Aiden Burnett Week 11

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Purpose

To understand the work done by Rogers et al., in order to inform our research project and gain more experience with journal club presentations and source evaluation.

Methods & Results

Searching the Scientific Literature Part 2: Evaluating Scientific Sources

  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).
    • Rogers TF, Zhao F, Huang D, Beutler N, Burns A, He WT, Limbo O, Smith C, Song G, Woehl J, Yang L, Abbott RK, Callaghan S, Garcia E, Hurtado J, Parren M, Peng L, Ramirez S, Ricketts J, Ricciardi MJ, Rawlings SA, Wu NC, Yuan M, Smith DM, Nemazee D, Teijaro JR, Voss JE, Wilson IA, Andrabi R, Briney B, Landais E, Sok D, Jardine JG, Burton DR. Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model. Science. 2020 Aug 21;369(6506):956-963. doi: 10.1126/science.abc7520.
    1. Provided a link to the abstract of the article on PubMed.
    2. Provided a link to the full text of the article in PubMed Central.
    3. Provided 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? Looked at the first page of the PDF version of the article for the © symbol.
      • The authors of the article.
    6. How is the article available:
      • Is the article available “open access”
        • Yes. It was published in Science which is an open access journal from AAAS.
    7. Is the article available online-only or both in print and online?
      • The article is available in both print and online.
  2. Evaluating the source--the journal
    1. Who is the publisher of the journal?
      • The American Association for the Advancement of Science (AAAS).
    2. Is the publisher for-profit or non-profit?
      • non-profit
    3. Is the publisher a scientific society?
      • AAAS includes many scientific societies within itself & acts as their own non-profit publisher.
    4. Does the publisher belong to the Open Access Publishers Association?
      • Yes.
    5. What country is the journal published in?
      • The United States of America
    6. How long has the journal been in operation? (e.g., browse the archive for the earliest article published)
      • They have been operating since 1880.
    7. Are articles in this journal peer-reviewed?
      • Yes, all 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?
      • 41.845
  3. Evaluating the source--the article
    1. Is the article a review or primary research article?
      • primary research article
    2. On what date was the article submitted?
      • May 12, 2020
    3. On what date was the article accepted?
      • June 11, 2020
    4. Did the article undergo any revisions before acceptance?
      • There are no listed revisions before acceptance so this doesn't appear to be the case.
    5. When was the article published?
      • June 15, 2020
    6. What is the approximate elapsed time between submission and publication?
      • 1 month and 4 day
    7. What are the institutions with which the authors are affiliated?
      • Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
      • Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
      • IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.
      • Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.
      • IAVI, New York, NY 10004, USA.
      • Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
      • Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
      • Department of Pathology, George Washington University, Washington, DC 20052, USA.
      • Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
      • Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology
    8. Have the authors published other articles on this subject?
      • Thomas F. Rogers & Fangzhu Zhao have published several previous articles on the topic.
    9. Is there a conflict of interest for any of the authors?
      • D.R.B., D.H., J.G.J., E.L., T.F.R., D.S., and F.Z. have invested in "pending patent applications describing the SARS antibodies". The other authors had no interests to declare.
    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?
      • Yes. The authors seem to bring a wealth of prior knowledge on the subject to this article. It is also published in a well respected journal.

