JT Correy Journal Week 11

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Purpose

The purpose of lab this week was to expand our understanding of the SARS-CoV-2 virus and also sharpen our abilities as a researcher. We were tasked with finding a peer-reviewed and published article, analyzing it, and preparing a presentation to show our understanding of the complex concepts.

Exercises

Article Information

  1. Now we will begin to evaluate your assigned article in three areas availability, the journal, and the article metadata. Again, provide a citation for the article in APA format, this time including the DOI. For the following questions, for information that is not available, answer n/a).
    • Article Title: The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity.
    • APA Citation: Li, Q., Wu, J., Nie, J., Zhang, L., Hao, H., Liu, S., ... & Qin, H. (2020). The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity. Cell, 182(5), 1284-1294. doi: 10.1016/j.cell.2020.07.012
    1. Provide a link to the abstract of the article on PubMed
    2. Provide a link to the full text of the article in PubMed Central
    3. Provide a link to the full text of the article (HTML format) from the publisher website.
    4. Provide a link to the full PDF version of the article from the publisher website.
    5. Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
      • Elsevier Inc.
    6. How is the article available to you:
      • Is the article available “open access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If YES, stop here.
        • The article is not open access.
      • If the article is not “open access” is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If YES, stop here.
        • The article does not appear to be open after a certain amount of time. It has only been published for about three months so it may be avaiable later but as of right now it is not.
      • Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: http://sq4ya5rf2q.search.serialssolutions.com/ If YES, stop here.
        • Yes, the article URL includes sciencedirect-com.electra.lmu.edu.

The Journal

    1. Who is the publisher of the journal?
      • Elsevier Inc.
    2. Is the publisher for-profit or non-profit?
      • For-profit.
    3. Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
      • Elsevier Inc. is not part of a scientific community.
    4. Does the publisher belong to the Open Access Publishers Association?
      • Elsevier Inc. is not a member of the Open Access Publishers Association.
    5. What country is the journal published in?
      • The Elsevier Foundation, Radarweg 29 1043 NX Amsterdam, Netherlands
    6. How long has the journal been in operation? (e.g., browse the archive for the earliest article published)
      • CELL was started in 1974
    7. Are articles in this journal peer-reviewed?
      • Yes, the articles are peer-reviewed.
    8. Provide a link to the scientific advisory board/editorial board of the journal.
    9. What is the journal impact factor (look to see if it is provided on the journal home page; often you can also find it through a Google search)?
      • 3.339

The Article

    1. Is the article a review or primary research article?
      • Primary Research Article
    2. On what date was the article submitted?
      • June 8, 2020
    3. On what date was the article accepted?
      • July 10, 2020
    4. Did the article undergo any revisions before acceptance?
      • Yes, the final revised form was submitted July 7, 2020
    5. When was the article published?
      • July 17, 2020
    6. What is the approximate elapsed time between submission and publication?
      • About 1 month.
    7. What are the institutions with which the authors are affiliated?
      • The main author,Qianqian Li, is affiliated with the Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China. Graduate School of Peking Union Medical College, No. 9 Dongdan Santiao, Dongcheng District, Beijing 100730, China
    8. Have the authors published other articles on this subject? (How will you find this out?)
      • Yes, the authors have published other articles on this topic and can be found here
    9. Is there a conflict of interest for any of the authors?
      • There are no noticeable conflict of interest for any of the authors.
    10. Make a recommendation--based just on the information you have gathered so far, is this a good article to evaluate further? Why or why not?
      • Given the confidence of the journal and the fact that the article was reviewed at least one time, I think it is fair to say this is a good article. That being said, the science community is learning more every day about SARS-CoV-2 so in the future there will probably be more detailed and accurate articles. But given the immediate need for research on the topic this is a good article.

Terms

Make a list of at least 10 biological terms for which you 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 (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page. Note that the citation should be to the exact page from which the definition was taken, not to the general home page of the the online dictionary.

  1. Glycosylation
    • A biochemical process where a glycan attaches to a protein, a lipid, or other organic molecule, especially through the catalytic action of certain enzymes (Biology Online)
  2. Nucleocapsid
    • the structure within a virus that comprises the proteinaceous capsid and the genomic nucleic acid (Cammack 2008).
  3. monoclonal antibody
    • Monoclonal antibodies are produced by a single clone of hybridoma cells and are therefore a single species of antibody molecule (Lackie 2007)
  4. GISAID database
    • A database that promotes the rapid sharing of data from all influenza viruses and the coronavirus causing COVID-19
  5. epitope
    • any immunological determinant group of an antigen (Cammack 2008)
  6. Vero
    • A cell line derived from the African Green Monkey (Lackie 2007)
  7. VeroE6
    • A specific line of Vero cells (Lackie 2007)
  8. polyclonal
    • an antibody that arises from the immune response to an immunogen (Cammack 2008)
  9. RLU
    • Relative Light Unit, a measurement of bioluminescence. (Berthold 2020)
  10. Antigenicity
      • the capacity of an agent to stimulate the formation of specific antibodies (cammack 2008)

Outline

Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.

