Cdominguez Week 8

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Assignment Page	Individual Journal Entries	Class Journal
BIOL368/S20:Week 1	user:cdominguez	BIOL368/S20:Class Journal Week 1
BIOL368/S20:Week 2	cdominguez Week 2	BIOL368/S20:Class Journal Week 2
BIOL368/S20:Week 3	cdominguez Week 3	BIOL368/S20:Class Journal Week 3
BIOL368/S20:Week 4	cdominguez Week 4	BIOL368/S20:Class Journal Week 4
BIOL368/S20:Week 5	cdominguez Week 5	BIOL368/S20:Class Journal Week 5
BIOL368/S20:Week 6	cdominguez Week 6	BIOL368/S20:Class Journal Week 6
BIOL368/S20:Week 8	cdominguez Week 8	BIOL368/S20:Bibliography
BIOL368/S20:Week 10	cdominguez Week 10	BIOL368/S20:Class Journal Week 10
BIOL368/S20:Week 11	cdominguez Week 11	BIOL368/S20:Class Journal Week 11
BIOL368/S20:Week 13	cdominguez Week 13	BIOL368/S20:Class Journal Week 13
BIOL368/S20:Week 14	cdominguez Week 14	BIOL368/S20:Class Journal Week 14

Purpose

To implement searching skills in the pursuit to learn data and information as scientists about HIV-1 gp120 that is valid and useful for our project investigating HIV-1 gp120 further.

Search Engine Questions

Using key words: "HIV env structure variation"

