BIOL368/S20:Sahil Patel Week 8

Purpose

The purpose of this assignment is to collaboratively create a shared annotated bibliography to help guide our research for the next part of the HIV project where we will investigate the structure and function of mutations in the gp120 protein.

Assignment

1. Google Scholar generated about 28,300 search results in 0.07 sec for the following input: "HIV-1 env structure mutation"

2. Record the top 10 papers, this time using APA format:

Reitz Jr, M. S., Wilson, C., Naugle, C., Gallo, R. C., & Robert-Guroff, M. (1988). Generation of a neutralization-resistant variant of HIV-1 is due to selection for a point mutation in the envelope gene. Cell, 54(1), 57-63.

Alfadhli, A., Mack, A., Ritchie, C., Cylinder, I., Harper, L., Tedbury, P. R., ... & Barklis, E. (2016). Trimer enhancement mutation effects on HIV-1 matrix protein binding activities. Journal of virology, 90(12), 5657-5664.

Dong, X. N., Xiao, Y., Dierich, M. P., & Chen, Y. H. (2001). N-and C-domains of HIV-1 gp41: mutation, structure and functions. Immunology Letters, 75(3), 215-220.

Davis, M. R., Jiang, J., Zhou, J., Freed, E. O., & Aiken, C. (2006). A mutation in the human immunodeficiency virus type 1 Gag protein destabilizes the interaction of the envelope protein subunits gp120 and gp41. Journal of virology, 80(5), 2405-2417.

Menéndez-Arias, L. (2009). Mutation rates and intrinsic fidelity of retroviral reverse transcriptases. Viruses, 1(3), 1137-1165.

Wilson, C., Reitz, M. S., Aldrich, K., Klasse, P. J., Blomberg, J., Gallo, R. C., & Robert-Guroff, M. (1990). The site of an immune-selected point mutation in the transmembrane protein of human immunodeficiency virus type 1 does not constitute the neutralization epitope. Journal of Virology, 64(7), 3240-3248.

Ratcliff, A. N., Shi, W., & Arts, E. J. (2013). HIV-1 resistance to maraviroc conferred by a CD4 binding site mutation in the envelope glycoprotein gp120. Journal of virology, 87(2), 923-934.

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).

Mansky, L. M., & Bernard, L. C. (2000). 3′-Azido-3′-deoxythymidine (AZT) and AZT-resistant reverse transcriptase can increase the in vivo mutation rate of human immunodeficiency virus type 1. Journal of Virology, 74(20), 9532-9539.

Dykes, C., Balakrishnan, M., Planelles, V., Zhu, Y., Bambara, R. A., & Demeter, L. M. (2004). Identification of a preferred region for recombination and mutation in HIV-1 gag. Virology, 326(2), 262-279.

3. Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:

Schuster, T. (2020). Analysis of the impact of codon choice on gene expression of HIV-1 (Doctoral dissertation).

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.

Suphaphiphat, K. (2019). Anti-viral immune response in the semen of cynomolgus macaques and inhibition of cell to cell transmission by broadly neutralizing antibodies in an SIV/SHIV model of infection (Doctoral dissertation, Université Paris-Saclay).

Zumblick, A. (2020). Restriktion von HERV-K (HML-2) durch IFI-16 (Master's thesis, Robert Koch-Institut).

Kubota, S., Ishikawa, T., Kawata, K., Hattori, T., & Nishida, T. (2020). Retrotransposons Manipulating Mammalian Skeletal Development in Chondrocytes. International Journal of Molecular Sciences, 21(5), 1564.

4. Filter your results using “Since 2019”, and record the top 5 papers, using APA format:

Fu, M., Hu, K., Hu, H., Ni, F., Du, T., Shattock, R. J., & Hu, Q. (2019). Antigenicity and immunogenicity of HIV-1 gp140 with different combinations of glycan mutation and V1/V2 region or V3 crown deletion. Vaccine, 37(51), 7501-7508.

Wu, N. R., Nicely, N. I., Lee, E. M., Reed, R. K., Watts, B. E., Cai, F., ... & Trama, A. M. (2019). Cooperation between somatic mutation and germline-encoded residues enables antibody recognition of HIV-1 envelope glycans. PLoS Pathogens, 15(12).