  1. What is the importance or significance of this work?
    • Given the current SARS-CoV-2 pandemic, any literature on the topic is exceedingly important. This paper specifically investigates some of the mutations that are already known as well as some potential mutations that are not found naturally yet. The article goes into significant detail into their findings and provides a great foundation for other articles to build off what they found.
  2. What were the limitations in previous studies that led them to perform this work?
    • The main limitation was just lack of knowledge about the SARS-CoV-2 pandemic. The research they did is fairly similar to other papers, they were just more specific on the exact mutations they chose to study. They also used 26 specific cell lines that I have not seen used in a SARS-CoV-2 study before.
  3. How did they overcome these limitations?
    • They were able to overcome the limitations by being very selective with the mutations they chose to study and the cell lines they chose to study them with. As SARS-CoV-2 is very understudies, any additional information is useful and they chose mutations and cell lines that they believed would be the most beneficial.
  4. What is the main result presented in this paper? (Hint: look at the last sentence of the introduction and restate it in plain English.)
    • The main finding that the study found was that glycosylation was the leading mutation of SARS-CoV-2 that led to differing reactions by antigens.
  5. What were the methods used in the study?
    • The research team first selected what virus RNA sequences from the GISAID database. They then split these into three subgroups based on the presence naturally and constructed psuedotyped viruses from the sequences. The team then infected the 26 cell lines with the different viruses. They then narrowed down the differences in the viruses and the corresponding effects they had. Following this they started adding 13 different monoclonal antibodies to the cell lines and analyzed the results. Lastly they related these results to the current SARS-CoV-2 RNA sequences.
  6. Briefly state the result shown in each of the figures and tables that you have been assigned in your group.
    • Figure 4 is a grid that displays the antigenicity of the different monoclonal antibodies on the different SARS-CoV-2 mutations in Huh-7 cells. There were 3-5 trials completed for each combination and the redder the square is the more efficient the antibody was. Supplemental figures 2 and 3 display the heat map in much more detail. They show the specific trials and highlight significant trials. They also display the serial dilutions for each monoclonal antibody.
  7. What are the important implications of this work?
    • This study did two major things. First it started the long process of predicting and analyzing how the SARS-CoV-2 will mutate and effect cells. Second, they analyzed how different antibodies interacted with SARS-CoV-2 and identified potentially useful antibodies.
  8. What future directions should the authors take?
    • There are two important directions the researchers could go from here. First, they could continue what they have been doing and study more variations in RNA sequencing, cell lines, and antibodies. Second, they could take the information they have and start moving from cells to more complex organisms and work their way up to human antibody and SARS-CoV-2 trials.
  9. Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any limitations or major flaws to the paper?
    • I think that this paper supported their conclusion very well. Granted there was lots of technical language and specific biological systems that I don’t yet understand so they could have errors there I did not catch. From what I understood everything made sense and the methods they used to narrow down the mutations to identify which antibodies are most effective seemed like very sound science.

Conclusion

I think that the lab this week was one of the more useful ones this semester. I feel like I learned a lot about being able to quickly digest and filter articles when we were selecting the article we wanted to present on. Our group had about ten different ones and we all had to quickly go through each one and decide if it fit the criteria and if it was something that we were all interested in. Being able to efficiently go through scientific writing is super useful and it will definitely come in handy in my future.

Powerpoint

Journal Club Presentation

References

  • Li, Q., Wu, J., Nie, J., Zhang, L., Hao, H., Liu, S., . . . Wang, Y. (2020). The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Cell, 182(5). doi:10.1016/j.cell.2020.07.012
  • Glycosylation - Definition and Examples - Biology Online Dictionary. (2020, August 05). Retrieved from https://www.biologyonline.com/dictionary/glycosylation
  • Oxford Dictionary of Biochemistry and Molecular Biology, by Richard Cammack et al., Oxford University Press, Oxford, 2006, pp. 692.
  • The Dictionary of Cell and Molecular Biology, by J. M. Lackie, Academic Press, 2007, pp. 273.
  • “Mission.” GISAID, www.gisaid.org/about-us/mission/.
  • Berthold Technologies GmbH & Co.KG. “RLU (Relative Light Unit) - Berthold Technologies.” Berthold Technologies GmbH & Co.KG, Berthold Technologies GmbH & Co.KG, 2 Nov. 2020, www.berthold.com/en/bioanalytic/knowledge/glossary/rlu/.
  • Oxford Dictionary of Biochemistry and Molecular Biology, by Richard Cammack et al., Oxford University Press, Oxford, 2006, pp. 316.
  • The Dictionary of Cell and Molecular Biology, by J. M. Lackie, Academic Press, 2007, pp. 442.
  • The Dictionary of Cell and Molecular Biology, by J. M. Lackie, Academic Press, 2007, pp. 442.
  • Oxford Dictionary of Biochemistry and Molecular Biology, by Richard Cammack et al., Oxford University Press, Oxford, 2006, pp. 794.
  • Oxford Dictionary of Biochemistry and Molecular Biology, by Richard Cammack et al., Oxford University Press, Oxford, 2006, pp. 62.
  • OpenWetWare. (2020). BIOL368/F20:Week 11. Retrieved 18 November 2020, from https://openwetware.org/wiki/BIOL368/F20:Week_11.

Acknowledgements

  • Yaniv Maddahi
    • We were in the same research group communicated and worked together both at the end of the week 11 lab and throughout the week to create our research project and assignment pages.
  • Macie Duran
    • We were in the same research group communicated and worked together both at the end of the week 11 lab and throughout the week to create our research project and assignment pages.
  • Fatimah Alghanem
    • We were in the same research group communicated and worked together both at the end of the week 11 lab and throughout the week to create our research project and assignment pages.
  • Dr. Dahlquist
    • Dr. Dahlquist served as a coach for how to begin our pages. She also instructed the class and provided us with the guiding homework document.
  • I copied and modified the protocol shown on the Week 11 page of our class OpenWetWare.

Jcorrey (talk) 23:38, 18 November 2020 (PST)


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