FunGals

From LMU BioDB 2019
Revision as of 18:38, 20 November 2019 by Knguye66 (talk | contribs) (→‎Week 12/13: add info)
Jump to navigation Jump to search

Effects of the Pesticide Thiuram:  Genome-wide Screening of Indicator Genes by Yeast DNA Microarray

Team Information
Project Manager: Michael Armas
Quality Assurance:  Iliana Crespin
Data Analysis: Emma Young, Kaitlyn Nguyen
Coder: Michael Armas

Methods and Results

Week 11

Setting up the Project

  • Selected Michael Armas as team's Project Manager.
  • Added the name of of selected project manager to the Project Manager guild page and Overview pages.
  • Named the team FunGals and created FunGals home page on the wiki.
  • The name of the team home page was the selected team name.
  • Created a link to team's page on the course Main page.
  • Created a template for FunGal with useful information and links that you will invoke on all pages that you will create for the project.
  • Created a category using team name and included it the FunGal template so that it is used on all pages created for the project. Also included the category "Group Projects" in the template.
  • Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
  • Each team member should reflect on the team's progress (Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks):
    • What worked? What didn't work? What will I do next to fix what didn't work?
      • Michael Armas: Working with this team is a great pleasure! Everyone on the team is pulling their weight and providing information that contributes to the group work. Next time, as the project manager, I want to be more organized and come up with interim deadlines to make sure we are not cramming right before the actual deadline. In fact, I would have something small due every day than procrastinate until the end. However, with this team, we are making it work and doing exceptional work!
      • Kaitlyn Nguyen: What worked this week is starting the presentation formatting early, thus allocating the rest of the time to "filling in the missing parts" of the powerpoint. What also worked this week was team communication via group-chats. What didn't work this week was starting the individual assignment later, leaving less time to practicing and fully understanding the material from the journal article for the presentation in class. To fix what didn't work, I will start my individual assignment much earlier, to leave the rest of the time to focus on collaborative teamwork and group assignments. Knguye66 (talk) 23:37, 13 November 2019 (PST)
      • Emma Young: The team seems to work really well together. I think in upcoming weeks we will really thrive in working together. A foundation for communication has already been established and we have already started reviewing each others work and providing constructive criticism and help where it is needed. The main issue this week was a matter of timing. With the amount of work we had to do in the time frame given we were not able to meet up due to busy and conflicting prior engagements. This meant that we did not reach our full potential of working together effectively as a group this week. Next week, we hopefully will be able to set better deadlines and be able to have the ability to plan out time to work on this in a less rushed manner.
      • Iliana Crespin: Overall, this group has been great. Everyone has worked together and understands what must be done. In addition, each member is understanding of the special circumstances before the deadline of this assignment. The only thing that didn't work out was how scattered each of us were because of all the assignments that had to be completed from other classes. In addition, mandated plans (school- or work-related) popped up which made it difficult to contribute equally. For the future, I will make sure to manage my time better, because I have work and school. Therefore, by doing a fair share of certain things before classes/work, I will be able to contribute more.Icrespin (talk) 23:46, 13 November 2019 (PST)

