Kvescio Week 8 Assignment

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Weekly Assignments

Class Journals

Purpose

  • The Purpose of this assignment was to become familiar with different scientific databases, and to be able to search for articles that are relevant to future research.

Assignment

Google Scholar

  1. Perform a search in Google Scholar .
    1. Record the number of “hits” you found: 23,800
    2. Record the top 10 papers, this time using APA format:
      • 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.
      • Delwart, E. L., Shpaer, E. G., Louwagie, J., McCutchan, F. E., Grez, M., Rubsamen-Waigmann, H., & Mullins, J. I. (1993). Genetic relationships determined by a DNA heteroduplex mobility assay: analysis of HIV-1 env genes. Science, 262(5137), 1257-1261.
      • Seaman, M. S., Janes, H., Hawkins, N., Grandpre, L. E., Devoy, C., Giri, A., ... & Bhattacharya, T. (2010). Tiered categorization of a diverse panel of HIV-1 Env pseudoviruses for assessment of neutralizing antibodies. Journal of virology, 84(3), 1439-1452.
      • 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.
      • Lu, S., Santoro, J. C., Fuller, D. H., Haynes, J. R., & Robinson, H. L. (1995). Use of DNAs expressing HIV-1 Env and noninfectious HIV-1 particles to raise antibody responses in mice. Virology, 209(1), 147-154.
      • Chen, C. J., Banerjea, A. C., Harmison, G. G., Haglund, K., & Schubert, M. (1992). Multitarget-ribozyme directed to cleave at up to nine highly conserved HIV-1 env RNA regions inhibits HIV-1 replication—potential effectiveness against most presently sequenced HIV-1 isolates. Nucleic acids research, 20(17), 4581-4589.
      • 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.
      • Sanders, R. W., Derking, R., Cupo, A., Julien, J. P., Yasmeen, A., de Val, N., ... & Golabek, M. (2013). A next-generation cleaved, soluble HIV-1 Env trimer, BG505 SOSIP. 664 gp140, expresses multiple epitopes for broadly neutralizing but not non-neutralizing antibodies. PLoS pathogens, 9(9).
      • 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
      • Ritola, K., Robertson, K., Fiscus, S. A., Hall, C., & Swanstrom, R. (2005). Increased human immunodeficiency virus type 1 (HIV-1) env compartmentalization in the presence of HIV-1-associated dementia. Journal of virology, 79(16), 10830-10834.
  2. Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:
    • Senapathi, J., Bommakanti, A., Mallepalli, S., Mukhopadhyay, S., & Kondapi, A. K. (2020). Sulfonate modified Lactoferrin Nanoparticles as drug carriers with dual activity against HIV-1. Colloids and Surfaces B: Biointerfaces, 110979.
    • Tartaglia, L. J., Gupte, S., Pastores, K. C., Trott, S., Abbink, P., Mercado, N. B., ... & Bondzie, E. A. (2020). Differential Outcomes Following Optimization of Simian-Human Immunodeficiency Viruses From Clades AE, B and C. Journal of Virology.
    • Heredia, J. D. (2019). Conformational engineering of human chemokine receptors and HIV-1 Env using deep mutational scanning (Doctoral dissertation, University of Illinois at Urbana-Champaign).
    • Shen, H., Zhang, Z., Li, S., & Gu, Y. (2020). Progress in HIV-1 Env trimer design. Sheng wu Gong Cheng xue bao= Chinese Journal of Biotechnology, 36(1), 25-32.
    • Bradley, T., Kuraoka, M., Yeh, C. H., Tian, M., Chen, H., Cain, D. W., ... & Barr, M. (2020). Immune checkpoint modulation enhances HIV-1 antibody induction. Nature Communications, 11(1), 1-16.
  3. Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
    • Nussenzweig, M., Bjorkman, P. J., Scharf, L., & Scheid, J. (2019). U.S. Patent No. 10,421,803. Washington, DC: U.S. Patent and Trademark Office.
    • Harrison, S. C., Chen, B., Barouch, D., Nkolola, J. P., & Seaman, M. S. (2020). U.S. Patent Application No. 16/579,025.
    • 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.
    • Haynes, B. F., Liao, H. X., Danishefsky, S., Park, P., Sodroski, J., Aussedat, B., & Vohra, Y. (2019). U.S. Patent No. 10,286,057. Washington, DC: U.S. Patent and Trademark Office.
    • Harrison, S. C., Chen, B., Barouch, D. H., Nkolola, J. P., & Seaman, M. S. (2019). U.S. Patent No. 10,463,729. Washington, DC: U.S. Patent and Trademark Office.
  4. Filter your results using “Since 2016”, and record the top 5 papers, using APA format:
    • 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.
    • Steinhardt, J. J., Guenaga, J., Turner, H. L., McKee, K., Louder, M. K., O’Dell, S., ... & Doria-Rose, N. A. (2018). Rational design of a trispecific antibody targeting the HIV-1 Env with elevated anti-viral activity. Nature communications, 9(1), 1-12.
    • 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.
    • Gorman, J., Soto, C., Yang, M. M., Davenport, T. M., Guttman, M., Bailer, R. T., ... & Druz, A. (2016). Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design. Nature structural & molecular biology, 23(1), 81.
    • Pancera, M., Kwong, P. D., Schön, A., Freire, E., Abrams, C., Blanchard, S. C., ... & Sodroski, J. G. (2018). Publisher Correction: The β20–β21 of gp120 is a regulatory switch for HIV-1 Env conformational transitions.
  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:
    • mutations gp120
    • HIV gp120
    • Structure-function mutation gp120
    • structure and function of 120
    • Structure of gp10
    • gp120
    • gp120 structure and function
    • gp120 structure function
    • mutation in the gp120 protein
    • HIV-1 gp120 protein
    • gp120 mutation structure
    • mutation in gp120
    • HIV gp120 mutation
    • HIV gp120 function
    • Record the search terms that have now been assigned specifically to you:HIV-1-ENV
      • HIV-1 env structure variation

