Jmenzago Week 8

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Purpose

The purpose of this assignment is to prepare for the next phase of the HIV research project by reading and reviewing scientific literature regarding structure-function implications of mutations of the gp120 protein.

Assignment

Google Scholar Search

  1. Perform a search in Google Scholar .
    1. Record the number of “hits” you found: 98,100
    2. Record the top 10 papers, this time using APA format:
      • Gristick, H. B., von Boehmer, L., West Jr, A. P., Schamber, M., Gazumyan, A., Golijanin, J., ... & Bjorkman, P. J. (2016). Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site. Nature structural & molecular biology, 23(10), 906.
      • Pancera, M., Zhou, T., Druz, A., Georgiev, I. S., Soto, C., Gorman, J., ... & Stewart-Jones, G. B. (2014). Structure and immune recognition of trimeric pre-fusion HIV-1 Env. Nature, 514(7523), 455-461.
      • Lee, J. H., Ozorowski, G., & Ward, A. B. (2016). Cryo-EM structure of a native, fully glycosylated, cleaved HIV-1 envelope trimer. Science, 351(6277), 1043-1048.
      • Do Kwon, Y., Pancera, M., Acharya, P., Georgiev, I. S., Crooks, E. T., Gorman, J., ... & Soto, C. (2015). Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env. Nature structural & molecular biology, 22(7), 522.
      • Julien, J. P., Cupo, A., Sok, D., Stanfield, R. L., Lyumkis, D., Deller, M. C., ... & Ward, A. B. (2013). Crystal structure of a soluble cleaved HIV-1 envelope trimer. Science, 342(6165), 1477-1483.
      • Stewart-Jones, G. B., Soto, C., Lemmin, T., Chuang, G. Y., Druz, A., Kong, R., ... & Bylund, T. (2016). Trimeric HIV-1-Env structures define glycan shields from clades A, B, and G. Cell, 165(4), 813-826.
      • Lyumkis, D., Julien, J. P., de Val, N., Cupo, A., Potter, C. S., Klasse, P. J., ... & Wilson, I. A. (2013). Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. Science, 342(6165), 1484-1490.
      • Blattner, C., Lee, J. H., Sliepen, K., Derking, R., Falkowska, E., de la Peña, A. T., ... & Peng, W. (2014). Structural delineation of a quaternary, cleavage-dependent epitope at the gp41-gp120 interface on intact HIV-1 Env trimers. Immunity, 40(5), 669-680.
      • Bartesaghi, A., Merk, A., Borgnia, M. J., Milne, J. L., & Subramaniam, S. (2013). Prefusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy. Nature structural & molecular biology, 20(12), 1352.
      • Tran, E. E., Borgnia, M. J., Kuybeda, O., Schauder, D. M., Bartesaghi, A., Frank, G. A., ... & Subramaniam, S. (2012). Structural mechanism of trimeric HIV-1 envelope glycoprotein activation. PLoS pathogens, 8(7).
  2. Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:
    • Wong, R. W., Balachandran, A., Cheung, P. K., Cheng, R., Pan, Q., Stoilov, P., ... & Cochrane, A. (2020). An activator of G protein-coupled receptor and MEK1/2-ERK1/2 signaling inhibits HIV-1 replication by altering viral RNA processing. PLoS pathogens, 16(2), e1008307.
