Yaniv Maddahi Journal Week 11

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Journal Club Presentation

Journal Club 2 Presentation

Purpose

  • The purpose of this lab is to do several things. Firstly, in this lab we developed our understanding of all of the moving parts and backbones of publishing an article. We analyzed the article, it's publisher, what type of organization it was, etc. We understood the different natures of publishing an article, distinguishing between open access and not. Further, and arguably what the main purpose is, to become independent thinkers, analyzing the articles, its source of publication, etc. We then chose our own journal article and went forth to create our own presentation.

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).
    • 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.
      • 2020 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 does not appear to be 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 appear to be free after a certain period of time has elapsed.
      • 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.
        • LMU does not appear to have bought a subscription for access.
      • Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99. Note that you don’t need to actually request it for this assignment.
        • The article does not appear to be behind a paywall.
    7. Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
      • The article is available in print and online and one can subscribe via the publisher website.

Evaluating the source--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)
      • It does not seem as if Elsevier Inc. is a scientific community.
    4. Does the publisher belong to the Open Access Publishers Association?
      • Elsevier Inc. does not appear to be part 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)
      • The paper was Published July, 2020
    7. Are articles in this journal 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

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?
      • 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?
      • A little over 1 month, between June 8th and July 17th there are approximately 39 days.
    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?
      • No, there do not appear to be any conflicts of interest for 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?
      • With regard to quality of work, depth of review, etc. It is hard to truly evaluate given the quick turnaround time for article submission and publication. I think it is worthy to continue evaluating this source to understand if the quality of the work falls short in any way given it's rushed nature.

Preparation for Journal Club 2

The paper you are assigned for Journal Club 2:

  • 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


10 Biological Terms

  1. Positive-strand RNA: Templates for both translation and replication, leading to interactions between host translation factors and RNA replication at multiple levels.
    • Ahlquist, P., Noueiry, A. O., Lee, W. M., Kushner, D. B., & Dye, B. T. (2003). Host factors in positive-strand RNA virus genome replication. Journal of virology, 77(15), 8181-8186.
  2. Trimers: a polymer formed from three molecules of a monomer
    • Biology Online. (2020) . Trimer - Definition and Examples - Biology Online Dictionary. Biology Articles, Tutorials & Dictionary Online.
  3. 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. (2020) . Glycosylation - Definition and Examples - Biology Online Dictionary. Biology Articles, Tutorials & Dictionary Online.
  4. Vector: A vehicle (e.g. a plasmid) used to transfer the genetic material such as DNA sequences from the donor organism to the target cell of the recipient organism.
    • Biology Online. (2020) . Vector - Definition and Examples - Biology Online Dictionary. Biology Articles, Tutorials & Dictionary Online.
  5. Pathogenic: Capable of causing disease.
    • Biology Online. (2020) . Pathogenic - Definition and Examples - Biology Online Dictionary. Biology Articles, Tutorials & Dictionary Online.
  6. Hemagglutinin: A substance that causes hemagglutination (i.e. the agglutination of red blood cells).
    • Biology Online. (2020) . Hemagglutinin - Definition and Examples - Biology Online Dictionary. Biology Articles, Tutorials & Dictionary Online.
  7. Pseudotyping: modular swapping of VAPs between viral strains.
    • Bergen, J., & Schaffer, D. (2017). 4.33 Engineering Viruses For Gene Therapy.
  8. Convalescent Serum: serum from patients recently recovered from a disease; useful for diagnosis by demonstrating a fourfold increase in specific antibodies or in preventing or modifying by passive immunization the same disease in exposed susceptible people.
    • convalescent serum. (2002) McGraw-Hill Concise Dictionary of Modern Medicine.
  9. Epitope: a localized region on the surface of an antigen capable of eliciting an immune response and of combining with a specific antibody to counter that response.
    • Epitopes. (2003). Miller-Keane Encyclopedia and Dictionary of Medicine, Nursing, and Allied Health, Seventh Edition.
  10. Vero Cell: lineage of cells used in cell cultures.
    • Vero. (2007). Miller-Keane Encyclopedia and Dictionary of Medicine, Nursing, and Allied Health, Seventh Edition.

