Mking44 Week 8

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Assignments

Individual Journal Entries

Class Journal Entries

Purpose

The purpose of this week's assignment was to compare several search engine and databases like Google Scholar, Web of Science, and PubMed in order to test different combinations of keywords relating to structure and mutations of HIV-1 gp120 protein. This will allow the student to find a relevant article on the structure-function of HIV-1 gp120 protein, and investigate the article as well as the source, in order to determine if it is relevant to one's own research project.

Methods and Results

  • Chosen keywords to search: HIV-1 gp120 structure variation
  • The following procedure was found on Week 8 Assignment. I provided answers to the steps and questions provided.

Google Scholar

  1. Perform a search in Google Scholar .
    1. Record the number of “hits” you found: about 28,500 results
    2. Record the top 10 papers, this time using APA format:
      • Fouchier, R. A., Groenink, M. A. R. T. I. J. N., Kootstra, N. A., Tersmette, M. A. T. T. H. I. J. S., Huisman, H. G., Miedema, F. R. A. N. K., & Schuitemaker, H. A. N. N. E. K. E. (1992). Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. Journal of virology, 66(5), 3183-3187.
      • Kwong, P. D., Wyatt, R., Majeed, S., Robinson, J., Sweet, R. W., Sodroski, J., & Hendrickson, W. A. (2000). Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Structure, 8(12), 1329-1339.
      • Hoffman, N. G., Seillier-Moiseiwitsch, F., Ahn, J., Walker, J. M., & Swanstrom, R. (2002). Variability in the human immunodeficiency virus type 1 gp120 Env protein linked to phenotype-associated changes in the V3 loop. Journal of virology, 76(8), 3852-3864.
      • Huang, C. C., Tang, M., Zhang, M. Y., Majeed, S., Montabana, E., Stanfield, R. L., ... & Wyatt, R. (2005). Structure of a V3-containing HIV-1 gp120 core. Science, 310(5750), 1025-1028.
      • Zhou, T., Xu, L., Dey, B., Hessell, A. J., Van Ryk, D., Xiang, S. H., ... & Burton, D. R. (2007). Structural definition of a conserved neutralization epitope on HIV-1 gp120. Nature, 445(7129), 732-737.
      • Jiang, X., Burke, V., Totrov, M., Williams, C., Cardozo, T., Gorny, M. K., ... & Kong, X. P. (2010). Conserved structural elements in the V3 crown of HIV-1 gp120. Nature structural & molecular biology, 17(8), 955.
      • Liu, J., Bartesaghi, A., Borgnia, M. J., Sapiro, G., & Subramaniam, S. (2008). Molecular architecture of native HIV-1 gp120 trimers. Nature, 455(7209), 109-113.
      • Rizzuto, C. D., Wyatt, R., Hernández-Ramos, N., Sun, Y., Kwong, P. D., Hendrickson, W. A., & Sodroski, J. (1998). A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding. Science, 280(5371), 1949-1953.
      • McLellan, J. S., Pancera, M., Carrico, C., Gorman, J., Julien, J. P., Khayat, R., ... & O’Dell, S. (2011). Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9. Nature, 480(7377), 336-343.
      • Zhou, T., Georgiev, I., Wu, X., Yang, Z. Y., Dai, K., Finzi, A., ... & Yang, Y. (2010). Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01. Science, 329(5993), 811-817.
  2. Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:
    • Verma, A., Schmidt, B. A., Elizaldi, S. R., Nguyen, N. K., Walter, K. A., Beck, Z., ... & Matyas, G. R. (2020). Impact of Th1 CD4 Follicular Helper T Cell Skewing on Antibody Responses to an HIV-1 Vaccine in Rhesus Macaques. Journal of Virology, 94(6).
    • Sant, A. J. (2019). Descripción general del reconocimiento de los linfocitos T: hacer que los microbios patógenos sean visibles para el sistema inmunitario. Inmunología Clínica: Principios Y Práctica, 93.
    • Schaeringer, K., Maxeiner, S., Schalla, C., Ruetten, S., Zenke, M., & Sechi, A. (2020). LSP1-myosin1e bi-molecular complex regulates focal adhesion dynamics and cell migration. bioRxiv.
    • Magadán, S. (2020). Adaptive Immune Receptor Repertoires, an overview of this exciting field. Immunology Letters.
    • Huang, D., Abbott, R. K., Havenar-Daughton, C., Skog, P., Al-Kolla, R., Groschel, B., ... & Volpi, S. A. (2020). B cells expressing authentic naive human VRC01-class BCRs can be primed and recruited to germinal centers in multiple independent mouse models. bioRxiv.
  3. Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
    • Lamers, S. L., Fogel, G. B., Nolan, D. J., Barbier, A. E., Rose, R., Singer, E. J., ... & McGrath, M. S. (2019). Emerging patterns in HIV-1 gp120 variable domains in anatomical tissues in the absence of a plasma viral load. AIDS research and human retroviruses, 35(6), 588-596.
    • Palmer, J., & Poon, A. F. (2019). Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes. Virus evolution, 5(2), vez022.
    • Vangala, R., Sivan, S. K., Peddi, S. R., & Manga, V. (2020). Computational design, synthesis and evaluation of new sulphonamide derivatives targeting HIV-1 gp120. Journal of Computer-Aided Molecular Design, 34(1), 39-54.
    • Kumar, S., Sarkar, A., Pugach, P., Sanders, R. W., Moore, J. P., Ward, A. B., & Wilson, I. A. (2019). Capturing the inherent structural dynamics of the HIV-1 envelope glycoprotein fusion peptide. Nature communications, 10(1), 1-10.
    • Qiu, T. (2019). Understanding Dynamic Structural Variations in HIV-1 Envelope Glycoprotein Gp120 (Doctoral dissertation, State University of New York at Stony Brook).
  4. Filter your results using “Since 2016”, and record the top 5 papers, using APA format:
    • Lamers, S. L., Fogel, G. B., Nolan, D. J., Barbier, A. E., Rose, R., Singer, E. J., ... & McGrath, M. S. (2019). Emerging patterns in HIV-1 gp120 variable domains in anatomical tissues in the absence of a plasma viral load. AIDS research and human retroviruses, 35(6), 588-596.
    • Palmer, J., & Poon, A. F. (2019). Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes. Virus evolution, 5(2), vez022.
    • Rathore, U. (2018). HIV-1 immunogen design: Envelope protein minimization, stabilization and glycan removal (Doctoral dissertation).
    • Munro, J. B., & Lee, K. K. (2018). Probing structural variation and dynamics in the HIV-1 Env fusion glycoprotein. Current HIV research, 16(1), 5-12.
    • Vangala, R., Sivan, S. K., Peddi, S. R., & Manga, V. (2020). Computational design, synthesis and evaluation of new sulphonamide derivatives targeting HIV-1 gp120. Journal of Computer-Aided Molecular Design, 34(1), 39-54.
  5. We will now make a list of the search terms that were used by each student in the class. Record the list written on the board here:
    • mutations gp120
    • HIV gp120
    • structure-function mutation gp120
    • structure and function of gp120
    • structure of gp120
    • gp120 structure function
    • mutations in the gp120 protein
    • HIV-1 gp120 protein mutation
    • gp120 mutation structure function
    • mutations in gp120
    • HIV gp120 mutations
    • HIV gp120 function
    • gp120
    • gp120 structure and function
    • Record the search terms that have now been assigned specifically to you:
      • HIV-1 gp120 structure variation

