Mpaniag1 Week 8

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Purpose

The purpose of this week's lab is to compare and analyze the strengths and weaknesses of different scholarly search engines and using the references found to study the relationship between structure and function of the HIV virus.

Methods and Results

Google Scholar

  • Open Google Scholar[1]
  • Maya's Phrase-HIV-1 gp120 structure mutation
  • Number of Hits-about 32,500 results
  • Top 10 Papers when sorted by relevance
    • Ogert, R. A., Ba, L., Hou, Y., Buontempo, C., Qiu, P., Duca, J., ... & Howe, J. A. (2009). Structure-function analysis of human immunodeficiency virus type 1 gp120 amino acid mutations associated with resistance to the CCR5 coreceptor antagonist vicriviroc. Journal of virology, 83(23), 12151-12163.
    • Ahmed, F. K., Clark, B. E., Burton, D. R., & Pantophlet, R. (2012). An engineered mutant of HIV-1 gp120 formulated with adjuvant Quil A promotes elicitation of antibody responses overlapping the CD4-binding site. Vaccine, 30(5), 922-930.
    • Yuan, Y., Maeda, Y., Terasawa, H., Monde, K., Harada, S., & Yusa, K. (2011). A combination of polymorphic mutations in V3 loop of HIV-1 gp120 can confer noncompetitive resistance to maraviroc. Virology, 413(2), 293-299.
    • Liu, S. Q., Liu, C. Q., & Fu, Y. X. (2007). Molecular motions in HIV-1 gp120 mutants reveal their preferences for different conformations. Journal of Molecular Graphics and Modelling, 26(1), 306-318.
    • Clayton, L. K., Sieh, M., Pious, D. A., & Reinherz, E. L. (1989). Identification of human CD4 residues affecting class II MHC versus HIV-1 gp120 binding. Nature, 339(6225), 548-551.
    • Suphaphiphat, P., Essex, M., & Lee, T. H. (2007). Mutations in the V3 stem versus the V3 crown and C4 region have different effects on the binding and fusion steps of human immunodeficiency virus type 1 gp120 interaction with the CCR5 coreceptor. Virology, 360(1), 182-190.
    • Doria-Rose, N. A., Georgiev, I., O'Dell, S., Chuang, G. Y., Staupe, R. P., McLellan, J. S., ... & Burton, D. R. (2012). A short segment of the HIV-1 gp120 V1/V2 region is a major determinant of resistance to V1/V2 neutralizing antibodies. Journal of virology, 86(15), 8319-8323.
    • 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.
    • Julien, J. P., Sok, D., Khayat, R., Lee, J. H., Doores, K. J., Walker, L. M., ... & Katpally, U. (2013). Broadly neutralizing antibody PGT121 allosterically modulates CD4 binding via recognition of the HIV-1 gp120 V3 base and multiple surrounding glycans. PLoS pathogens, 9(5).
    • Auwerx, J., François, K. O., Covens, K., Van Laethem, K., & Balzarini, J. (2008). Glycan deletions in the HIV-1 gp120 V1/V2 domain compromise viral infectivity, sensitize the mutant virus strains to carbohydrate-binding agents and represent a specific target for therapeutic intervention. Virology, 382(1), 10-19.
  • Top 5 Papers when sorted by date
    • Li, X., Liu, Q., Sheng, T., Liu, J., & Wang, X. Pyridin-2 (1 H)-ones as HIV-1 NNRTIs: a combinatorial optimization strategy.
    • Stejskal, L., Lees, W. D., Moss, D. S., Palor, M., Bingham, R. J., Shepherd, A. J., & Grove, J. (2020). Flexibility and intrinsic disorder are conserved features of hepatitis C virus E2 glycoprotein. PLOS Computational Biology, 16(2), e1007710.
    • Paula, T. P. D. Avaliação do impacto da galectina-1 sobre a infecção experimental por vírus Zika (Doctoral dissertation, Universidade de São Paulo).
    • Philipson, B., & Milone, M. C. (2020). T Cell Engineering and the Rise of CAR-T Cell Therapies. In Second Generation Cell and Gene-based Therapies (pp. 69-90). Academic Press.
    • Dick, A., & Cocklin, S. (2020). Bioisosteric Replacement as a Tool in Anti-HIV Drug Design. Pharmaceuticals, 13(3), 36.
  • Top 5 Papers when filtered using "Since 2019"
    • Gawron, M. A., Duval, M., Carbone, C., Jaiswal, S., Wallace, A., Martin, J. C., ... & Luban, J. (2019). Human Anti–HIV-1 gp120 Monoclonal Antibodies with Neutralizing Activity Cloned from Humanized Mice Infected with HIV-1. The Journal of Immunology, 202(3), 799-804.
    • Zhuang, M., Vassell, R., Yuan, C., Keller, P. W., Ling, H., Wang, W., & Weiss, C. D. (2019). Mutations that increase the stability of the postfusion gp41 conformation of the HIV-1 envelope glycoprotein are selected by both an X4 and R5 HIV-1 virus to escape fusion inhibitors corresponding to heptad repeat 1 of gp41, but the gp120 adaptive mutations differ between the two viruses. Journal of virology, 93(11), e00142-19.
    • 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.
    • Yuan, C., Wang, J. Y., Zhao, H. J., Li, Y., Li, D., Ling, H., & Zhuang, M. (2019). Mutations of Glu560 within HIV-1 Envelope Glycoprotein N-terminal heptad repeat region contribute to resistance to peptide inhibitors of virus entry. Retrovirology, 16(1), 1-11.
    • Henderson, R., Watts, B. E., Ergin, H. N., Anasti, K., Parks, R., Xia, S. M., ... & Wiehe, K. (2019). Selection of immunoglobulin elbow region mutations impacts interdomain conformational flexibility in HIV-1 broadly neutralizing antibodies. Nature communications, 10(1), 1-14.
  • Top 5 Papers when filtered using "Since 2016"
    • Chan, K. W., Pan, R., Costa, M., Gorny, M. K., Wang, S., Lu, S., & Kong, X. P. (2018). Structural comparison of human anti-HIV-1 gp120 V3 monoclonal antibodies of the same gene usage induced by vaccination and chronic infection. Journal of virology, 92(18), e00641-18.
    • Gawron, M. A., Duval, M., Carbone, C., Jaiswal, S., Wallace, A., Martin, J. C., ... & Luban, J. (2019). Human Anti–HIV-1 gp120 Monoclonal Antibodies with Neutralizing Activity Cloned from Humanized Mice Infected with HIV-1. The Journal of Immunology, 202(3), 799-804.
    • Zhuang, M., Vassell, R., Yuan, C., Keller, P. W., Ling, H., Wang, W., & Weiss, C. D. (2019). Mutations that increase the stability of the postfusion gp41 conformation of the HIV-1 envelope glycoprotein are selected by both an X4 and R5 HIV-1 virus to escape fusion inhibitors corresponding to heptad repeat 1 of gp41, but the gp120 adaptive mutations differ between the two viruses. Journal of virology, 93(11), e00142-19.
    • Rathore, U., Purwar, M., Vignesh, V. S., Das, R., Kumar, A. A., Bhattacharyya, S., ... & La Branche, C. C. (2018). Bacterially expressed HIV-1 gp120 outer-domain fragment immunogens with improved stability and affinity for CD4-binding site neutralizing antibodies. Journal of Biological Chemistry, 293(39), 15002-15020.
    • Tam, K., Schultz, M., Reyes-Robles, T., Vanwalscappel, B., Horton, J., Alonzo, F., ... & Torres, V. J. (2016). Staphylococcus aureus leukocidin LukED and HIV-1 gp120 target different sequence determinants on CCR5. MBio, 7(6), e02024-16.
  • Phrases from the class
    • 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
    • Mutation in gp120
    • HIV gp120 mutation

