Dcartmel Week 8

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Purpose

The purpose of this assignment is to utilize different search engines to search for scientific literature and become familiar with the search tools that each search engine provides to make finding scientific articles more efficient.

Assignment

  1. Warm up exercise (announced in class).
    • I searched keywords gp120, structure, and function.
  2. Perform a search in Google Scholar.
    • My keywords were: HIV, env, structure, mutation
    1. Record the number of “hits” you found: 42,800
    2. Record the top 10 papers, this time using APA format:
      • Blish, C. A., Nguyen, M. A., & Overbaugh, J. (2008). Enhancing exposure of HIV-1 neutralization epitopes through mutations in gp41. PLoS medicine, 5(1).
      • Olsen, H. S., Nelbock, P., Cochrane, A. W., & Rosen, C. A. (1990). Secondary structure is the major determinant for interaction of HIV rev protein with RNA. Science, 247(4944), 845-848.
      • Zanini, F., & Neher, R. A. (2013). Quantifying selection against synonymous mutations in HIV-1 env evolution. Journal of virology, 87(21), 11843-11850.
      • Venkateshand, L. K., & Chinnadurai, G. (1990). Mutants in a conserved region near the carboxy-terminus of HIV-1 Rev identify functionally important residues and exhibit a dominant negative phenotype. Virology, 178(1), 327-330.
      • Boyd, D. F., Peterson, D., Haggarty, B. S., Jordan, A. P., Hogan, M. J., Goo, L., ... & Overbaugh, J. (2015). Mutations in HIV-1 envelope that enhance entry with the macaque CD4 receptor alter antibody recognition by disrupting quaternary interactions within the trimer. Journal of virology, 89(2), 894-907.
      • Bu, Z., Ye, L., Vzorov, A., Taylor, D., Compans, R. W., & Yang, C. (2004). Enhancement of immunogenicity of an HIV Env DNA vaccine by mutation of the Tyr-based endocytosis motif in the cytoplasmic domain. Virology, 328(1), 62-73.
      • Wang, C. T., & Barklis, E. (1993). Assembly, processing, and infectivity of human immunodeficiency virus type 1 gag mutants. Journal of virology, 67(7), 4264-4273.
      • Tedbury, P. R., Ablan, S. D., & Freed, E. O. (2013). Global rescue of defects in HIV-1 envelope glycoprotein incorporation: implications for matrix structure. PLoS pathogens, 9(11).
      • Kang, S. M., Quan, F. S., Huang, C., Guo, L., Ye, L., Yang, C., & Compans, R. W. (2005). Modified HIV envelope proteins with enhanced binding to neutralizing monoclonal antibodies. Virology, 331(1), 20-32.
      • Desmezieres, E., Gupta, N., Vassell, R., He, Y., Peden, K., Sirota, L., ... & Weiss, C. D. (2005). Human immunodeficiency virus (HIV) gp41 escape mutants: cross-resistance to peptide inhibitors of HIV fusion and altered receptor activation of gp120. Journal of virology, 79(8), 4774-4781.
  3. Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:
    • Kwon, E. H., Musema, G. M., Boelter, J., Townsend, S., Tshala-Katumbay, D., Kayembe, P. K., ... & Wood, C. (2020). HIV-1 subtypes and drug resistance mutations among female sex workers varied in different cities and regions of the Democratic Republic of Congo. PloS one, 15(2), e0228670.
    • Le, C. B., LiWang, P., & Colvin, M. E. (2020). In-Silico Exploration of Antiviral Lectin Griffithsin. Biophysical Journal, 118(3), 505a.
    • Antanasijevic, A., Ueda, G., Copps, J., Brouwer, P. J., Huang, D., Allen, J. D., ... & Ketas, T. J. (2020). Structural and functional evaluation of de novo-designed, two-component nanoparticle carriers for HIV Env trimer immunogens. BioRXiv.
    • Yang, Y. R., McCoy, L. E., van Gils, M. J., Andrabi, R., Turner, H. L., Yuan, M., ... & Polveroni, T. M. (2020). Autologous neutralizing antibody responses to an HIV envelope glycan hole are not easily broadened in rabbits. Journal of Virology.
    • Renner, T. (2020). Uncovering the Complexity of a Simple Retrovirus: A Study of Glycosylated Gag and Flow Virometry (Doctoral dissertation, Université d'Ottawa/University of Ottawa).
  4. Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
    • Van Duyne, R., Kuo, L. S., Pham, P., Fujii, K., & Freed, E. O. (2019). Mutations in the HIV-1 envelope glycoprotein can broadly rescue blocks at multiple steps in the virus replication cycle. Proceedings of the National Academy of Sciences, 116(18), 9040-9049.
    • Flemming, A. (2020). bnAbs for HIV: shepherding towards improbable mutations. Nature Reviews Immunology, 20(2), 71-71.
    • Dingens, A. S., Arenz, D., Weight, H., Overbaugh, J., & Bloom, J. D. (2019). An antigenic atlas of HIV-1 escape from broadly neutralizing antibodies distinguishes functional and structural epitopes. Immunity, 50(2), 520-532.
    • Tedbury, P. R., Novikova, M., Alfadhli, A., Hikichi, Y., Kagiampakis, I., KewalRamani, V. N., ... & Freed, E. O. (2019). HIV-1 matrix trimerization-impaired mutants are rescued by matrix substitutions that enhance envelope glycoprotein incorporation. Journal of Virology, 94(1).
    • Yokoyama, M., Koma, T., Kotani, O., Sato, H., Adachi, A., & Nomaguchi, M. (2019). Concomitant enhancement of HIV-1 replication potential and neutralization-resistance in concert with three adaptive mutations in Env V1/C2/C4 domains. Frontiers in microbiology, 10, 2.
  5. Filter your results using “Since 2016”, and record the top 5 papers, using APA format:
    • Weiss, C. (2017). D-111 Coordinated gp41 and gp120 mutations conferring an open conformation of Env and their consequences on Env function. Jaids Journal of Acquired Immune Deficiency Syndromes, 74, 49.
    • Van Duyne, R., Kuo, L. S., Pham, P., Fujii, K., & Freed, E. O. (2019). Mutations in the HIV-1 envelope glycoprotein can broadly rescue blocks at multiple steps in the virus replication cycle. Proceedings of the National Academy of Sciences, 116(18), 9040-9049.
    • Flemming, A. (2020). bnAbs for HIV: shepherding towards improbable mutations. Nature Reviews Immunology, 20(2), 71-71.
    • Dingens, A. S., Arenz, D., Weight, H., Overbaugh, J., & Bloom, J. D. (2019). An antigenic atlas of HIV-1 escape from broadly neutralizing antibodies distinguishes functional and structural epitopes. Immunity, 50(2), 520-532.