    • Bontempo, A., Garcia, M. M., Rivera, N., & Cayabyab, M. J. (2020). A Systematic Approach to HIV-1 Vaccine Immunogen Selection. AIDS Research and Human Retroviruses, (ja).
    • 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.
    • Silver, Z. A., Antonopoulos, A., Haslam, S. M., Dell, A., Dickinson, G. M., Seaman, M. S., & Desrosiers, R. C. (2020). Discovery of O-Linked Carbohydrate on HIV-1 Envelope and Its Role in Shielding against One Category of Broadly Neutralizing Antibodies. Cell Reports, 30(6), 1862-1869.
    • Barnes, C. O. (2020). Structures of Natively-Glycosylated HIV-1 Envelope Trimers Define Antibody-Mediated Neutralization of HIV-1. Biophysical Journal, 118(3), 3a.
  3. Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
    • 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.
    • Chuang, G. Y., Zhou, J., Acharya, P., Rawi, R., Shen, C. H., Sheng, Z., ... & Doria-Rose, N. A. (2019). Structural survey of broadly neutralizing antibodies targeting the HIV-1 Env trimer delineates epitope categories and characteristics of recognition. Structure, 27(1), 196-206.
    • Lu, M., Ma, X., Castillo-Menendez, L. R., Gorman, J., Alsahafi, N., Ermel, U., ... & Zhou, T. (2019). Associating HIV-1 envelope glycoprotein structures with states on the virus observed by smFRET. Nature, 568(7752), 415-419.
    • Yang, Z., Wang, H., Liu, A. Z., Gristick, H. B., & Bjorkman, P. J. (2019). Asymmetric opening of HIV-1 Env bound to CD4 and a coreceptor-mimicking antibody. Nature structural & molecular biology, 26(12), 1167-1175.
    • 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.
  4. Filter your results using “Since 2016”, and record the top 5 papers, using APA format:
    • Gristick, H. B., von Boehmer, L., West Jr, A. P., Schamber, M., Gazumyan, A., Golijanin, J., ... & Bjorkman, P. J. (2016). Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site. Nature structural & molecular biology, 23(10), 906.
    • Lee, J. H., Ozorowski, G., & Ward, A. B. (2016). Cryo-EM structure of a native, fully glycosylated, cleaved HIV-1 envelope trimer. Science, 351(6277), 1043-1048.
    • Sarkar, A., Bale, S., Behrens, A. J., Kumar, S., Sharma, S. K., de Val, N., ... & Ward, A. B. (2018). Structure of a cleavage-independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer. Nature communications, 9(1), 1-14.
    • Stewart-Jones, G. B., Soto, C., Lemmin, T., Chuang, G. Y., Druz, A., Kong, R., ... & Bylund, T. (2016). Trimeric HIV-1-Env structures define glycan shields from clades A, B, and G. Cell, 165(4), 813-826.
    • Guenaga, J., Dubrovskaya, V., De Val, N., Sharma, S. K., Carrette, B., Ward, A. B., & Wyatt, R. T. (2016). Structure-guided redesign increases the propensity of HIV Env to generate highly stable soluble trimers. Journal of virology, 90(6), 2806-2817.
  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:
    • mutation 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 proteins
    • HIV-1 gp120 protein mutation
    • gp120 mutation structure function
    • Record the search terms that have now been assigned specifically to you:
      • HIV, env, structure