Annotated Bibliography

  1. Braconi, D., Bernardini, G., & Santucci, A. (2016). Saccharomyces cerevisiae as a model in ecotoxicological studies: A post-genomics perspective. Journal of Proteomics, 137, 19-34. DOI: 10.1016/j.jprot.2015.09.001
  2. Hinkle, K. L., & Olsen, D. (2018). Exposure to the lampricide TFM elicits an environmental stress response in yeast. FEMS yeast research, 19(1), foy121. doi: 10.1093/femsyr/foy121
  3. Iwahashi, Y., Hosoda, H., Park, J. H., Lee, J. H., Suzuki, Y., Kitagawa, E., ... & Iwahashi, H. (2006). Mechanisms of patulin toxicity under conditions that inhibit yeast growth. Journal of agricultural and food chemistry, 54(5), 1936-1942. doi: 10.1021/jf052264g.
  4. Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
  5. Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
  6. Kitagawa, E., Momose, Y., & Iwahashi, H. (2003). Correlation of the Structures of Agricultural Fungicides to Gene Expression in Saccharomyces cerevisiaeupon Exposure to Toxic Doses. Environmental Science & Technology, 37(12), 2788–2793. doi: 10.1021/es026156b
  7. Lu Yu, Na Guo, Rizeng Meng, Bin Liu, Xudong Tang, Jing Jin, Yumei Cui, Xuming Deng. Allicin-induced global gene expression profile of Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 2010, 88 (1) , 219-229. DOI: 10.1007/s00253-010-2709-x.
  8. Pierron, A., Mimoun, S., Murate, L. S., Loiseau, N., Lippi, Y., Bracarense, A. P. F., ... & Oswald, I. P. (2016). Intestinal toxicity of the masked mycotoxin deoxynivalenol-3-β-D-glucoside. Archives of toxicology, 90(8), 2037-2046. doi: 10.1007/s00204-015-1592-8

Week 12/13

Milestone 3: Getting the data ready for analysis

  1. Downloaded and examined the microarray dataset, compared it to the samples and experiment described in the journal club article.
    • Kitagawa et al. (2002)
    • downloaded and unzipped
    • file was downloaded but was PLC format
    • Mike figured out how to drag and drop it one to excel to open the file
  2. Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.
    • Table was created in excel
  3. Come up with consistent column headers that summarize this information
    • -
      • For example, the Dahlquist Lab microarray data used strain_LogFC_timepoint-replicate number, as in wt_LogFC_t15-1.
  4. Organize the data in a worksheet in an Excel workbook so that:
    • MasterIndex is in the first column, ID is in the second column
    • Data columns are to the right, in increasing chronological order, using the column header pattern you created
    • Replicates are grouped together
  5. Data analysts (DA) set-up the ANOVA worksheet via referencing Week 8
    • Followed the steps for the ANOVA: Part I, Benjamini, Bonferroni, and p-value correction, as well as, perform a quick sanity check
  6. DAs begin setting up for STEM analysis to complete the first stage of milestones and deliverables
  • Each team member should reflect on the team's progress (Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks):

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

Data and Files

Week 11

Week 12/13

Milestones

Tasks to be completed Due Date
Team Journal Assignment, write down Methods and Results for Week 12/13
  • Coder/designer: find out the column names and edit them, sample to data relationship table
  • Data Analysis: ANOVA analysis and set-up, STEM set-up (will run STEM on Thursday)
  • QA: make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
 Thursday, 12:00am, 11/19/19
Tuesday, 12:00am, 11/26/19
Thursday, 12:00am, 11/28/19
Tuesday, 12:00am, 12/03/19
Thursday, 12:00am, 12/05/19
Final Presentation Tuesday, 12:00am, 12/10/19
Report submitted Friday, 4:00 pm, 12/13/19

Acknowledgements

This section is in acknowledgement to partner Michael Armas, Iliana Crespin, Emma Young, and Kaitlyn Nguyen. I would also like to acknowledge Dr. Dahlquist for introducing and teaching the topic and direction of this assignment.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
Marmas (talk) 23:40, 13 November 2019 (PST) Icrespin (talk) 23:46, 13 November 2019 (PST)

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source." Eyoung20 (talk) 23:57, 13 November 2019 (PST)

Information and Links

FunGals Links
BIOL Databases Main Page FunGals: Project Overview Page Final Project Deliverables Requirements FunGals: Final Project Deliverables
Assignment Pages Week 11 Week 12/13 Week 15

User Pages

Knguye66 
Marmas
Icrespin
Eyoung20

Template Page

Template:FunGals

References

-Week 11-

-Week 12/13-

Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2019/index.php?title=FunGals&oldid=7133"