Yeo, J. Y., Goh, G. R., Su, C. T. T., & Gan, S. K. E. (2020). The determination of HIV-1 RT mutation rate, its possible allosteric effects, and its implications on drug resistance.

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.

Pan, J., Peng, H., Chen, B., & Harrison, S. C. (2020). Cryo-EM structure of full-length HIV-1 Env bound with the Fab of antibody PG16. Journal of Molecular Biology.

5. Filter your results using “Since 2016”, and record the top 5 papers, using APA format:

Alfadhli, A., Mack, A., Ritchie, C., Cylinder, I., Harper, L., Tedbury, P. R., ... & Barklis, E. (2016). Trimer enhancement mutation effects on HIV-1 matrix protein binding activities. Journal of virology, 90(12), 5657-5664.

Fu, M., Hu, K., Hu, H., Ni, F., Du, T., Shattock, R. J., & Hu, Q. (2019). Antigenicity and immunogenicity of HIV-1 gp140 with different combinations of glycan mutation and V1/V2 region or V3 crown deletion. Vaccine, 37(51), 7501-7508.

Wu, N. R., Nicely, N. I., Lee, E. M., Reed, R. K., Watts, B. E., Cai, F., ... & Trama, A. M. (2019). Cooperation between somatic mutation and germline-encoded residues enables antibody recognition of HIV-1 envelope glycans. PLoS Pathogens, 15(12).

Zanini, F., Puller, V., Brodin, J., Albert, J., & Neher, R. A. (2017). In vivo mutation rates and the landscape of fitness costs of HIV-1. Virus evolution, 3(1), vex003.

Lemmin, T., Soto, C., & Kwong, P. D. (2017). Insights into the Dynamics of the HIV-1 Env Glycan Shield. Biophysical Journal, 112(3), 322a.

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:

HIV
HIV-1
gp120
env
structure
mutation
variation

Record the search terms that have now been assigned specifically to you:

HIV-1
env
structure
mutation

7. Now access the PubMed database by using the LMU-specific link. Perform an unrestricted search on your assigned keywords.

Total number of hits: 217
Record the top 10 papers (you don't need to do APA format for this):

Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque CD4 and CCR5.

Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody.

Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope.

Associating HIV-1 envelope glycoprotein structures with states on the virus observed by smFRET.

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.

Concomitant Enhancement of HIV-1 Replication Potential and Neutralization-Resistance in Concert With Three Adaptive Mutations in Env V1/C2/C4 Domains.

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.

Molecular mechanism of HIV-1 resistance to sifuvirtide, a clinical trial-approved membrane fusion inhibitor.

8/9. Perform a title/abstract search on your assigned keywords.

Record the total number of hits: No Results
Record the top 10 papers (you don't need to do APA format for this): N/A

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.

Do you find any new articles that you did not find before on PubMed? Yes, I found several articles that I had not seen earlier.
List up to 5 new articles that were found on the author name search:

Self-controlled amount and pacing of practice facilitate learning of a sequential timing task.

Aiken CA, Post PG, Hout MC, Fairbrother JT. J Sports Sci. 2020 Feb;38(4):405-415. doi: 10.1080/02640414.2019.1704498. Epub 2019 Dec 19. PMID: 31856697 Similar articles Select item 31413124

Dominant Negative MA-CA Fusion Protein Is Incorporated into HIV-1 Cores and Inhibits Nuclear Entry of Viral Preintegration Complexes.

Anderson-Daniels J, Singh PK, Sowd GA, Li W, Engelman AN, Aiken C. J Virol. 2019 Oct 15;93(21). pii: e01118-19. doi: 10.1128/JVI.01118-19. Print 2019 Nov 1. PMID: 31413124 Similar articles Select item 31167922

A Novel Phenotype Links HIV-1 Capsid Stability to cGAS-Mediated DNA Sensing.

Siddiqui MA, Saito A, Halambage UD, Ferhadian D, Fischer DK, Francis AC, Melikyan GB, Ambrose Z, Aiken C, Yamashita M. J Virol. 2019 Jul 30;93(16). pii: e00706-19. doi: 10.1128/JVI.00706-19. Print 2019 Aug 15. PMID: 31167922 Free PMC Article Similar articles Select item 30947724

Functional analysis of the secondary HIV-1 capsid binding site in the host protein cyclophilin A.

