BIOL368/F16:Week 14

This journal entry is due on Tuesday, December 6 at midnight PDT (Monday night/Tuesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

Individual Journal Assignment

• Store this journal entry as "username Week 14" (i.e., this is the text to place between the square brackets when you link to this page).
• Create the following set of links. These links should all be in your personal template; then use the template on your journal entry.
  • Link to your journal entry from your user page.
  • Link back from your journal entry to your user page.
  • Link to this assignment from your journal entry.
  • Don't forget to add the "BIOL368/F16" category to the end of your wiki page.

Part 1: Biological Databases (In class activity for November 22)

Each year, the journal Nucleic Acids Research (NAR) devotes the first issue in January to biological databases. The goal of this assignment is to dive into the deep end of the pool and experience the breadth and depth of biological databases available on the Web. This "Part 1" assignment is worth a total of 20 points (as part of the information literacy points for the course).

Read

• Rigden, D. J., Fernández-Suárez, X. M., & Galperin, M. Y. (2016). The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. Nucleic acids research, 44(D1), D1-D6. doi: 10.1093/nar/gkv1356
• Slides from DataONE.org
  • DataONE: Why Data Management
• DataONE: Data Sharing

Assignment: Database Profile

• For this exercise, you will work individually. Choose a database from this issue; each person should choose a different database to profile.
  • Zach - HPSC
  • Isai - SIDER
  • Anu - eggNOG
  • Avery - Withdrawn
  • Will - International Nucleic Acid Sequence Database ^-^
  • Courtney - BindingDB
  • Mia - CancerResource
  • Shivum - Panther
  • Matt O. - DIDA
  • Matt A. - MitoAge
  • Colin - KEGG
  • Jordan - IC4R
• Nucleic Acids Research Database Issue Table of Contents 2016
• Answer the questions below on your Week 14 individual journal page.
• In class on Tuesday, November 29, each person will give a 5-minute lightning talk (worth 3 points) to tell the rest of the class about his or her database. You will use your wiki page and the database web page itself for the presentation (no PowerPoint slides).
• Read the article about the database from the Nucleic Acids Research journal and then go online to the database itself. When you answer the questions below, provide a hyperlink to the page that you got the information from (there must be at least one link per answer).
  1. What database did you access? (link to the home page of the database)
  2. What is the purpose of the database?
  3. What biological information does it contain?
  4. What species are covered in the database?
  5. What biological questions can it be used to answer?
  6. What type (or types) of database is it (sequence, structure, model organism, or specialty [what?]; primary or “meta”; curated electronically, manually [in-house], manually [community])?
  7. What individual or organization maintains the database?
  8. What is their funding source(s)?
  9. Is there a license agreement or any restrictions on access to the database?
  10. How often is the database updated? When was the last update?
  11. Are there links to other databases?
  12. Can the information be downloaded? And in what file formats?
  13. Evaluate the “user-friendliness” of the database.
      • Is the Web site well-organized?
      • Does it have a help section or tutorial?
      • Run a sample query. Do the results make sense?
• Some Definitions
  • Electronic curation occurs when someone writes a program to add information to a database record from another database.
  • Manual curation occurs when a human reviews the information being added to a record to validate it as true.
  • In-house is when the human works for the database organization.
  • Community is when the database allows members of the scientific community that don't work for the database organization to add information to the record.

Part 2: Revising Journal Club Slides (In-class Activity for Tuesday, November 29 and Week 14 Assignment)

Homework Partners for Weeks 14 and 15

• Matt A., Matt O., Mia, Colin: Hebly (2014); Δswi4 Dahlquist lab data
• Shivum, Isai, Anu, Will: Tai et al. (2007); Δgln3 Dahlquist lab data
• Avery, Courtney, Jordan, Zach: Schade et al. (2004); wt Dahlquist lab data

Journal Club Papers

• Hebly, M., de Ridder, D., de Hulster, E. A., de la Torre Cortes, P., Pronk, J. T., & Daran-Lapujade, P. (2014). Physiological and transcriptional responses of anaerobic chemostat cultures of Saccharomyces cerevisiae subjected to diurnal temperature cycles. Applied and environmental microbiology, 80(14), 4433-4449. doi: 10.1128/AEM.00785-14
  • PowerPoint slides for Hebly et al. (2014)
• Schade, B., Jansen, G., Whiteway, M., Entian, K. D., & Thomas, D. Y. (2004). Cold Adaptation in Budding Yeast. Molecular Biology of the Cell, 15(12), 5492-5502. doi: 10.1091/mbc.E04-03-0167
  • PowerPoint slides for Schade et al. (2004)
• Tai, S. L., Daran-Lapujade, P., Walsh, M. C., Pronk, J. T., & Daran, J. M. (2007). Acclimation of Saccharomyces cerevisiae to low temperature: a chemostat-based transcriptome analysis. Molecular Biology of the Cell, 18(12), 5100-5112. doi: 10.1091/mbc.E07-02-0131
  • PowerPoint slides for Tai et al. (2007)

