BIOL368/F20:Week 6

This journal entry is due on Thursday, October 15, at 12:01am Pacific time.

Overview

The learning objectives for this assignment are:

• To use bioinformatics tools to answer your own questions about the spike protein-ACE2 interaction.
• To communicate the results of your research in a scientific presentation with a clear and consistent message.

Individual Journal Assignment

Homework Partners

• You will be expected to consult with your partner, in order to complete the assignment.
• Each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).
• You must give the details of the interaction with your partner in the Acknowledgments section of your journal assignment.
• Homework partners for this week are the same as last week:
  • Fatimah & Kam
  • Nathan & Macie
  • Aiden & Anna
  • JT & Yaniv
  • Owen & Ian
  • Taylor & Nida

Format and Content Checklist

1. Store this journal entry as "username Week 6" (i.e., this is the text to place between the square brackets when you link to this page).
2. Write something in the summary field each time you save an edit. You are aiming for 100%.
3. Invoke the template that you made as part of the Week 1 assignment on your individual page.
4. Purpose: a statement of the scientific purpose of the assignment. Note that this is different than the learning objective stated on the assignment page. What science will be discovered by completing this assignment?
5. Combined Methods/Results (Electronic Lab Notebook): documentation of your workflow for this exercise. It should include:
   • The protocol you followed in enough detail for someone else to be able to conduct the same investigation. There should be enough detail provided so that you or another person could re-do it based solely on your notebook. You may copy protocol instructions on your page and modify them as to what you actually did, as long as you provide appropriate attribution.
   • Answers to any specific questions posed in the exercise.
   • Screenshots and images to document your answers.
   • Data and files: links to all data and files used and generated.
     • It is a critical skill for data and computer literacy to back-up your data and files in at least two ways:
       • Upload the files to this wiki.
       • Upload the files to Box.
       • Back them up on your personal flash drive.
     • References to data and files should be made within the methods and results section. In addition to these inline links, create a "Data and Files" section of your notebook to make a list of the files generated in this exercise.
6. Scientific Conclusion: a summary statement of the main result of exercise/research. It should mirror the purpose. Length should be 2-3 sentences, up to a paragraph.
7. Acknowledgments section (see Week 1 assignment for more details.)
   • You must acknowledge your homework partner with whom you worked, giving details of the nature of the collaboration. You should include when and how you met and what content you worked on together.
   • Acknowledge anyone else you worked with who was not your assigned partner. This could be the instructor, the TA, other students in the class, or even other students or faculty outside of the class.
   • 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 copied any part of the assignment or protocol and then modified it, acknowledge that here and also include a formal citation in the Reference section.
   • You must also include this statement:
   • "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
   • Sign your Acknowledgments section with your wiki signature (four tildes, ~~~~).
8. References section (see Week 1 assignment for more details.)
   • Use the APA format.
   • Cite this assignment page.
   • Cite any protocols that you copied and modified (this must also be noted in the Acknowledgments section).
   • Cite any other methods, software, websites, data, facts, images, documents (including the scientific literature) that was used to generate content on your page.
   • Do not include extraneous references that you do not cite or use on your page.

Background

Week 3 Journal Club article:

• Wan, Y., Shang, J., Graham, R., Baric, R. S., & Li, F. (2020). Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. Journal of virology, 94(7). DOI: 10.1128/JVI.00127-20

Other SARS-CoV-2 structure articles:

• Walls, A. C., Park, Y. J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell. DOI: 10.1016/j.cell.2020.02.058
• Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C. L., Abiona, O., ... & McLellan, J. S. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science, 367(6483), 1260-1263. DOI: 10.1126/science.abb2507
• Yan, R., Zhang, Y., Li, Y., Xia, L., Guo, Y., & Zhou, Q. (2020). Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science, 367(6485), 1444-1448. doi: 10.1126/science.abb2762

Data, Databases, and Tools

• UniProt
• NCBI Structure Database
  • Wan et al. (2020)
    • Figure 1A SARS-CoV RBD (year 2002) complexed with human ACE2: 2AJF
    • Figure 1C SARS-CoV RBD (optimized for human ACE2 recognition) and human ACE2: 3SCI
    • Figure 4B SARS-CoV RBD (optimized for civet ACE2 recognition) and civet ACE2: 3SCK
  • Other spike protein structures:
    • SARS-CoV-2:spike protein, Yan et al. (2020) 6M17
    • spike protein only, Walls et al. (2020): 6VXX or 6VYB
    • spike protein only, Wrapp et al. (2020): 6VSB
• Phylogeny.fr
• MN908947: Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1 genome sequence
  • QHD43416.1: spike protein
• NCBI Virus SARS-CoV-2 Data Hub (sequences)
• NCBI SARS-CoV-2 Resources page
• COVID-19 Data Portal
• GISAID: Global Initiative on Sharing All Influenza Data
• See also, sequences from the Week 4 and Week 4 talk pages

Scope of the Coronavirus Research Project 1

1. You will answer your research question from Week 5 using the bioinformatics tools with which you practiced during the in-class activities for Weeks 4 and 5.
   • You must create a multiple sequence alignment and tree using Phylogeny.fr (or other equivalent software).
   • You must also use iCn3D to create at least one structure figure illustrating your project results.
2. You will prepare a presentation that you will give in class for Week 7 (October 15) showing your results.
   • Your presentation will be 15 minutes long (approximately 15 slides, one per minute). Include:
     • Title slide
     • Outline slide
     • Background that led you to ask your research question (you will need to provide some summary of the Wan et al. (2020) article for this)
     • Your question
     • How you answered your question, method/results
     • Interpretation of your results; answer to your question
     • Future directions
   • Upload your slides to the OpenWetWare wiki by the Week 6 journal assignment deadline.
     • You may make changes to your slides in advance of your presentation in the afternoon, but you will be graded on what you upload by the journal deadline.
     • The format for your slides can be .pdf or .pptx.
       • Note that to upload .pptx files to the wiki, you will need to zip them. See the Help page for instructions if you don't know how to do this.
     • Both partners should link to the exact same file. I.e., don't upload duplicate files with different names.
     • Please follow the Presentation Guidelines PowerPoint on Brightspace for how to format your slides.
     • Your presentation will also be graded on the following Presentation Rubric.

Shared Journal Assignment

• Compose your journal entry in the shared Class Journal Week 6 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
• Create a header with your name, and then answer the questions in your own section of the page.
• You do not need to invoke your template on the class journal page.
• Any Acknowledgments and References you need to make should go in the appropriate sections on your individual journal page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the category "BIOL368/F20" to the end of the wiki page (if someone has not already done so).

Reflect

1. In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
2. What is still not clear to you after having concluded this project?
3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project? You will have the opportunity to conduct a second, more in-depth research project in the latter part of the semester.