    • Tedbury, P. R., Novikova, M., Alfadhli, A., Hikichi, Y., Kagiampakis, I., KewalRamani, V. N., ... & Freed, E. O. (2019). HIV-1 matrix trimerization-impaired mutants are rescued by matrix substitutions that enhance envelope glycoprotein incorporation. Journal of Virology, 94(1).
  6. 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 in gp120
    • HIV gp120 mutation
    • mutations gp120
    • HIV gp120
    • structure-function mutation gp120
    • structure and function of gp120
    • structure of gp120
    • gp120
    • gp120 structure and function
    • gp120 structure function
    • mutations in the gp120 protein
    • HIV-1 gp120 protein mutation
    • gp120 mutation structure function
    • HIV gp120 function
    • Record the search terms that have now been assigned specifically to you:
      • HIV env structure mutation
  7. 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: 233
    • Record the top 10 papers (you don't need to do APA format for this):
      1. Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque CD4 and CCR5.
      2. Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody.
      3. Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope.
      4. Associating HIV-1 envelope glycoprotein structures with states on the virus observed by smFRET.
      5. Cell-cell and virus-cell fusion assay-based analyses of alanine insertion mutants in the distal α9 portion of the JRFL gp41 subunit from HIV-1.
      6. Concomitant Enhancement of HIV-1 Replication Potential and Neutralization-Resistance in Concert With Three Adaptive Mutations in Env V1/C2/C4 Domains.
      7. Structural Constraints at the Trimer Apex Stabilize the HIV-1 Envelope in a Closed, Antibody-Protected Conformation.
      8. Display of the HIV envelope protein at the yeast cell surface for immunogen development.
      9. CRISPR/Cas9 gene editing for the creation of an MGAT1-deficient CHO cell line to control HIV-1 vaccine glycosylation.
      10. Molecular mechanism of HIV-1 resistance to sifuvirtide, a clinical trial-approved membrane fusion inhibitor.
  8. Perform a title/abstract search on your assigned keywords.
    • Record the total number of hits: 43
    • Record the top 10 papers (you don't need to do APA format for this):
      1. Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope. Review
      2. Structure-Based Design of a Soluble Prefusion-Closed HIV-1 Env Trimer with Reduced CD4 Affinity and Improved Immunogenicity.
      3. HIV Vaccine Design to Target Germline Precursors of Glycan-Dependent Broadly Neutralizing Antibodies. Review
      4. HIV-1 Envelope Glycoprotein Trafficking through the Endosomal Recycling Compartment Is Required for Particle Incorporation.
      5. Structural Constraints at the Trimer Apex Stabilize the HIV-1 Envelope in a Closed, Antibody-Protected Conformation.
      6. Coevolution Analysis of HIV-1 Envelope Glycoprotein Complex.
      7. A Neutralizing Antibody Recognizing Primarily N-Linked Glycan Targets the Silent Face of the HIV Envelope.
      8. Concomitant Enhancement of HIV-1 Replication Potential and Neutralization-Resistance in Concert With Three Adaptive Mutations in Env V1/C2/C4 Domains.
      9. Conformational properties of the third variable loop of HIV-1AD8 envelope glycoprotein in the liganded conditions.
      10. Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth.
  9. Add the word “Review” to any articles that are review articles that you listed in question 8.
  10. 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. Author chosen : Eric O. Freed
    • Do you find any new articles that you did not find before on PubMed?
      • Yes there were new articles that I did not find on PubMed.
    • List up to 5 new articles that were found on the author name search:
      1. Freed, E. O. (1998). HIV-1 gag proteins: diverse functions in the virus life cycle. Virology, 251(1), 1-15.
      2. Van Duyne, R., Kuo, L. S., Pham, P., Fujii, K., & Freed, E. O. (2019). Mutations in the HIV-1 envelope glycoprotein can broadly rescue blocks at multiple steps in the virus replication cycle. Proceedings of the National Academy of Sciences, 116(18), 9040-9049.
      3. Freed, E. O. (2001). HIV-1 replication. Somatic cell and molecular genetics, 26(1-6), 13-33.
      4. Ono, A., & Freed, E. O. (2001). Plasma membrane rafts play a critical role in HIV-1 assembly and release. Proceedings of the National Academy of Sciences, 98(24), 13925-13930.
      5. Li, F., Goila-Gaur, R., Salzwedel, K., Kilgore, N. R., Reddick, M., Matallana, C., ... & Allaway, G. P. (2003). PA-457: a potent HIV inhibitor that disrupts core condensation by targeting a late step in Gag processing. Proceedings of the National Academy of Sciences, 100(23), 13555-13560.
  11. Now access the Web of Science database. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits: 215
    • Record the top 10 papers (you don't need to use APA format for this):
      1. Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody
      2. Refolding Dynamics of gp41 from Pre-fusion to Pre-hairpin States during HIV-1 Entry
      3. HIV-1 Matrix Trimerization-Impaired Mutants Are Rescued by Matrix Substitutions That Enhance Envelope Glycoprotein Incorporation
      4. Cooperation between somatic mutation and germline-encoded residues enables antibody recognition of HIV-1 envelope glycans
      5. Replication of HIV-1 envelope protein cytoplasmic domain variants in permissive and restrictive cells
      6. Harnessing Avidity: Quantifying the Entropic and Energetic Effects of Linker Length and Rigidity for Multivalent Binding of Antibodies to HIV-1
      7. Topological analysis of the gp41 MPER on lipid bilayers relevant to the metastable HIV-1 envelope prefusion state
      8. A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance
      9. Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies
      10. Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope
  12. Articles added to class page:
    • Blish, C. A., Nguyen, M. A., & Overbaugh, J. (2008). Enhancing exposure of HIV-1 neutralization epitopes through mutations in gp41. PLoS medicine, 5(1).