PubMed

  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: 1424
    • Record the top 10 papers (you don't need to do APA format for this):
      1. Differential Outcomes Following Optimization of Simian-Human Immunodeficiency Viruses From Clades AE, B and C.
      2. Comparison of shortened mosaic HIV-1 vaccine schedules: a randomised, double-blind, placebo-controlled phase 1 trial (IPCAVD010/HPX1002) and a preclinical study in rhesus monkeys (NHP 17-22).
      3. Immune checkpoint modulation enhances HIV-1 antibody induction.
      4. Diversity and function of maternal HIV-1-specific antibodies at the time of vertical transmission.
      5. [Progress in HIV-1 Env trimer design].
      6. CCR10 expression is required for the adjuvant activity of the mucosal chemokine CCL28 when delivered in the context of an HIV-1 Env DNA vaccine.
      7. Discovery of O-Linked Carbohydrate on HIV-1 Envelope and Its Role in Shielding against One Category of Broadly Neutralizing Antibodies.
      8. Late boosting of the RV144 regimen with AIDSVAX B/E and ALVAC-HIV in HIV-uninfected Thai volunteers: a double-blind, randomised controlled trial.
      9. Neonatal Rhesus Macaques Have Distinct Immune Cell Transcriptional Profiles following HIV Envelope Immunization.
      10. Immunogenicity of HIV-1 Vaccines Expressing Chimeric Envelope Glycoproteins on the Surface of Pr55 Gag Virus-Like Particles.
  2. Perform a title/abstract search on your assigned keywords.
    • Record the total number of hits: 1410
    • Record the top 10 papers (you don't need to do APA format for this):
      1. Differential Outcomes Following Optimization of Simian-Human Immunodeficiency Viruses From Clades AE, B and C.
      2. Comparison of shortened mosaic HIV-1 vaccine schedules: a randomised, double-blind, placebo-controlled phase 1 trial (IPCAVD010/HPX1002) and a preclinical study in rhesus monkeys (NHP 17-22).
      3. Immune checkpoint modulation enhances HIV-1 antibody induction.
      4. CpG Frequency in the 5' Third of the env Gene Determines Sensitivity of Primary HIV-1 Strains to the Zinc-Finger Antiviral Protein.
      5. Glycan Profiles of gp120 Protein Vaccines from Four Major HIV-1 Subtypes Produced from Different Host Cell Lines under Non-GMP or GMP Conditions.
      6. CCR10 expression is required for the adjuvant activity of the mucosal chemokine CCL28 when delivered in the context of an HIV-1 Env DNA vaccine.
      7. Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements.
      8. Novel transmitted/founder SHIVs for HIV latency and cure research.
      9. Publisher Correction: Asymmetric opening of HIV-1 Env bound to CD4 and a coreceptor-mimicking antibody.
      10. IFITM3 Reduces Retroviral Envelope Abundance and Function and Is Counteracted by glycoGag.
  3. Add the word “Review” to any articles that are review articles that you listed in question 8.
      1. [Progress in HIV-1 Env trimer design]. Review
  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. Harrison SC
    • 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. Correction: The structure of the Ctf19c/CCAN from budding yeast.
      2. Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate.
      3. Cryoelectron Microscopy Structure of a Yeast Centromeric Nucleosome at 2.7 Å Resolution.
      4. Cryo-EM Structure of Full-length HIV-1 Env Bound With the Fab of Antibody PG16.
      5. Structure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor.