PubMed

  1. Now access the PubMed database by using the LMU-specific link. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits: 102
    • Record the top 10 papers (you don't need to do APA format for this):
      1. The lipid membrane of HIV-1 stabilizes the viral envelope glycoproteins and modulates their sensitivity to antibody neutralization.
      2. Humoral Response to the HIV-1 Envelope V2 Region in a Thai Early Acute Infection Cohort.
      3. Signal peptide of HIV envelope protein impacts glycosylation and antigenicity of gp120.
      4. Protein structural disorder of the envelope V3 loop contributes to the switch in human immunodeficiency virus type 1 cell tropism.
      5. Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model.
      6. The utility of protein structure as a predictor of site-wise dN/dS varies widely among HIV-1 proteins.
      7. HIV Subtypes B and C gp120 and Methamphetamine Interaction: Dopaminergic System Implicates Differential Neuronal Toxicity.
      8. Negatively charged glyconanoparticles modulate and stabilize the secondary structures of a gp120 V3 loop peptide: toward fully synthetic HIV vaccine candidates.
      9. Structure and immune recognition of trimeric pre-fusion HIV-1 Env.
      10. Functional analyses reveal extensive RRE plasticity in primary HIV-1 sequences selected under selective pressure.
  2. Perform a title/abstract search on your assigned keywords.
    • Record the total number of hits: 0
    • Record the top 10 papers (you don't need to do APA format for this):
      1. N/A
  3. Add the word “Review” to any articles that are review articles that you listed in question 8.
    • N/A
  4. Pick an author that shows up in multiple citations (if there isn’t one, just pick a last author from one of the papers) and perform an author search on the name.
    • Haim H.
    • Do you find any new articles that you did not find before on PubMed?
      1. Yes
    • List up to 5 new articles that were found on the author name search:
      1. Phenotypic and immunologic comparison of clade B transmitted/founder and chronic HIV-1 envelope glycoproteins.
      2. Contribution of intrinsic reactivity of the HIV-1 envelope glycoproteins to CD4-independent infection and global inhibitor sensitivity.
      3. Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer.
      4. Modeling virus- and antibody-specific factors to predict human immunodeficiency virus neutralization efficiency.
      5. Induction of a Tier-1-Like Phenotype in Diverse Tier-2 Isolates by Agents That Guide HIV-1 Env to Perturbation-Sensitive, Nonnative States.