Article Outline

  1. What is the importance or significance of this work?
    • SARS-COV-2 has been an increasingly dangerous and prevalent virus that has been sweeping the globe for over a year now. It originated in Asia and over the months and now year has been seen in countries across the globe. People have died, and those who survived saw side effects that have been negatively impacting their lives. There have been appearances of SARS-CoV in the past although it seems none were as serious as this seems to be. The article states that “as of July 3, 2020, 216 countries have reported COVID-19 cases, with more than 10 million confirmed cases and approximately 518,000 deaths”. Thus it is clear that it is important to try to find mutations that could impact infectivity and further impact virality and severity of dangers posed by the virus.
  2. What were the limitations in previous studies that led them to perform this work?
    • Most other work has acknowledged the variations of SARS-CoV and the possible mechanisms to explain the varying infectivity although it seems none have gone into depth regarding specific mutation and more importantly glycosylation.
  3. How did they overcome these limitations?
    • The researchers decided to investigate 80 variants and 26 glycosylation site modifications for the infectivity and reactivity to a panel of neutralizing antibodies and sera from convalescent patients.
  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 researchers investigated the biological significance of natural variants and subsequent amino acid and glycosylation changes in SARS-CoV-2. They generated 106 mutants and analyzed both their infectivity as well as their reactivity to antibodies. They found that some of the variants and N-linked glycan deleted mutants have come to evolve and pose relatively major alterations in both their infectivity and antigenicity.
  5. What were the methods used in the study?
    • The researchers began with a Site-directed mutagenesis which included the implantation of recombinant plasmid containing the gene for SARS-CoV-2. This plasmid was used as a template for site-directed mutagenesis PCR and used to transform E. coli cells. After the site-directed mutagenesis, production and titration of pseudotyped viruses was performed, in which pseudotyped viruses incorporated with spike protein from with SARS-CoV-2, variants, or mutants were constructed. Most of the cell lines used were cultured in Dulbecco’s modified Eagle medium (DMEM), including Homo Sapien kidney tissue, liver tissue, and gallbladder tissue). All expressed human ACE2. Human serum samples from 10 convalescent patients in Wuhan and Shandong were collected for the study as well.
  6. Briefly state the result shown in each of the figures and tables that you have been assigned in your group.
      • Figure 1. Illustration of Amino Acid Changes Selected for this study.This figure has 3 categories: A, B, and C. Figure A depicts variants and combined variants with D614G across the entire S gene excluding the RBD region. Figure B depicts the variants in RBD. Mutants at the 22 glycosylation sites. The groups depicted in category C are those that are induced mutation at the 22 glycosylation sites, combinations of glycosylation sites, and naturally occurring variants. The high frequency amino acid change sites are highlighted in red. The figure depicts the different Amino Acid residues undergoing mutations.
    • Figure 2. Selection of Susceptible Cell Lines. 26 cell lines were infected with the pseudotyped viruses and were diluted and analyzed. The results were obtained from three independent experiments. Part A shows results for SARS-CoV-2 and B for VSV G. Although almost all cell lines were generally susceptible to infection by VSV G pseudotyped virus, SARS-CoV-2 pseudotyped virus could efficiently infect certain cell lines including three human cell lines.
  8. What are the important implications of this work?
    • This work is important for several reasons. Besides the fact that SARS-CoV-2 is currently taking over the world and has caused an enormous outbreak of deaths, illnesses, and economic downfalls, the idea of mutations that could have greater infectivity poses an incredible threat. There have been previous generations of SARS-CoV in society and the idea of new strains being discovered with varying degrees of severity is incredibly important and should be monitored closely. The danger potential for this could be enormous.
  9. What future directions should the authors take?
    • I think the authors, having discovered the different areas of variation among SARS-CoV-2 and the mutations with their subsequent effects on infectivity, should now go to find possible solutions to terminate these strains. Especially after having declared that these newer strains are more infectious and more resistant to antibodies, it would behoove the authors to find a solution before these mere lab experiments become a reality.
  10. 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 the authors did a very good job at supporting their conclusions and showing their work. The methods section was very well detailed and included all necessary information to replicate the experiment. Further, the figures and tables were extremely well thought out and detailed and supported the writing very well. I appreciated the detailed nature of the article and the nuances it presented with regard to the mutations of the bacteria.

Conclusion

  • In this lab we were able to analyze our journal article and come forth to not only analyze its content but also the backbone of it, including publisher and surrounding information on the journal and publishing company. We further analyzed the article for its content and created our own outline of it. Lastly, we created our own journal club presentation and were able to discuss our respective figures. By doing all of this, we have been able to develop our skills in analyzing work and going through the process of picking a journal and presenting it to our peers.

Acknowledgements

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Yaniv Maddahi (talk) 08:09, 19 November 2020 (PST)

References

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