PubMed Search

  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: 1140
    • Record the top 10 papers (you don't need to do APA format for this):
      1. The impact of sustained immunization regimens on the antibody response to oligomannose glycans. Nguyen DN, Redman RL, Horiya S, Bailey JK, Xu B, Stanfield RL, Temme JS, LaBranche CC, Wang S, Rodal AA, Montefiori DC, Wilson IA, Krauss IJ.
      2. Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque CD4 and CCR5. Roop JI, Cassidy NA, Dingens AS, Bloom JD, Overbaugh J.
      3. A Systematic Approach to HIV-1 Vaccine Immunogen Selection. Bontempo A, Garcia MM, Rivera N, Cayabyab MJ.
      4. Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody. Schommers P, Gruell H, Abernathy ME, Tran MK, Dingens AS, Gristick HB, Barnes CO, Schoofs T, Schlotz M, Vanshylla K, Kreer C, Weiland D, Holtick U, Scheid C, Valter MM, van Gils MJ, Sanders RW, Vehreschild JJ, Cornely OA, Lehmann C, Fätkenheuer G, Seaman MS, Bloom JD, Bjorkman PJ, Klein F.
      5. Autologous neutralizing antibody responses to an HIV envelope glycan hole are not easily broadened in rabbits. Yang YR, McCoy LE, van Gils MJ, Andrabi R, Turner HL, Yuan M, Cottrell CA, Ozorowski G, Voss J, Pauthner M, Polveroni TM, Messmer T, Wilson IA, Sanders RW, Burton DR, Ward AB.
      6. Cryo-EM Structure of Full-length HIV-1 Env Bound With the Fab of Antibody PG16. Pan J, Peng H, Chen B, Harrison SC.
      7. Spontaneous Glycan Reattachment Following N-Glycanase Treatment of Influenza and HIV Vaccine Antigens. Keating CL, Kuhn E, Bals J, Cocco AR, Yousif AS, Matysiak C, Sangesland M, Ronsard L, Smoot M, Moreno TB, Okonkwo V, Setliff I, Georgiev I, Balazs AB, Carr SA, Lingwood D.
      8. The Envelope-Based Fusion Antigen GP120C14K Forming Hexamer-Like Structures Triggers T Cell and Neutralizing Antibody Responses Against HIV-1. Raman SC, Mejías-Pérez E, Gomez CE, García-Arriaza J, Perdiguero B, Vijayan A, Pérez-Ruiz M, Cuervo A, Santiago C, Sorzano COS, Sánchez-Corzo C, Moog C, Burger JA, Schorcht A, Sanders RW, Carrascosa JL, Esteban M.
      9. Flow Cytometry Analysis of HIV-1 Env Conformations at the Surface of Infected Cells and Virions: Role of Nef, CD4, and SERINC5. Staropoli I, Dufloo J, Ducher A, Commere PH, Sartori-Rupp A, Novault S, Bruel T, Lorin V, Mouquet H, Schwartz O, Casartelli N.
      10. Refolding Dynamics of gp41 from Pre-fusion to Pre-hairpin States during HIV-1 Entry. Lin M, Da LT.
  2. Perform a title/abstract search on your assigned keywords.
    • Record the total number of hits: 38
    • 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. Roop JI, Cassidy NA, Dingens AS, Bloom JD, Overbaugh J.
      2. Cryo-EM Structure of Full-length HIV-1 Env Bound With the Fab of Antibody PG16. Pan J, Peng H, Chen B, Harrison SC.
      3. Impact of HIV-1 Diversity on Its Sensitivity to Neutralization. Stefic K, Bouvin-Pley M, Braibant M, Barin F. (Review)
      4. Vaccine-induced V1V2-specific antibodies control and or protect against infection with HIV, SIV and SHIV. Zolla-Pazner S, Alvarez R, Kong XP, Weiss S.
      5. Concomitant Enhancement of HIV-1 Replication Potential and Neutralization-Resistance in Concert With Three Adaptive Mutations in Env V1/C2/C4 Domains. Doi N, Yokoyama M, Koma T, Kotani O, Sato H, Adachi A, Nomaguchi M.
      6. Optimized protocol for detection of native, full-length HIV-1 envelope on the surface of transfected cells. Altman JB, Liu X, Itri V, Zolla-Pazner S, Powell RLR.
      7. The first structure of HIV-1 gp120 with CD4 and CCR5 receptors. Guan Y.
      8. Meeting Review: 2018 International Workshop on Structure and Function of the Lentiviral gp41 Cytoplasmic Tail. Fernandez MV, Freed EO.
      9. Mapping of Neutralizing Antibody Epitopes on the Envelope of Viruses Obtained from Plasma Samples Exhibiting Broad Cross-Clade Neutralization Potential Against HIV-1. Cheedarla N, Sundaramurthi JC, Hemalatha B, Anangi B, Nesakumar M, Ashokkumar M, Vidya Vijayan KK, Tripathy SP, Swaminathan S, Vaniambadi SK, Ramanathan DV, Hanna LE.
      10. Rational Design of DNA-Expressed Stabilized Native-Like HIV-1 Envelope Trimers. Aldon Y, McKay PF, Allen J, Ozorowski G, Felfödiné Lévai R, Tolazzi M, Rogers P, He L, de Val N, Fábián K, Scarlatti G, Zhu J, Ward AB, Crispin M, Shattock RJ.
  3. Add the word “Review” to any articles that are review articles that you listed in question 8.
  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.
    • used Overbaugh J.
    • Do you find any new articles that you did not find before on PubMed?
      • yes
    • List up to 5 new articles that were found on the author name search:
      1. Knowns and Unknowns of Assaying Antibody-Dependent Cell-Mediated Cytotoxicity Against HIV-1. Lewis GK, Ackerman ME, Scarlatti G, Moog C, Robert-Guroff M, Kent SJ, Overbaugh J, Reeves RK, Ferrari G, Thyagarajan B.
      2. CD4-HIV-1 Envelope Interactions: Critical Insights for the Simian/HIV/Macaque Model. Sharma A, Overbaugh J.
      3. The Role of Immune Responses in HIV Mother-to-Child Transmission. Milligan C, Slyker JA, Overbaugh J.
      4. HIV transmission biology: translation for HIV prevention. Ronen K, Sharma A, Overbaugh J.
      5. HIV infection. Deeks SG, Overbaugh J, Phillips A, Buchbinder S.