PubMed

  • Open PubMed[2]
  • Number of Hits-225 results
  • Top 10 Papers
    • Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque CD4 and CCR5.
    • Characterization of resistance to a potent D-peptide HIV entry inhibitor.
    • Griffithsin Retains Anti-HIV-1 Potency with Changes in gp120 Glycosylation and Complements Broadly Neutralizing Antibodies PGT121 and PGT126.
    • Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope
    • Concomitant Enhancement of HIV-1 Replication Potential and Neutralization-Resistance in Concert With Three Adaptive Mutations in Env V1/C2/C4 Domains.
    • Systematic mutational analysis of human neutrophil α-defensin HNP4.
    • Human Anti-HIV-1 gp120 Monoclonal Antibodies with Neutralizing Activity Cloned from Humanized Mice Infected with HIV-1.
    • Structural Constraints at the Trimer Apex Stabilize the HIV-1 Envelope in a Closed, Antibody-Protected Conformation.
    • Display of the HIV envelope protein at the yeast cell surface for immunogen development.
    • CRISPR/Cas9 gene editing for the creation of an MGAT1-deficient CHO cell line to control HIV-1 vaccine glycosylation.
  • Top 10 Papers when you perform a title abstract search
    • NO results were available
  • Results from Review search
    • NO results were available
  • Author Search-Overbaugh J
    • Yes, I found new papers when I performed a specific author search.
      • Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque CD4 and CCR5.
      • Diversity and function of maternal HIV-1-specific antibodies at the time of vertical transmission.
      • Dynamics of HIV DNA reservoir seeding in a cohort of superinfected Kenyan women.
      • Schistosomiasis was not associated with higher HIV-1 plasma or genital set point viral loads among HIV seroconverters from four cohort studies.
      • Virological failure in children living with HIV on antiretroviral therapy: correlates and predictive value of clinical measurements and CD4 cell count.