Peng W, Shi J, Márquez CL, Lau D, Walsh J, Faysal KMR, Byeon CH, Byeon IL, Aiken C, Böcking T. Retrovirology. 2019 Apr 4;16(1):10. doi: 10.1186/s12977-019-0471-4. PMID: 30947724 Free PMC Article Similar articles Select item 30567984

PF74 Inhibits HIV-1 Integration by Altering the Composition of the Preintegration Complex.

Balasubramaniam M, Zhou J, Addai A, Martinez P, Pandhare J, Aiken C, Dash C. J Virol. 2019 Mar 5;93(6). pii: e01741-18. doi: 10.1128/JVI.01741-18. Print 2019 Mar 15. PMID: 30567984 Free PMC Article Similar articles

11. Now access the Web of Science database. Perform an unrestricted search on your assigned keywords.

Total number of hits: 198
Record the top 10 papers (you don't need to use APA format for this):

Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody

By: Schommers, Philipp; Gruell, Henning; Abernathy, Morgan E.; et al. CELL Volume: 180 Issue: 3 Pages: 471-+ Published: FEB 6 2020

Refolding Dynamics of gp41 from Pre-fusion to Pre-hairpin States during HIV-1 Entry

By: Lin, Mengna; Da, Lin-Tai JOURNAL OF CHEMICAL INFORMATION AND MODELING Volume: 60 Issue: 1 Pages: 162-174 Published: JAN 2020

HIV-1 Matrix Trimerization-Impaired Mutants Are Rescued by Matrix Substitutions That Enhance Envelope Glycoprotein Incorporation

By: Tedbury, Philip R.; Novikova, Mariia; Alfadhli, Ayna; et al. JOURNAL OF VIROLOGY Volume: 94 Issue: 1 Article Number: e01526-19 Published: JAN 2020

Cooperation between somatic mutation and germline-encoded residues enables antibody recognition of HIV-1 envelope glycans

By: Wu, Nelson R.; Nicely, Nathan I.; Lee, Esther M.; et al. PLOS PATHOGENS Volume: 15 Issue: 12 Article Number: e1008165 Published: DEC 2019

Replication of HIV-1 envelope protein cytoplasmic domain variants in permissive and restrictive cells

By: Staubus, August O.; Alfadhli, Ayna; Barklis, Robin Lid; et al. VIROLOGY Volume: 538 Pages: 1-10 Published: DEC 2019

Harnessing Avidity: Quantifying the Entropic and Energetic Effects of Linker Length and Rigidity for Multivalent Binding of Antibodies to HIV-1

By: Einav, Tal; Yazdi, Shahrzad; Coey, Aaron; et al. CELL SYSTEMS Volume: 9 Issue: 5 Pages: 466-+ Published: NOV 27 2019

Topological analysis of the gp41 MPER on lipid bilayers relevant to the metastable HIV-1 envelope prefusion state

By: Wang, Yi; Kaur, Pavanjeet; Sun, Zhen-Yu J.; et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volume: 116 Issue: 45 Pages: 22556-22566 Published: NOV 5 2019

A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance

By: Skittrall, Jordan P.; Ingemarsdotter, Carin K.; Gog, Julia R.; et al. PLOS COMPUTATIONAL BIOLOGY Volume: 15 Issue: 9 Article Number: e1007345 Published: SEP 2019

Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies

By: LaBranche, Celia C.; Henderson, Rory; Hsu, Allen; et al. PLOS PATHOGENS Volume: 15 Issue: 9 Article Number: e1008026 Published: SEP 2019

Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope

Associated Data By: Schoofs, Till; Barnes, Christopher O.; Suh-Toma, Nina; et al. IMMUNITY Volume: 50 Issue: 6 Pages: 1513-+ Published: JUN 18 2019

12. Shared articles to the class shared bibliography page.

13. Davis, M. R., Jiang, J., Zhou, J., Freed, E. O., & Aiken, C. (2006). A mutation in the human immunodeficiency virus type 1 Gag protein destabilizes the interaction of the envelope protein subunits gp120 and gp41. Journal of virology, 80(5), 2405-2417.