Web of Science Search

  1. Now access the Web of Science database. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits: 1,128
    • 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. Schommers, Philipp; Gruell, Henning; Abernathy, Morgan E.; et al.
      2. Spontaneous Glycan Reattachment Following N-Glycanase Treatment of Influenza and HIV Vaccine Antigens. Keating, Celina L.; Kuhn, Eric; Bals, Julia; et al.
      3. Boosting with AIDSVAX B/E Enhances Env Constant Region 1 and 2 Antibody-Dependent Cellular Cytotoxicity Breadth and Potency. Easterhoff, David; Pollara, Justin; Luo, Kan; et al.
      4. The lipid membrane of HIV-1 stabilizes the viral envelope glycoproteins and modulates their sensitivity to antibody neutralization. Salimi, Hamid; Johnson, Jacklyn; Flores, Manuel G.; et al.
      5. Refolding Dynamics of gp41 from Pre-fusion to Pre-hairpin States during HIV-1 Entry. Lin, Mengna; Da, Lin-Tai
      6. Segmentation by classification: A novel and reliable approach for semiautomatic selection of HIV/SIV envelope spikes. Banerjee, Chaity; Dutta, Moumita; Liu, Xiuwen; et al.
      7. In Vivo Validation of the Viral Barcoding of Simian Immunodeficiency Virus SIVmac239 and the Development o New Barcoded SIV and Subtype B and C Simian-Human Immunodeficiency Viruses. Khanal, Sirish; Fennessey, Christine M.; O'Brien, Sean P.; et al.
      8. SOS and IP Modifications Predominantly Affect the Yield but Not Other Properties of SOSIP.664 HIV-1 Env Glycoprotein Trimers. Ringe, Rajesh P.; Colin, Philippe; Torres, Jonathan L.; et al.
      9. HIV-1 Matrix Trimerization-Impaired Mutants Are Rescued by Matrix Substitutions That Enhance Envelope Glycoprotein Incorporation. Tedbury, Philip R.; Novikova, Mariia; Alfadhli, Ayna; et al.
      10. The Tryptophan-Rich Motif of HIV-1 gp41 Can Interact with the N-Terminal Deep Pocket Site: New Insights into the Structure and Function of gp41 and Its Inhibitors. Zhu, Yuanmei; Ding, Xiaohui; Yu, Danwei; et al.

