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

Milestone 1: Annotated Bibliography

• The Coder/Designer will work with their teams to develop an annotated bibliography of papers relating to their team's assigned paper.

Milestone 2: Journal Club Presentation

• The Coder/Designer will work with their teams to create and deliver a Journal Club presentation about to their team's assigned paper.

Milestone 3: Working Environment Setup

Coder/Designer work will require the following software/accounts. The Seaver 120 lab computers are already set up for this; this list is provided for Coders/Designers who need to work on a different computer or outside of the lab.

• Microsoft Access
• Box account (provided by LMU)
  • Databases created by the teams will be kept in a "BIOL367_Fall2019 > Final Project Database" Box folder.
  • Coder/Designer guild members have rights as editor to this folder; all others in the class can only view/download.
  • This folder will serve as as the version control mechanism for the Coder/Designer guild.

Milestone 4: Design a Database to Store Time-course Microarray Data from four sources

• Designer/Coders will work with the QA's to create a MS Access Database to store the yeast time-course microarray data for the dataset being analyzed by the Data Analysts.
• The starting point will be the database already used for the Week 10 assignment, which can be found here on Box.
  • This database is already populated with tables for the Dahlquist Lab microarray data, degradation rates from Neymotin et al. (2014), and initial guesses for production rates.
    • You may need to change the table names of these existing tables so that they make sense with the overall database design.
  • You will need to add one or more expression tables for the expression data from your team's article.
    • Work with your team's QA and Data Analysts to determine appropriate column headings for the expression table.
  • You will also need to create one or more tables with metadata about the other tables because now the database will contain data from multiple sources, not just one.
    • A major part of the design work will be to figure out what information needs to be in the metadata table so that queries can be easily and uniquely performed on the data.
    • Think about what information would someone need to know to be able to understand how the dataset works. Consult with the QA and Data Analysts to figure out the sample-data relationships and how that should be encoded.

Milestone 5: Build an individual database for your team

• Once the design work has been completed, you need to actually import the data into the database.
• Initially, each team will have their own database so that the QA and Data analysts can validate and use the database.

Milestone 6: Validation and Quality Assurance on Database

• The QA will perform quality assurance to make sure that the database is correct and accurate.
  • In particular, the QA needs to make sure that all of the rows of data were imported into the database for the expression table(s).
  • The QA will make sure that both the ID (SGD systematic name) and Standard Names are included in each expression table and are correct.
• QA's will communicate to the Coder/Designers any changes needed to the database.

Milestone 7: Merge completed databases into a single database for the class

• As a guild, the Coder/Designers will merge their separate databases into a final product.
• With the QA's finalize the database schema diagram

Data/Files

Sulfiknights Deliverables

Journal Club Presentation 11/14/19

Team Feedback

Naomi Tesfaiohannes

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

• What worked?

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

• What didn't work?

My time management due to other coursework

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

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

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

References

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