Preparation for Journal Club 2

  1. 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. Antibody- any glycoprotein of the immunoglobulin family that is capable of combining noncovalently, reversibly, and in a specific manner with a specific manner with a corresponding antigen. (Oxford University Press, 2000)
    2. monoclonal antibodies- identical antibodies that are made in large amounts in the laboratory. (Biology online, 2020)
    3. convalescent- serum from patients recently recovered from a disease; useful in preventing or modifying by passive immunization the same disease in exposed susceptible individuals (Biology Online, 2020)
    4. epitope- the part of an antigenic molecule to which the t-cell receptor responds, a site on a large molecule against which an antibody will be produced and to which it will bind (Biology Online, 2020)
    5. titers- a measure of the concentration or activity of an active substance, e.g. an antibody, in a solution, usually expressed as the highest dilution of the solution in which the activity can be detected. By convention, if the highest dilution giving activity is 100‐fold, the titre is said to be 100 (Oxford Dictionary of Biochemistry and Microbiology, 2020)
    6. prophylactic- an agent that prevents the development of a condition or disease (Oxford Dictionary of Biochemistry and Microbiology, 2020)
    7. syncytium- An epithelium or tissue characterized by cytoplasmic continuity, or a large mass of cytoplasm not separated into individual cells and containing many nuclei. (Biology Online, 2020)
    8. HeLa cell line- An established line of human epithelial cells derived from a cervical caracinoma (from a black American woman called Henrietta lacks).These cells are used for virus cultivation and antitumour drug screening assays. (Biology Online, 2020)
    9. Antigen- an antigen refers to any substance that triggers an immune response. This response is intended to naturally protect the body from harmful entities, such as disease-causing microbes and neoplastic growth. (Biology Online, 2020)
    10. luciferase- Any of the group of enzymes that act on the oxidation of luciferin of bioluminescent organisms. (Biology Online, 2020)
    11. exocytosis- When materials leave the cell by the membrane “spitting it out”. (Biology Online, 2020)
    12. virion- A single virus particle, complete with coat. (Biology Online, 2020)
  2. 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.
    • I'm sorry but I'm not going to be able to write a full summary. I'll accept the point loss involved. I want to make sure I do my best on the group presentation for my partners but I've had an emotionally exhausting week and I honestly don't have the motivation to do both.
    • What is the importance or significance of this work?
      • They found that passive exposure to antibodies inoculated from humans infected with SARS-CoV-2 is able to render immunity to syrian hamsters. This gives hope and information to vaccine researchers (and everyone else).
    • What were the limitations in previous studies that led them to perform this work? How did they overcome these limitations?
      • There weren't necessarily limitations that they had to overcome, so much as there was a subject with needed to be studied. No prior studies had explored the efficacy of antibodies from SARS-CoV-2 infected humans in combatting infection in others. They sought to remedy this as such studies are useful in the search for vaccines.
    • What is the main result presented in this paper?
      • Neutralizing antibodies are able to provide protection from SARS-CoV-2!
    • What were the methods used in the study?
      • Humans who were naturally infected with SARS-CoV-2 were found. Monoclonal antibodies were isolated from these individuals and they were subject to neutralization assays. The two most effective of these were used to treat Syrian hamsters. These hamsters, and a control group, were then exposed to SARS-CoV-2. The progress of their infections were monitored through weight loss and lung tissue viral load.
    • Briefly state the result shown in each of the figures and tables that you have been assigned in your group.
      • Figure 5 illustrates the results of their infecting syrian hamsters with SARS-CoV-2 after various treatments. Hamsters treated with higher concentrations (max of 2 mg/ml) of neutralizing antibodies were found to have experiences no/less weight loss and lower viral load than hamsters treated with the control (anti-dengue fever antibodies) and lower concentration anti-SARS-CoV-2 antibodies.
    • What are the important implications of this work?
      • A vaccine is possible!
    • What future directions should the authors take?
      • They should treat a group of animals with low concentrations of anti-SARS-CoV-2 antibodies. In the current experiment they found that these animals experienced more (but statistically insignificant) weight loss than the control treated animals. This may be indicative of antibody-mediated enhanced disease and is worth looking into.
    • 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 their conclusions were well supported. The hamsters treated with 2mg/ml of neutralizing antibodies clearly exhibited a greater resistance to SARS-CoV-2. They experienced no weight loss and lower viral loads in lung tissue than the control hamsters.

Journal Club Presentation

Presentation Slides (PDF)

Scientific Conclusion

Treatment with anti-SARS-CoV-2 antibodies are able to combat in in otherwise unexposed individuals. This means that this is a fertile ground for research hoping to develop a vaccine against this virus.

Acknowledgments

I worked with my partners Taylor Makela, Anna Horvath, and Nida Patel during class (over Zoom) to decide on and discuss our journal article.

  • I copied and modified the procedures shown on the Week 11 page.
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Aiden Burnett (talk) 23:47, 17 November 2020 (PST)

References

  1. Rogers, T. F., Zhao, F., Huang, D., Beutler, N., Burns, A., He, W. T., Limbo, O., Smith, C., Song, G., Woehl, J., Yang, L., Abbott, R. K., Callaghan, S., Garcia, E., Hurtado, J., Parren, M., Peng, L., Ramirez, S., Ricketts, J., Ricciardi, M. J., … Burton, D. R. (2020). Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model. Science (New York, N.Y.), 369(6506), 956–963. https://doi.org/10.1126/science.abc7520
  2. Oxford Dictionary of Biochemistry and Molecular Biology. (2006). Antibody. Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. Oxford University Press. Retrieved November 14, 2020, from https://www-oxfordreference-com.electra.lmu.edu/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-1267?rskey=KO820V&result=1
  3. Biology Online. (2020). Monoclonal Antibodies. Retrieved 17 November 2020, from https://www.biologyonline.com/dictionary/monoclonal-antibodies
  4. Biology Online. (2020). Convalescent. Retrieved 17 November 2020, from https://www.biologyonline.com/dictionary/convalescents
  5. Biology Online. (2020). Epitope. Retrieved 17 November 2020, from https://www.biologyonline.com/dictionary/epitope
  6. Oxford Dictionary of Biochemistry and Molecular Biology. (2006). Titre. Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. Oxford University Press. Retrieved November 17, 2020, from https://www-oxfordreference-com.electra.lmu.edu/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-19642
  7. Oxford Dictionary of Biochemistry and Molecular Biology. (2006). Prophylactic. Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. Oxford University Press. Retrieved November 17, 2020, from https://www-oxfordreference-com.electra.lmu.edu/view/10.1093/acref/9780198788454.001.0001/acref-9780198788454-e-7392?rskey=ClWg5E&result=1
  8. Biology Online. (2020). Syncytium. Retrieved 17 November 2020, from https://www.biologyonline.com/dictionary/syncytium
  9. Biology Online. (2020). Hela. Retrieved 17 November 2020, from https://www.biologyonline.com/dictionary/hela
  10. Biology Online. (2020). Antigen. Retrieved 17 November 2020, from https://www.biologyonline.com/dictionary/antigen
  11. Biology Online. (2020). Luciferase. Retrieved 17 November 2020, from https://www.biologyonline.com/dictionary/luciferase
  12. Biology Online. (2020). Exocytosis. Retrieved 17 November 2020, from https://www.biologyonline.com/dictionary/exocytosis
  13. Biology Online. (2020). Virion. Retrieved 17 November 2020, from https://www.biologyonline.com/dictionary/virion

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