Analysis of Assigned Article

  1. We will now create a shared bibliography for the entire class. Go through the search results that you have found and add articles to the class shared bibliography page.
    • Only add articles that are unique (everyone will be adding to the page and we do not want redundant articles)
    • Put review articles and primary research articles in their respective sections. If the article does not fit either of those two categories, place it in the other articles section.
    • Add the articles in APA format (re-find them in Google Scholar to easily obtain APA format, if necessary). Add your wiki signature to the end of the citation.
    • Ideally, each student will contribute 2-3 unique articles.
  2. Now that we have our shared bibliography, each student will be assigned one article. Record the citation for your article in APA format:
    • Roop, J. I., Cassidy, N. A., Dingens, A. S., Bloom, J. D., & Overbaugh, J. (2020). Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque CD4 and CCR5. Viruses, 12(2), 241.
    • In Web of Science, search for the specific article that you have been assigned.
      • How many cited references does that article have?
        • n/a (not available on Web of Science)
      • How many articles have cited the article you have been assigned?
        • n/a (not available on Web of Science), likely 0 since it was published this year
  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
      • advantages - easy to use, able to generate citations, produces a wide range of results
      • disadvantages - not all articles are available for use, unable to see if article have been peer reviewed, unable to see if articles are primary literature or reviews
    • PubMed
      • advantages - provides a list of similar articles, more filters allowing for more specific search results
      • disadvantages - does not provide many articles
    • Web of Science
      • advantages - best of the three for focusing searches and finding information about articles
      • disadvantages - expensive
  4. What impact does choice of keywords have on your results?
    • Keyword choice has a significant impact on search results. Broader, more generic keywords will result in a larger list of results, and vice versa for more specific keywords. Also, the order and arrangement of keywords in the search bar can make a difference in results produced.
  5. 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).
    • Roop, J. I., Cassidy, N. A., Dingens, A. S., Bloom, J. D., & Overbaugh, J. (2020). Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque CD4 and CCR5. Viruses, 12(2), 241. https://doi.org/10.3390/v12020241
    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
      • n/a
    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.
      • The authors
    6. How is the article available to you:
      • The article is open access.
  6. Evaluating the source--the journal
    1. Who is the publisher of the journal?
      • MDPI
    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)
      • no
    4. Does the publisher belong to the Open Access Publishers Association?
      • yes
    5. What country is the journal published in?
      • Switzerland
    6. How long has the journal been in operation? (e.g., browse the archive for the earliest article published)
      • since 2009
    7. Are articles in this journal peer-reviewed?
      • yes
    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)?
      • 3.811
  7. 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?
      • 27 December 2019
    3. On what date was the article accepted?
      • 19 February 2020
    4. Did the article undergo any revisions before acceptance?
      • not stated that there were any revisions
    5. When was the article published?
      • 21 February 2020
    6. What is the approximate elapsed time between submission and publication?
      • 2 days
    7. What are the institutions with which the authors are affiliated?
      • Fred Hutchinson Cancer Research Center
        • Divisions of Human Biology
        • Basic Sciences
    8. Have the authors published other articles on this subject? (How will you find this out?)
      • Searched by author on PubMed to find out
      • Roop J. I.: no
      • Overbaugh J.: yes
    9. Is there a conflict of interest for any of the authors?
      • there is no conflict of interest, according to 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.
      • HIV-1 strains do not replicate well in Rhesus macaque cells due to a non-synonymous mutation in macaque CD4 that restricts HIV-1 env-mediated entry. Several induced mutations from this study have been found in gp120 that enhance binding of HIV-1 to macaque CD4.
    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 that it would be interesting to do a journal club on this article. Based on the abstract, it could provide useful information about the structure-function relationship of the mutations in the gp120 sequence of HIV-1. The journal is open access since the publisher has been committed to that movement in the research community, so the class will be able to easily read the article. There were no conflicts of interest, and the chief overseeing researcher (Julie Overbaugh) has published other articles on the subject. However, the article is new so there is no information about its relevance to HIV research. The journal and publisher are also relatively new, the former being created just over 10 years ago and the latter being established in 1996. The impact factor of the journal (3.811) is decent, but nothing notable. Because everything from the publisher to the article is fairly new, it is difficult to really get an idea of the quality of the article, but I think it would be interesting to give it a shot.
  8. Copy your 1-2 sentence statement about the relevance and the recommendation (plus justification) and paste into the class shared bibliography as a bullet point underneath your assigned paper.

Scientific Conclusion

The purpose of this assignment was to look for research articles that could be useful for upcoming projects on the structure-function relationship of gp120 using different search engines. This exercise highlighted how many factors can play into information literacy. While I had an idea that the way were used keywords made a difference in search results, it wasn't really apparent to me of how much of a difference they can make until this assignment. This assignment also showed me how much of an influence different search engines had on search results and access to articles. This was something I had completely overlooked and it was interesting to see how different results were between the search engines despite me using the same keywords. I also did not know about the open access issue in the research community and thought that was interesting and cool to learn about.

Acknowledgements

  • My homework partner for the week was Drew Cartmel
    • We discussed over text the advantages and disadvantages of using the different search engines from the assignment
  • I followed the protocol on BIOL368/S20:Week_8 to complete this page
    • Syntax for assignment questions copied from this page
  • I asked [User: Nyeo2 | Nicholas Yeo]] how to make text bold on the wiki page
  • Google Scholar, PubMed LMU-specific link, and Web of Science were used to search for articles
  • I used MDPI and Viruses to get information about the journal and publisher for my article
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Jmenzago (talk) 13:14, 26 March 2020 (PDT)

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