Web of Science

  1. Now access the Web of Science database. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits: 79
    • Record the top 10 papers (you don't need to use APA format for this):
      1. The lipid membrane of HIV-1 stabilizes the viral envelope glycoproteins and modulates their sensitivity to antibody neutralization
      2. Strain-Dependent Activation and Inhibition of Human Immunodeficiency Virus Entry by a Specific PF-68742 Stereoisomer
      3. Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies
      4. Signal peptide of HIV envelope protein impacts glycosylation and antigenicity of gp120
      5. Insights into the molecular mechanism underlying CD4-dependency and neutralization sensitivity of HIV-1: a comparative molecular dynamics study on gp120s from isolates with different phenotypes
      6. Protein structural disorder of the envelope V3 loop contributes to the switch in human immunodeficiency virus type 1 cell tropism
      7. Chemical optimization of macrocyclic HIV-1 inactivators for improving potency and increasing the structural diversity at the triazole ring
      8. Determinants of HIV-1 CD4-Independent Brain Adaptation
      9. Antigenicity-defined conformations of an extremely neutralization-resistant HIV-1 envelope spike
      10. Evidence of Divergent Amino Acid Usage in Comparative Analyses of R5-and X4-Associated HIV-1 Vpr Sequences

Shared Bibliography

  • Class bibliography was created (Shared Bibliography), and 3 articles were cited in APA format
    1. Rizzuto, C. D., Wyatt, R., Hernández-Ramos, N., Sun, Y., Kwong, P. D., Hendrickson, W. A., & Sodroski, J. (1998). A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding. Science (New York, N.Y.), 280(5371), 1949–1953. https://doi.org/10.1126/science.280.5371.1949
    2. Fouchier, R. A., Groenink, M., Kootstra, N. A., Tersmette, M., Huisman, H. G., Miedema, F., & Schuitemaker, H. (1992). Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. Journal of virology, 66(5), 3183–3187. Mking44 (talk) 15:07, 5 March 2020 (PST)
    3. O'Connell, R. J., Kim, J. H., & Excler, J. L. (2014). The HIV-1 gp120 V1V2 loop: structure, function and importance for vaccine development. Expert review of vaccines, 13(12), 1489–1500. https://doi.org/10.1586/14760584.2014.951335 Mking44 (talk) 15:11, 5 March 2020 (PST)

Assigned Article with Questions

  1. Selected Article in APA format:
    • Rizzuto, C. D., Wyatt, R., Hernández-Ramos, N., Sun, Y., Kwong, P. D., Hendrickson, W. A., & Sodroski, J. (1998). A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding. Science (New York, N.Y.), 280(5371), 1949–1953. https://doi.org/10.1126/science.280.5371.1949
  2. In Web of Science, search for the specific article that you have been assigned.
    • How many cited references does that article have?
      • 49
    • How many articles have cited the article you have been assigned?
      • 716
  3. What are the relative merits of searching with Google Scholar, PubMed, and Web of Science? Name two advantages and disadvantages for each.
    • Google Scholar: quick to access, organized, don't need to be very skilled or knowledgeable to use, can cite quickly
    • Google Scholar: can't see directly which is a review and which is a clinical trial, not everything is truly scholarly
    • PubMed: free to access, lots of ways to modify search
    • PubMed: not as many articles since it restricts it to pubmed central, need to explore for a little first in order to use the database properly
    • Web of Science: organized, more detailed and narrow searches
    • Web of Science: not as good as keyword searching, have to pay for it
  4. What impact does choice of keywords have on your results?
    • If you put the word 'and' between two keywords, it will only pull up results that include both words. Also, the more specific/ more keywords you have, the more specific the result will be and might not get as many results; this is especially observed in Web of Science and PubMed.
  5. Now we will begin to evaluate your assigned article in three areas availability, the journal, and the article metadata.
    • Rizzuto, C. D., Wyatt, R., Hernández-Ramos, N., Sun, Y., Kwong, P. D., Hendrickson, W. A., & Sodroski, J. (1998). A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding. Science (New York, N.Y.), 280(5371), 1949–1953. https://doi.org/10.1126/science.280.5371.1949
    1. PubMed: https://pubmed.ncbi.nlm.nih.gov/9632396
    2. PubMed Central: N/A
    3. Full Text Link: https://science.sciencemag.org/content/280/5371/1949.long
    4. PDF: https://science.sciencemag.org/content/280/5371/1949.full.pdf
    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.
      • 1998 The Authors
    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.
        • It 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.
        • No, it is not free after a certain period of time.
      • 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, LMU pays a fee for Science Magazine.
      • 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.
        • N/A
      • 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.
        • It is both in print and online.