Background Reading on Microarrays

• Brown, P.O. & Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays Nature Genetics 21: 33-37.
• Campbell, A.M. and Heyer, L.J. (2003), “Chapter 4: Basic Research with DNA Microarrays”, in Discovering Genomics, Proteomics, and Bioinformatics, Cold Spring Harbor Laboratory Press, pp. 107-124. (Available on MyLMUConnect)

Journal Club and Microarray Data Analysis Mini-Project

• For the next two weeks, we will perform a DNA microarray analysis mini-project based on data from the Dahlquist Lab.
• During the final exam period, your group will give a combined journal club, data analysis presentation where you will discuss a published microarray paper and then compare your data analysis results to it.
  • Your Week 14 assignment is to prepare the journal club definitions, outline, and revisions to the slides provided to you.
  • In class during Week 15, we will perform the DNA microarray data analysis that you will then compare to the results from the journal club article.

Journal Club Instructions

• Unlike the previous journal club preparations in this course, you will work on this as a group. For this part of the assignment, designate one group member's individual wiki page as the group page. The other members of the group should then link to that page from their own individual pages. All four members of the group should then work together on the shared page.
• Compile a list of at least 30 biological terms for which at least one member of the group did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries. List the citation(s) for the dictionary(s) you use, one per definition.
• Create a shared 3-4 page outline of the article. Your outline can be in any form you choose. It does not have to be complete sentences, but it should answer the questions listed below and have enough information so that I can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. Your outline should address the following points:
  • What is the main result presented in this paper?
  • What is the importance or significance of this work?
  • What were the limitations in previous studies that led them to perform this work?
  • How did they treat the yeast cells (what experiment were they doing?)
    • Draw a diagram or flow chart of the experimental design.
    • What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
    • What media did they grow them in? What temperature? What type of incubator? For how long?
    • What controls did they use?
    • How many replicates did they perform per treatment or timepoint?
  • What method did they use to prepare the RNA, label it and hybridize it to the microarray? (very brief description)
  • What mathematical/statistical method did they use to analyze the data? (very brief description)
  • Are the data publicly available for download? From which web site?
  • Briefly state the result shown in each of the figures and tables.
  • How does this work compare with previous studies?
  • What are the important implications of this work?
  • What future directions should the authors take?
  • 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?
• During the final exam period of finals week, your group will give a PowerPoint presentation that combines the journal club for this article with the data analysis you will do next week.
  • Your group will be given slides prepared by previous students to revise for your presentation.
  • You have been graded on three presentation so far and should be familiar with the Presentation Guidelines and Grading Rubric. You are required to revise the presentations you have been given to make them better. Remember the following:
    • The title of your paper should be the title of your presentation; the complete bibliographic reference to the paper should also appear on the title slide in APA format. This will serve as the citation for the information in your presentation. Any figures or information from additional sources need to be cited separately on the slide and included in the list of references at the end of the presentation in APA format.
    • For the body of your presentation, you need to have an outline, one or more introductory slides, and then a slide for each of the figures and tables in your article. Do not have a separate section of your presentation for Methods. Instead, show each of the results (figures/tables) and just explain the methods used to obtain those results on that slide. You will then end with a discussion, conclusion, and evaluation of the quality of the paper. Please address the questions stated above for your outline in your presentation.
  • Instructions on how to include the slides from the microarray analysis you will perform yourselves will be provided next week.

Academic Honesty

As discussed in class, each weekly individual journal assignment needs to conclude with an Acknowledgments and References section.

Acknowledgments

In this section, you need to acknowledge anyone who assisted you with your assignment, either in person, electronically, or even anonymously without their knowledge (see below).

1. You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. An appropriate statement could be (but is not limited to) the following:
   • I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
     • Sign this statement with your wiki signature.
2. Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
3. If you copied wiki syntax or a particular style from another wiki page, acknowledge that here. Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style. If you need to reference content, use your References section (see below).
4. You must also include this statement unless otherwise noted: "While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source."

References

• In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising. This includes, but is not limited to:
  • data
  • facts
  • images
  • documents, including the scientific literature
• The references in this section should be accompanied by in text citations on your page that refer to these references.
• The references should be formatted according to the APA guidelines.
• For more detailed guidelines, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.

Shared Journal Assignment

• Store your journal entry in the shared BIOL368/F16:Class Journal Week 14 page. If this page does not exist yet, go ahead and create it.
• Link to the shared journal entry from your user page; this should be part of your template.
• Link the shared journal page to this assignment page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the "BIOL368/F16" category to the end of the wiki page (if someone hasn't done it first).

View

• Watch the video "Deception at Duke" from CBS 60 Minutes.

Re-read (or Read)

• Slides from DataONE.org
  • DataONE: Why Data Management
  • DataONE: Data Sharing

Reflection

• Answer the following questions:
  • Were you aware of the Duke case of research fraud before viewing this video?
  • What are your initial reactions to hearing the case?
  • What role did data sharing play in uncovering the fraud?
  • What additional information would you like to know about the Duke case in particular?
• Please feel free to respond or comment on your classmates' reflections.