How many cited references does that article have? 88
How many articles have cited the article you have been assigned? 50

14. What are the relative merits of searching with Google Scholar, PubMed, and Web of Science? Name two advantages and disadvantages for each.

Google Scholar (Advantages): Provides citations in a variety of styles, as well as the number of times an article has been cited. Google scholar gives the most search result with the most flexibility with keywords.
Google Scholar (Disadvantages): Did not have the option for me to only search for peer reviewed articles, also it does not rank search results on the number of times the keywords searched appear in the article.

PubMed (advantages): Pubmed provides access to other databases offered by the NLM (National Library of Medicine). PubMed allows the largest number of keywords per search and filters out non peer-reviewed articles. Pubmed (disadvantages): Pubmed focuses on medical and biomedical sciences but has limited information on other sciences. Pubmed is the only database of the three that does not provide citation analysis. Web of Science (advantages):Web of Science covers the oldest publications, because its indexed and archived records go back to 1900. Easily access the number of times an article was cites as well as track citation history. Web of Science (disadvantages): Updated less frequently than the others (around once a week). Search engine is not as intuitive as pubmed and not even close to google scholar.

15. What impact does choice of keywords have on your results?

The number of keywords inputted give more accurate results and filters based on title first, then number of times keywords are found within the article.
The conjunction 'and' when put between words brings search results including both those words.

16. 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).

https://www.ncbi.nlm.nih.gov/pubmed/?term=A+mutation+in+the+human+immunodeficiency+virus+type+1+Gag+protein+destabilizes+the+interaction+of+the+envelope+protein+subunits+gp120+and+gp41.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1395406/
https://jvi.asm.org/content/80/5/2405
https://jvi.asm.org/content/jvi/80/5/2405.full-text.pdf
American Society for Microbiology
Open Access
Available both print and online

17. Evaluating the source--the journal

Journal of Virology
For profit
In collaboration with the American Society of Virology
not a member of the Open Access Publishers Association
USA
Since February of 1967
Yes they are peer reviewed
https://jvi.asm.org/content/board-editors
4.324 (2018)

18. Evaluating the source--the article

Primary research article
Received 13 October 2005
Accepted 8 December 2005
March 2006, did go through some revision but not to any data/figures
about 4 months
Vanderbilt University Chair/Professor of Immunology, Microbiology, Pathology
Current projects of the Aiken lab include:

HIV-1 capsid structure and function (Cell 139:780-90, 2009; Nature 497:643-6, 2013). Role of host cell proteins in HIV-1 infection (J. Virol. 82:12001-8, 2008; J. Virol. 87:422-32, 2013). Mechanism of HIV-1 restriction by TRIM5alpha (PLos Pathog. 4(5):e1000074, 2008; J. Virol. 84:6564-69, 2010; PLos Path 7:e1002009, 2011; J. Virol. 87:9271-8, 2013). Identification and mechanisms of HIV-1 capsid inhibitors (J. Virol. 85:542-9, 2011). Conformational Masking of HIV-1 Env proteins during virion maturation (PLoS Pathog 7:e1002234, 2011).

Initial interactions between HIV-1 particles and target cells occur between gp120 and CD4. CD4 binding elicits a conformational change within gp120 that reveals a binding site for the viral coreceptor. Subsequent engagement of coreceptor initiates further conformational changes in gp41 that lead to membrane fusion.
I believe that this article would be good for a journal club because it pertains to prior topics discussed, but it may be a bit too long since this journal does not have a limit on the page count.

Conclusion

By doing this assignment, I learned quite a bit about the way in which biologists conduct research. I always knew that there were different sources but I never cared to inquire about the credibility of the journal or the article, including the authors and publishers. This also gave me some key insight for when I personally do research. Now, I will know whether I want to use Google Scholar, PubMed, or the Web of Science and by assessing the pros and cons of each, our class has an edge over other young researchers who would probably just guess with where to start, much like I used to. Therefore, I believe that it is important to assess and evaluate the journal and article as well as the authors and publishers before we begin to read in article because that establishes credibility and trust with the work.

Acknowledgments

I would like to thank Dr. Dahlquist for being a wonderful instructor.
Except for what is noted above, this individual journal entry was completed by me and not copied from another source.