1. Warm Up Excercise
2. Google Scholar Results
   1. Record the number of “hits” you found: 33,200
   2. Record the top 10 papers, this time using APA format:
      • White, T. A., Bartesaghi, A., Borgnia, M. J., Meyerson, J. R., De la Cruz, M. J. V., Bess, J. W., ... & Subramaniam, S. (2010). Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: strain-dependent variation in quaternary structure. PLoS pathogens, 6(12).
      • Merk, A., & Subramaniam, S. (2013). HIV-1 envelope glycoprotein structure. Current opinion in structural biology, 23(2), 268-276.
      • 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.
      • Steckbeck, J. D., Craigo, J. K., Barnes, C. O., & Montelaro, R. C. (2011). Highly Conserved Structural Properties of the C-terminal Tail of HIV-1 gp41 Protein Despite Substantial Sequence Variation among Diverse Clades IMPLICATIONS FOR FUNCTIONS IN VIRAL REPLICATION. Journal of Biological Chemistry, 286(31), 27156-27166.
      • Guttman, M., Cupo, A., Julien, J. P., Sanders, R. W., Wilson, I. A., Moore, J. P., & Lee, K. K. (2015). Antibody potency relates to the ability to recognize the closed, pre-fusion form of HIV Env. Nature communications, 6(1), 1-11.
      • Payne, S. L., Fang, F. D., Liu, C. P., Dhruva, B. R., Rwambo, P., Issel, C. J., & Montelaro, R. C. (1987). Antigenic variation and lentivirus persistence: variations in envelope gene sequences during EIAV infection resemble changes reported for sequential isolates of HIV. Virology, 161(2), 321-331.
      • Korber, B., & Gnanakaran, S. (2009). The implications of patterns in HIV diversity for neutralizing antibody induction and susceptibility. Current Opinion in HIV and AIDS, 4(5), 408.
      • 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.
      • Zolla-Pazner, S., & Cardozo, T. (2010). Structure–function relationships of HIV-1 envelope sequence-variable regions refocus vaccine design. Nature reviews Immunology, 10(7), 527-535.
      • 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.
3. Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:
   • Kmiec, D., Nchioua, R., Sherrill-Mix, S., Stürzel, C. M., Heusinger, E., Braun, E., ... & Sauter, D. (2020). CpG Frequency in the 5′ Third of the env Gene Determines Sensitivity of Primary HIV-1 Strains to the Zinc-Finger Antiviral Protein. mBio, 11(1).
   • Salimi, H., Johnson, J., Flores, M. G., Zhang, M. S., O'Malley, Y., Houtman, J. C., ... & Haim, H. (2020). The lipid membrane of HIV-1 stabilizes the viral envelope glycoproteins and modulates their sensitivity to antibody neutralization. Journal of Biological Chemistry, 295(2), 348-362.
   • Yolitz, J. (2019). Variations in protein processing lead to variations in structure and function of the HIV-1 envelope protein (Doctoral dissertation, Johns Hopkins University).
   • Staropoli, I., Dufloo, J., Ducher, A., Commere, P. H., Sartori-Rupp, A., Novault, S., ... & Casartelli, N. (2020). Flow Cytometry Analysis of HIV-1 Env Conformations at the Surface of Infected Cells and Virions: Role of Nef, CD4, and SERINC5. Journal of Virology, 94(6).
   • Trinh, H. V., Gohain, N., Pham, P. T., Hamlin, C., Song, H., Sanders-Buell, E., ... & Robb, M. L. (2019). Humoral Response to the HIV-1 Envelope V2 Region in a Thai Early Acute Infection Cohort. Cells, 8(4), 365.
4. Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
   • Yolitz, J. (2019). Variations in protein processing lead to variations in structure and function of the HIV-1 envelope protein (Doctoral dissertation, Johns Hopkins University).
   • 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.
   • 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.
   • Ward, A. B. (2019). Playing Chess with HIV. Immunity, 50(2), 283-285.
   • Zhu, C., Dukhovlinova, E., Council, O., Ping, L., Faison, E. M., Prabhu, S. S., ... & Kincer, L. P. (2019). Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies. Nature communications, 10(1), 1-10.
5. Filter your results using “Since 2016”, and record the top 5 papers, using APA format:
   • 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.
   • Chuang, G. Y., Zhou, J., Rawi, R., Shen, C. H., Sheng, Z., West, A. P., ... & Louder, M. K. (2018). Structural survey of HIV-1-neutralizing antibodies targeting Env trimer delineates epitope categories and suggests vaccine templates. BioRxiv, 312579.
   • 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.
   • Yolitz, J., Schwing, C., Chang, J., Van Ryk, D., Nawaz, F., Wei, D., ... & Fauci, A. S. (2018). Signal peptide of HIV envelope protein impacts glycosylation and antigenicity of gp120. Proceedings of the National Academy of Sciences, 115(10), 2443-2448.
   • Yolitz, J. (2019). Variations in protein processing lead to variations in structure and function of the HIV-1 envelope protein (Doctoral dissertation, Johns Hopkins University).
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
   • mutations gp120
   • HIV gp 120
   • structure-function mutation gp120
   • structure and function of gp120
   • structure of gp120
   • gp120
   • gp120 structure and function
   • gp120 structure function
   • mutations in the gp120 function
   • HIV-1 gp120 protein mutation
   • gp120 mutation structure function
   • HIV gp120 mutation
   • HIV gp120 function
   • Record the search terms that have now been assigned specifically to you:
     • "HIV env structure variation"
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:92
   • 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. Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies.
     4. Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons.
     5. Structural Survey of Broadly Neutralizing Antibodies Targeting the HIV-1 Env Trimer Delineates Epitope Categories and Characteristics of Recognition.
     6. NGS combined with phylogenetic analysis to detect HIV-1 dual infection in Romanian people who inject drugs.
     7. Signal peptide of HIV envelope protein impacts glycosylation and antigenicity of gp120.
     8. Probing Structural Variation and Dynamics in the HIV-1 Env Fusion Glycoprotein.
     9. Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model.
     10. Rev-RRE Functional Activity Differs Substantially Among Primary HIV-1 Isolates.
8. 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. No result papers
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: Salimi H
    • Do you find any new articles that you did not find before on PubMed? 31 new papers
    • List up to 5 new articles that were found on the author name search:
      1. Mechanisms of Pathogen Invasion into the Central Nervous System.
      2. Encephalitic Alphaviruses Exploit Caveola-Mediated Transcytosis at the Blood-Brain Barrier for Central Nervous System Entry.
      3. How is the association between urinary prostate cancer antigen 3 (PCA3) levels and Gleason scores in patients suspicious of prostate cancer?
      4. Feasibility, complication and long-term follow-up of the newly nelaton based urethral dilation method, retrospective study.
      5. Increased advanced glycation end products in hypertrophied ligamentum flavum of diabetes mellitus patients.
11. Now access the Web of Science database. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits: 58
    • 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. Humoral Response to the HIV-1 Envelope V2 Region in a Thai Early Acute Infection Cohort
      4. Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies
      5. Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons
      6. Signal peptide of HIV envelope protein impacts glycosylation and antigenicity of gp120
      7. Probing Structural Variation and Dynamics in the HIV-1 Env Fusion Gly- coprotein
      8. 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
      9. Chemical optimization of macrocyclic HIV-1 inactivators for improving potency and increasing the structural diversity at the triazole ring
      10. Determinants of HIV-1 CD4-Independent Brain Adaptation

Shared Bibliography Article Questions

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.

My articles are:

• Salimi, H., Johnson, J., Flores, M. G., Zhang, M. S., O'Malley, Y., Houtman, J. C., ... & Haim, H. (2020). The lipid membrane of HIV-1 stabilizes the viral envelope glycoproteins and modulates their sensitivity to antibody neutralization. Journal of Biological Chemistry, 295(2), 348-362.
• Haim, H., Strack, B., Kassa, A., Madani, N., Wang, L., Courter, J. R., ... & Smith III, A. B. (2011). Contribution of intrinsic reactivity of the HIV-1 envelope glycoproteins to CD4-independent infection and global inhibitor sensitivity. PLoS pathogens, 7(6).
• Yolitz, J. (2019). Variations in protein processing lead to variations in structure and function of the HIV-1 envelope protein (Doctoral dissertation, Johns Hopkins University).