Web of Science

  1. Now access the Web of Science database. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits: 1540
    • Record the top 10 papers (you don't need to use APA format for this):
      1. Neutralizing Antibody Induction by HIV-1 Envelope Glycoprotein SOSIP Trimers on Iron Oxide Nanoparticles May Be Impaired by Mannose Binding Lectin
      2. P2X1 Selective Antagonists Block HIV-1 Infection through Inhibition of Envelope Conformation-Dependent Fusion
      3. Flow Cytometry Analysis of HIV-1 Env Conformations at the Surface of Infected Cells and Virions: Role of Nef, CD4, and SERINC5
      4. Metastable HIV-1 Surface Protein Env Sensitizes Cell Membranes to Transformation and Poration by Dual-Acting Virucidal Entry Inhibitors
      5. Chemokine-Adjuvanted Plasmid DNA Induces Homing of Antigen-Specific and Non-Antigen-Specific B and T Cells to the Intestinal and Genital Mucosae
      6. Cryo-EM Structure of Full-length HIV-1 Env Bound With the Fab of Antibody PG16
      7. Discovery of O-Linked Carbohydrate on HIV-1 Envelope and Its Role in Shielding against One Category of Broadly Neutralizing Antibodies
      8. Anti-HIV-1 antibodies trigger non-lytic complement deposition on infected cells
      9. Neonatal Rhesus Macaques Have Distinct Immune Cell Transcriptional Profiles following HIV Envelope Immunization
      10. Boosting with AIDSVAX B/E Enhances Env Constant Region 1 and 2 Antibody-Dependent Cellular Cytotoxicity Breadth and Potency
  2. 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.
  3. Now that we have our shared bibliography, each student will be assigned one article. Record the citation for your article in APA format:
  • 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. https://www.ncbi.nlm.nih.gov/pubmed/26098315.
  • In Web of Science, search for the specific article that you have been assigned.
    • How many cited references does that article have? 87
    • How many articles have cited the article you have been assigned? 176

Comparing search engines

  • 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
    • Advantages to Google Scholar is that it is easy to use, and the APA citation is easily obtained.
  • Google Scholar: disadvantages
    • Disadvantages include the fact that not all articles on Google Scholar may be "scholarly", and it does not allow users to limit results to either peer reviewed or full text materials or by discipline.
  • PubMed: advantages
    • PubMed is easily accessible for everyone. There are also good advance searches, and the articles can be sorted by their article type, publication dates, text availability, species, and more.
  • Pubmed: disadvantages
    • PubMed may try to charge the publisher or user a large and unnecessary fee. PubMed has limited free access to full texts and articles.
  • Web of Science: advantages
    • The Web of Science has more complex and focused search options, and options to filter searches and make advanced searches. There is also the option to analyze results. Articles are of high quality.
    • Somewhat higher data quality.
  • Web of Science: disadvantages
    • Must be logged in with an institution.
  1. What impact does choice of keywords have on your results?
  2. 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).
    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
    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.
    6. How is the article available to you:
      • Is the article available “open access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If YES, stop here.
      • 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? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
  3. Evaluating the source--the journal
    1. Who is the publisher of the journal?
    2. Is the publisher for-profit or 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)
    4. Does the publisher belong to the Open Access Publishers Association?
    5. What country is the journal published in?
    6. How long has the journal been in operation? (e.g., browse the archive for the earliest article published)
    7. Are articles in this journal peer-reviewed?
    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)?
  4. Evaluating the source--the article
    1. Is the article a review or primary research article?
    2. On what date was the article submitted?
    3. On what date was the article accepted?
    4. Did the article undergo any revisions before acceptance?
    5. When was the article published?
    6. What is the approximate elapsed time between submission and publication?
    7. What are the institutions with which the authors are affiliated?
    8. Have the authors published other articles on this subject? (How will you find this out?)
    9. Is there a conflict of interest for any of 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.
    11. Make a recommendation--based on the information you have gathered, should we do a journal club on this article? Why or why not?
    12. 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

Acknowledgements

  • I had a zoom meeting with Dr. Dahlquist to discuss the assignment
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

(Kvescio (talk) 07:35, 11 May 2020 (PDT))

References

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