Web of Science

  • Open Web of Science[3]
  • Number of Hits-230 results
  • Top 10 Papers
    • The Genetic Diversity of HIV-1 Quasispecies Within Primary Infected Individuals
    • Refolding Dynamics of gp41 from Pre-fusion to Pre-hairpin States during HIV-1 Entry
    • Griffithsin Retains Anti-HIV-1 Potency with Changes in gp120 Glycosylation and Complements Broadly Neutralizing Antibodies PGT121 and PGT126
    • Topological analysis of the gp41 MPER on lipid bilayers relevant to the metastable HIV-1 envelope prefusion state
    • Characterization of resistance to a potent d-peptide HIV entry inhibitor
    • Conformational Engineering of HIV-1 Env Based on Mutational Tolerance in the CD4 and PG16 Bound States
    • Systematic mutational analysis of human neutrophil alpha-defensin HNP4
    • Relative Binding Affinity Prediction of Charge-Changing Sequence Mutations with FEP in Protein-Protein Interfaces
    • Identification of a Helical Segment within the Intrinsically Disordered Region of the PCSK9 Prodomain
    • Human Anti-HIV-1 gp120 Monoclonal Antibodies with Neutralizing Activity Cloned from Humanized Mice Infected with HIV-1

Specific Article Assignment

  • Specific Article-Ogert, R. A., Ba, L., Hou, Y., Buontempo, C., Qiu, P., Duca, J., ... & Howe, J. A. (2009). Structure-function analysis of human immunodeficiency virus type 1 gp120 amino acid mutations associated with resistance to the CCR5 coreceptor antagonist vicriviroc. Journal of virology, 83(23), 12151-12163. DOI: 10.1128/JVI.01351-09
  • Number of Cited References
    • 60
  • Number of Times Cited
    • 29

Number 14 Assignment

  • Google Scholar Advantages-Provides citation and familiar/easy to use
  • Google Scholar Disadvantages-Can only sort by date and relevance and cannot tell if a source is a review or primary literature
  • PubMed Advantages-Extensive Filters/allows for specificity and Labels Reviews/easy to differentiate
  • PubMed Disadvantages- Limited access to free full-text journals and much more complicated when trying to use the filters and look for specifics
  • Web of Science Advantages-Tagged for the function i.e. review article and easy to re-find a paper, making it easy when doing research
  • Web of Science Disadvantages- Only searches the abstract and tagging information and need to have institution access

Number 15 Assignment

  • Keywords can vastly change your search results, for instance, all of us students chose different phrases to use to search when looking up the same topic and got vastly different numbers for search results.

Number 16 Assignment

Number 17 Assignment

  • Publisher-American Society for Microbiology
  • Non-Profit or For Profit-Non Profit
  • Scientific Society-Yes, American Society for Microbiology
  • Open Access Publishers Association-No
  • Country of Publication-USA
  • Journal Operation-Since February 1967
  • Peer Reviewed-Yes
  • Link to editorial Board-https://jvi.asm.org/content/board-editors
  • Impact Factor-4.324

Number 18 Assignment

  • Primary or Review-Review
  • Received-1 July 2009
  • Accepted-14 September 2009
  • Revisions-No revisions were stated
  • Published Date-Published online November 4, 2009
  • Time Elapsed between Submission and Publication- 4 months
  • Authors Affiliation- Schering-Plough Research Institute
  • Authors Multiple Papers-Yes, Ogert RA has published multiple papers regarding HIV
  • Conflict of Interest-No
  • Abstract Summary- In this study, the authors looked at vicriviroc, a coreceptor antagonist of CCR5 that is used in treatment for HIV-1. The results of the study should that the VCV-resistant virus modified itself to use the drug-bound receptor, increasing the reliance on the N-terminus of CCR5.
  • Journal Club Recommendation-No we should not use this article for journal club because of the article was not organized in a manner that was easy to follow along with.
  • Copy and Paste into class BIB

Conclusion

Before Week 8"s class the only search engine I used for a majority of my projects was google scholar unless I was told to do otherwise. Week 8's class taught me the shortcomings of google scholar and how I can use other search engines to narrow down my search and find the best possible paper for my projects. For instance, I did not know PubMed stated when a paper was a Review, which is very helpful information when a professor is asking for a primary literature article, with this tool you do not have to open the paper and check for each one if it is a review or not. A feature that I knew before this class but that was also mentioned in class was the fact that google scholar gives citations, which is very helpful when including references on a paper.

Acknowledgements

  • I worked with my homework partner, Madeleine B. King, and Nathan On throughout the class and compared search techniques.
  • I copied and modified the protocol shown in the Week 8 page
  • I copied links from search engines from the Week 8 page
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source

Mpaniag1 (talk) 13:07, 24 March 2020 (PDT)

References

Classwork

Assignments

Journals

Class Journals

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