    • Zanini, F., & Neher, R. A. (2013). Quantifying selection against synonymous mutations in HIV-1 env evolution. Journal of virology, 87(21), 11843-11850.
  13. Citation of article in APA format
    • Zanini, F., & Neher, R. A. (2013). Quantifying selection against synonymous mutations in HIV-1 env evolution. Journal of virology, 87(21), 11843-11850.
    • This article has 48 cited references.
    • This article has been cited by 24 articles.
  14. Merits of using Google Scholar, PubMed, and Web of science.
    • Google Scholar advantages
      1. One advantage is that this search engine provides a wide range of results from the keywords that are entered.
      2. One advantage is that this search engine allows you to use a citation button that creates a citation for the particular articles you find.
    • Google Scholar disadvantages
      1. Some of the articles that are provided from a search may not be available without a form of subscription to the specific publishers/journal.
      2. There is no way to search for only peer reviewed articles which forces individuals to make determinations concerning an articles credibility.
    • PubMed advantages
      1. One advantage of PubMed is that on the abstract page of an article, there is a provided list of related articles that makes it easier to find similar papers.
      2. One advantage of PubMed is that there are more filters when searching such as the type of article and the text availability.
    • PubMed disadvantages
      1. One disadvantage of PubMed is that there is no built-in feature that allows you to cite the articles you are using in different formats.
      2. One disadvantage of PubMed is that you are provided with fewer results than other search engines such as Google Scholar.
    • Web of Science advantages
      1. One advantage of Web of Science is that keywords from your search are highlighted in each of the article's titles, which might make finding relevant articles faster for the user.
      2. One advantage of Web of Science is that there is an additional search bar that allows the user to refine the results that they already have from an original keyword search.
    • Web of Science disadvantages
      1. One disadvantage of Web of Science is that it takes longer than other search engines to provide results to a keyword search.
      2. One disadvantage of Web of Science is that it is expensive for users to use and is only readily available to individuals associated with universities or other institutions that pay for the service.
  15. The choice of keywords has a large impact on the results that are provided. For example, using more than one keyword can refine your search results and can provide you with more relevant articles. Using specific keywords rather than broad terms can also provide you with better results, for example in this assignment the term env was used instead of just the word gene, which is more specific for the topic that we are researching.
  16. Citation of assigned article in APA format with DOI:
  17. Evaluating the source--the journal
    1. Who is the publisher of the journal? The American Society for Microbiology.
    2. Is the publisher for-profit or non-profit? For-profit
    3. Is the publisher a scientific society? Yes, the publisher is a scientific society.
    4. Does the publisher belong to the Open Access Publishers Association? No, this publisher does not belong 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? Since 1967
    7. Are the articles in this journal peer reviewed? Yes, the articles in this journal are peer reviewed.
    8. Provide a link to the scientific advisory board/editorial board of the journal: https://jvi.asm.org/content/board-editors
    9. What is the journal impact factor? 4.324
  18. Evaluating the source--the article
    1. Is the article a review or a primary research article? Primary research article.
    2. On what date was this article submitted? June 6th, 2013.
    3. On what date was the article accepted? August 20th, 2013.
    4. Did the article undergo any revisions before acceptance? No, this article did not undergo any revisions before acceptance.
    5. When was the article published? October 3rd, 2013.
    6. What is the approximate elapsed time between submission and publication? Four months.
    7. What are the institutions in which the authors are affiliated? The authors Fabio Zanini and Richard A. Neher are both affiliated with the Evolutionary Dynamics and Biophysics group and Max Planck Institute for Developmental Biology.
    8. Yes, both of these authors have published other articles on this subject. I found this out by doing an author search for both of these individuals, which reveled that they have published papers that are related to this topic.
    9. Is there a conflict of interest for any of the authors? There does not appear to be a conflict of interest between the two authors of this article because they both are affiliated with the same institution and both have published papers that have investigated topics similar to this article.
    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.
      • In terms of the structure-function relationship of mutations in the HIV-1 gp120 protein, this article found that synonymous mutations that were located around gp120 loops in RNA were more likely to be lost than synchronous mutations that were located elsewhere on RNA strands.This observation of selection against synonymous mutations showed that this process slowed down the rate of evolution of the HIV-1 protein.
    11. Make a recommendation--based on the information you have gathered, should we do a journal club on this article? Why or why not?
      • Based on the information I have gathered about this article, I think that it would be worthwhile to do a journal club on this article because it investigated how synonymous mutations on the HIV-1 protein relate to the rate of evolution of the protein as a whole and I think that this is very relevant to the topic of the original paper by Markham et al.

