the septin ring. 7B: CDC11-GFP localization is affected during K+ starvation. 7C: CDC11 protein levels are constant during starvation. 7D: CDC11 not properly localized in cells grown 60 min
## '''How does this work compare with previous studies?''' This work demonstrates that lack of potassium actually causes a fast and persistent increase in intracellular ammonium concentration.
## '''What are the important implications of this work?''' There is a significant amount of change in cells occur even during the retention of more than necessary potassium.
## '''What future directions should the authors take?''' The authors could separate the methods into their own research projects to prevent intervention or confusion with implementing new methods into the same project.
## '''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 only problem that I found with reading the results and the article in general is that, the authors inserted new techniques or analysis without much explanation, or the insertion of a new analysis method was not placed in the right spot of the article.

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

==Conclusion==

==Data/Files==
[[Media:Dramir36_The_short-term_response_of_yeast_to_potassium_starvation.pdf| The short-term response of yeast to potassium starvation]]

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x
*Biology Online. (2019). Biology Dictionary. https://www.biology-online.org/dictionary/Main_Page

==Acknowledgments==

Dramir36 Week 11

2019-11-14T22:29:32Z

Dramir36: /* Data/Files */ added PowerPoint onto individual page, although PowerPoint was on team page as well

File:Dramir36 The short-term response of yeast to potassium starvation.pdf

2019-11-14T22:27:19Z

Dramir36:

Dramir36 Week 11

2019-11-14T08:09:43Z

Dramir36: /* Outline of Journal Article */ answered questions

Skinny Genes

2019-11-14T07:37:38Z

Dramir36: /* David's Reflection */ answered questions

{{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.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.

===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)

Template:Dramir36

2019-11-14T07:28:17Z

Dramir36: edited team link

[[User:Dramir36]] [[template:Dramir36]] [[Skinny Genes]]

*'''Week 1'''

::[[Week 1]]

::[[Class Journal Week 1]]

*'''Week 2'''

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*'''Week 10'''

::[[Week 10]]

::[[Class Journal Week 10]]

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*'''Week 11'''

::[[Week 11]]

::[[Dramir36 Week 11]]

*'''Week 12'''

*'''Week 13'''

*'''Week 14'''

*'''Week 15'''

[[Category:Journal Entry]]

Dramir36 Week 11

2019-11-12T23:16:30Z

Dramir36: /* Outline of Journal Article */ added questions

Dramir36 Week 11

2019-11-12T23:12:04Z

Dramir36: /* 10 definitions of biological terms */ added the rest of terms

Dramir36 Week 11

2019-11-12T22:42:06Z

Dramir36: /* 10 definitions of biological terms */ added some terms

Dramir36 Week 11

2019-11-12T01:12:36Z

Dramir36: /* References */ added biology link

==Purpose==
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==

==Outline of Journal Article==

==Annotated Bibliography==

==Conclusion==

==Data/Files==

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x
*Biology Online. (2019). Biology Dictionary. https://www.biology-online.org/dictionary/Main_Page

==Acknowledgments==

Dramir36 Week 11

2019-11-12T01:09:29Z

Dramir36: /* References */ changed link

Dramir36 Week 11

2019-11-07T23:57:11Z

Dramir36: /* References */ added website

==Purpose==
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==

==Outline of Journal Article==

==Annotated Bibliography==

==Conclusion==

==Data/Files==

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11

==Acknowledgments==

Dramir36 Week 11

2019-11-07T23:54:20Z

Dramir36: /* Purpose */ removed bullet

Dramir36 Week 11

2019-11-07T23:53:47Z

Dramir36: /* Purpose */ added info

==Purpose==
* Everyone will contribute to [[Week_11#Whole_Team_Journal_Assignment:_Creating_a_Team_Wiki_Page | Creating your team's home page,]] and in the process, getting yourselves organized for the final project.
* To learn how to search the primary literature.
* To prepare and give a journal club presentation.

==10 definitions of biological terms==

==Outline of Journal Article==

==Annotated Bibliography==

==Conclusion==

==Data/Files==

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x

==Acknowledgments==

Dramir36 Week 11

2019-11-07T23:51:28Z

Dramir36: /* References */ added journal

==Purpose==

==10 definitions of biological terms==

==Outline of Journal Article==

==Annotated Bibliography==

==Conclusion==

==Data/Files==

==References==
*Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x

==Acknowledgments==

Template:Dramir36

2019-11-07T23:43:51Z

Dramir36: moved team link

[[User:Dramir36]] [[template:Dramir36]] [[Skinny Gene Team Page]]

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[[Category:Journal Entry]]

Template:Dramir36

2019-11-07T23:42:56Z

Dramir36: added team page

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[[Category:Journal Entry]]

Dramir36 Week 11

2019-11-07T23:40:40Z

Dramir36: /* 10 biological terms */ added to title

==Purpose==

==10 definitions of biological terms==

==Outline of Journal Article==

==Annotated Bibliography==

==Conclusion==

==Data/Files==

==References==

==Acknowledgments==

Dramir36 Week 11

2019-11-07T23:24:19Z

Dramir36: added titles

==Purpose==

==10 biological terms==

==Outline of Journal Article==

==Annotated Bibliography==

==Conclusion==

==Data/Files==

==References==

==Acknowledgments==

Template:Dramir36

2019-11-07T23:20:07Z

Dramir36: edit link

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Template:Dramir36

2019-11-07T23:19:43Z

Dramir36: inserted links to week 11

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