Evaluating the source--the journal

  1. Who is the publisher of the journal?
    • The American Association for the Advancement of Science
  2. Is the publisher for-profit or non-profit?
    • Non-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)
    • Yes it is a scientific society.
  4. Does the publisher belong to the Open Access Publishers Association?
    • Yes it belongs to the Open Access Publishers Association.
  5. What country is the journal published in?
    • United States
  6. How long has the journal been in operation? (e.g., browse the archive for the earliest article published)
    • July 3rd, 1880
  7. Are articles in this journal peer-reviewed?
    • They 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)?

Evaluating the source--the article

  1. Is the article a review or primary research article?
    • It is primary research article
  2. On what date was the article submitted?
    • May 15, 1998
  3. On what date was the article accepted?
    • May 27, 1998
  4. Did the article undergo any revisions before acceptance?
    • There were no revisions before acceptance
  5. When was the article published?
    • Jun 19, 1998
  6. What is the approximate elapsed time between submission and publication?
    • About a month
  7. What are the institutions with which the authors are affiliated?
    • Cancer Institute, Department of Pathology as well as Department of Immunology and Infectious Diseases , Harvard Medical School
    • Howard Hughes Medical Institute, Columbia University, New York, NY
  8. Have the authors published other articles on this subject? (How will you find this out?)
    • By going onto to the PubMed article link provided above, and clicking on the author's name. I found that they have published four other papers on the subject of HIV
      • Mutagenic stabilization and/or disruption of a CD4-bound state reveals distinct conformations of the human immunodeficiency virus type 1 gp120 envelope glycoprotein
      • Fine definition of a conserved CCR5-binding region on the human immunodeficiency virus type 1 glycoprotein 120
      • A V3 loop-dependent gp120 element disrupted by CD4 binding stabilizes the human immunodeficiency virus envelope glycoprotein trimer
      • Contribution of virion ICAM-1 to human immunodeficiency virus infectivity and sensitivity to neutralization
  9. Is there a conflict of interest for any of the authors?
    • There is no conflict of interest for any of the authors.
  10. Read the abstract. Write 1-2 sentences about the relevance of this article to understanding the structure-function relationship of mutations in the HIV-1 gp120 protein.
    • By using different mutants of the gp120 protein, the authors of this paper discovered a highly conserved gp120 structure that is adjacent to the V3 loop as well as contains neutralization antibodies. This structure can be used as a drug target or a starting point for preventing HIV diseases.
  11. Make a recommendation--based on the information you have gathered, should we do a journal club on this article? Why or why not?
    • I think the article has a potential spot for being used as a journal club article; it seems very interesting, not too complex as a paper, and cited by many people. However, I also think it is too old to use (1998), since Markham et. al was written in 1998 as well. I think it would be more interesting to hear from a more recent paper about HIV-1.

Scientific Conclusion

By performing this exercise, I learned about how to utilize different search engines and databases, and being aware of the pros and cons of each one. For example, it is good to recognize that Google Scholar is easy to access and will give you a lot of results, but these articles aren't necessarily scholarly. Therefore, PubMed and Web of Science can be good alternatives to find scholarly articles. I had previous knowledge on how to do better searches in these databases, but I never tried the same search on different engines, or compared different combinations of keywords. It's interesting how some of the class got 32,000 results, but some people only got half that, just by the change of one or two words. Therefore, performing multiple searches using different combinations of words is important to find the articles that you need.

Acknowledgments

  • I copied and modified the protocol from Week 8 for this assignment.
  • I asked Maya questions about some of the protocol.
  • I checked with Nathan about the answers to some of the journal questions since we both used an article from Science Magazine.
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Mking44 (talk) 07:05, 7 March 2020 (PST)

References

  1. OpenWetWare. (2020). BIOL368/S20:Week 8. Retrieved March 7, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_8
  2. Google Scholar. (2020). Retrieved March 7, 2020, from https://scholar.google.com/
  3. PubMed - NCBI. (2020). Retrieved March 7, 2020, from https://www.ncbi.nlm.nih.gov/pubmed
  4. Web of Science Core Collection. (2020). Retrieved March 7, 2020, from http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS
  5. Rizzuto, C. D., Wyatt, R., Hernández-Ramos, N., Sun, Y., Kwong, P. D., Hendrickson, W. A., & Sodroski, J. (1998). A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding. Science (New York, N.Y.), 280(5371), 1949–1953. https://doi.org/10.1126/science.280.5371.1949
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