1. Now that we have our shared bibliography, each student will be assigned one article. Record the citation for your article in APA format:
   • In Web of Science, search for the specific article that you have been assigned.
     • How many cited references does that article have? 94 times
     • How many articles have cited the article you have been assigned? 71 times
2. What are the relative merits of searching with Google Scholar, PubMed, and Web of Science? Name two advantages and disadvantages for each.
   • Google Scholar: convenience of using familiar interface and a lot of possible results
   • Google Scholar: not many filtering options and variability of result based on text
   • PubMed: more filtered through and ability to search based on title/abstract
   • Pubmed: does not help with citation and yields no results sometimes due to specificity
   • Web of Science: less results that are more filtered through and ability to add more filters
   • Web of Science: less results could result in dead end quicker and only available through LMU link
3. What impact does choice of keywords have on your results? The impact is great based on choice of keyword more particularly with Google Scholar. It is clear that with Google Scholar the addition or deletion of a word causes results that differ by the thousands. Since PubMed and Web of Science give more limited results, the difference is also big as it will give a more refined result based on your keywords.
4. 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).

• My article: Haim, H., Strack, B., Kassa, A., Madani, N., Wang, L., Courter, J. R., ... & Smith III, A. B. (2011). Contribution of intrinsic reactivity of the HIV-1 envelope glycoproteins to CD4-independent infection and global inhibitor sensitivity. PLoS pathogens, 7(6). DOI: 10.1371/journal.ppat.1002101.

1. 1. Provide a link to the abstract of the article on PubMed:https://www.ncbi.nlm.nih.gov/pubmed/?term=Contribution+of+intrinsic+reactivity+of+the+HIV-1+envelope+glycoproteins+to+CD4-independent+infection+and+global+inhibitor+sensitivity.
   2. Provide a link to the full text of the article in PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121797/
   3. Provide a link to the full text of the article (HTML format) from the publisher website: https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1002101
   4. Provide a link to the full PDF version of the article from the publisher website: https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1002101&type=printable
   5. Who owns the rights to the article? Haim et al.
   6. How is the article available to you:
      • Is the article available “open access”? YES
      • 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.
      • 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.
      • 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.
   7. Is the article available online-only or both in print and online? Available online only
2. Evaluating the source--the journal
   1. Who is the publisher of the journal? PLOS Pathogens
   2. Is the publisher for-profit or non-profit? Non-profit
   3. Is the publisher a scientific society? No
   4. Does the publisher belong to the Open Access Publishers Association? Yes
   5. What country is the journal published in? All countries
   6. How long has the journal been in operation? 2005
   7. Are articles in this journal peer-reviewed? Yes
   8. Provide a link to the scientific advisory board/editorial board of the journal: https://journals.plos.org/plospathogens/s/editorial-board
   9. What is the journal impact factor? 6.158
3. 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? January 20, 2011
   3. On what date was the article accepted? April 18, 2011
   4. Did the article undergo any revisions before acceptance? Does not say
   5. When was the article published? June 23, 2011
   6. What is the approximate elapsed time between submission and publication? 5 months
   7. What are the institutions with which the authors are affiliated? Harvard Medical School, University of Pennsylvania
   8. Have the authors published other articles on this subject? Lead author is a part of 14 other papers related to HIV-1. The last author had 200 papers he has worked on that included many related to HIV-1.
   9. Is there a conflict of interest for any of the authors? No conflicting interests
   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. This paper discusses specific HIV variants and how their requirement for CD4 binding changes glycoproteins. It speaks on how CD4 requirements changes reactivity of glycoproteins and causes sesitivity to neutralization by antibodies.
   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 do not think that it would be a good journal club article. It is fairly complicated and the language in which it is written seems to be on a professional level that would include a lot of knowledge on background information and specific dynamics of HIV mechanisms.

Conclusion

At the beginning of lab today, I felt that I had known a decent amount about searching biological literature and evaluating sources based on my knowledge from taking "Biological Databases". I knew that we had other search engines that offer other benefits that Google Scholar does not. However, the biggest take away from today's lab was the legitimacy of publishers and journals. I have learned that I should be more actively critical about the journals and publishers in which papers are being published and not assume that it is academically valid.

Acknowledgments

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

Cdominguez (talk) 14:48, 5 March 2020 (PST)

References

• Google Scholar. (2020). Google Scholar. Retrieved March 5, 2020, from https://scholar.google.com/.
• OpenWetWare. (2020). BIOL368/S20:Week 8. Retrieved March 5, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_8.
• PubMed. (2020). PubMed. Retrieved March 5, 2020, from https://www.ncbi.nlm.nih.gov/pubmed?holding=calmulib.
• Web of Science. (2020). Web of Science. Retrieved March 5, 2020, from http://apps.webofknowledge.com/WOS_GeneralSearch_input.doproduct=WOS&search_mode=GeneralSearch&SID=5B2dLyJmepJiIyQnSaI&preferencesSaved=.