Sulfiknights

Sulfiknight Links
BIOL Databases Main Page	Sulfiknights: Project Overview Page	Final Project Deliverables Requirements	Sulfiknights: Final Project Deliverables	Members	Project Manager & Quality Assurance: Naomi Tesfaiohannes	Quality Assurance: Joey Nimmers-Minor	Data Analysis: Ivy-Quynh Macaraeg & Marcus Avila	Designer: DeLisa Madere
				Assignment Pages	Week 11	Week 12/13	Week 15

Template:Sulfiknights

Week 12/13 Milestones

Project Manager

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

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

Ntesfaio (talk) 20:44, 21 November 2019 (PST)

Quality Assurance

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

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

Ntesfaio (talk) 18:40, 23 November 2019 (PST)

Team Journal Assignments

Week 12/13

Naomi Tesfaiohannes

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

What worked?

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

What didn't work?

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

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

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

Ntesfaio (talk) 21:20, 25 November 2019 (PST)

Ivy Macaraeg

1. What worked?
   • We figured out what we needed to be working on, and that helped get us going even more than before.
2. What didn't work?
   • We had some trouble organizing the data in a way that would be clear but compatible with future programs.
3. What will I do next to fix what didn't work?
   • I think sticking to the directions and making sure that we are thorough will help us.

John Nimmers-Minor

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

What worked?

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

What didn't work?

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

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

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

DeLisa Madere

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

Marcus Avila

1. What worked?
   • We did a good job dividing the work and ensuring that everything was done.
2. What didn't work?
   • We struggled with communication because it seemed each person had a lot going on as the break was approaching.
3. What will I do next time to fix what didn't work?
   • Next time I will try to do a better job with communicating with my team members.

Mavila9 (talk) 23:59, 25 November 2019 (PST)

Week 11

Naomi Tesfaiohannes

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

• What worked?

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

• What didn't work?

My time management due to other coursework

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

Have a better control of what work I put in each day for this assignment

Ntesfaio (talk) 00:08, 14 November 2019 (PST)

Joey Nimmers-Minor

• What worked?

Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.

• What didn't work?

Waiting until the last minute to do the assignment because every member of the team had tests to get through this week

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

I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.

Jnimmers (talk) 00:08, 14 November 2019 (PST)

Marcus Avila

1. What worked?
   • The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.
2. What didn't work?
   • I believe the amount of time given to complete the individual outline and group presentation was insufficient.
3. What will I do next to fix what didn't work?
   • Next time I will allocate more time to the assignment.

Mavila9 (talk) 17:24, 15 November 2019 (PST)

DeLisa Madere

What Worked?

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

What didn't work?

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

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

• Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.

Ivy Macaraeg

• What worked?

  -I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out.

• What didn't work?

  -All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it.

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

  -Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.

Imacarae (talk) 00:12, 14 November 2019 (PST)

Annotated Bibliography Sources

DeLisa Madere

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

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

Naomi Tesfaiohannes

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

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

Ivy Macaraeg

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

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

Marcus Avila

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

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

John Nimmers-Minor

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

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

Data/Files

Journal Club Presentation 11/14/19

• Other files can be found on our deliverables page

Sulfiknights Meta Data Sheet

Expression and Degradation Sheet of Thorsen & Dahlquist Data

References

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