Scientific Conclusion

What I learned from completing this exercise was that there are a lot more resources available that can be used to find scientific literature. Before this exercise, I thought that Google Scholar was one of the only search engines that could be used to find scientific literature, however after completing this exercise, I learned that there is also PubMed and Web of Science, each having their own benefits separate from Google Scholar. An important concept that I learned through this assignment was that other search engines can provide more efficient methods to finding the most relevant scientific literature for the topics that you are researching.

Acknowledgements

I worked with my homework partner Jack P. Menzagopian to complete this assignment. We texted each other on 3/25/2020 to discuss the pros and cons of using the different search engines.

I copied and modified the Week 8 assignment page.

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

Dcartmel (talk) 18:19, 25 March 2020 (PDT)

References

OpenWetWare. (2020). BIOL368/S20:Week 8. Retrieved March 25, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_8.

Zanini, F., & Neher, R. A. (2013). Quantifying selection against synonymous mutations in HIV-1 env evolution. Journal of virology, 87(21), 11843-11850. Retrieved March 25, 2020 from https://jvi.asm.org/content/87/21/11843.short.

American Society for Microbiology. (2020). Journal of Virology. Retrieved March 25, 2020 from https://jvi.asm.org/.

Google Scholar. (2020). Google Scholar. Retrieved on March 25, 2020, from https://scholar.google.com/.

PubMed. (2020). PubMed. Retrieved on March 25, 2020, from http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib.

Web of Science. (2020). Web of Science. Retrieved on March 25, 2020. from http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS.

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