Anuvarsh Week 10

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Class Notes

Notes from 11/03/2015

Two papers we need to find:

  1. Genome Sequence Paper
  2. Microarray Data/Paper
    • Several requirements for this data to make it work with our project.
    • Rank the papers what we want to do 1-8 (2 papers/person)
    • Dr. Dahlquist will confirm which paper matches all of our criteria, and we will proceed with that paper.
    • Our ELN will include the process that we used to find our papers and the annotated biblio. from our genome paper and the one or two microarray papers.
      • Then we copy our annotated biblios onto the team page and rank the microarray papers
  • Find LibGuide here.

Notes from 11/05/2015

  • May be helpful to go to a Microarray Database and search for data on our species and then find corresponding papers.
    • Not cut and dry, some data may not have papers linked.
  • Always used the advanced search - especially on PubMed.
  • Web of Science has a link called "## Cited References" which, when clicked on, presents a list of links that lead to the articles that the original article references.
  • Web of Science, like Google Scholar, also has a "Cited By" link that indicates which articles have cited the original article.


Electronic Lab Notebook

Find Genome Paper

  • PubMed
    • Searching "Burkholderia cenocepacia genome" returned 150 results.
    • Searching "Burkholderia cenocepacia genome[Title/Abstract]" returned 5 results.
    • Filtering by publication date (last 5 years) returns 3 results.
    • Advanced Search Options:
      • The advanced search options used included requiring the search term to be in the title and abstract and filtering by year.
      • Requiring the search term to be in the title/abstract helped cut down the most number of results. It is incredibly beneficial if the exact topic of the desired paper is known.
  • Google Scholar
    • Searching "Burkholderia cenocepacia genome" returned 18,100 results.
    • Filtering by "no patents" returned 17,800 results.
    • Searching "allintitle: Burkholderia cenocepacia genome" with the same filter as above returns 17 results.
    • Advanced Search Options:
      • The advanced search options used included filtering to remove patents from the search results and requiring search terms to be in the title of the articles.
      • Requiring the search term to be in the title/abstract cut down most of the excess search results here. Having the no patent filter is also incredibly helpful in determining whether the results we have are actually journal articles that we want.
  • Web of Science
    • Searching "Burkholderia cenocepacia genome" by Topic returned 188 results.
    • Searching "Burkholderia cenocepacia genome" by Title returned 22 results.
    • Searching these results with the term "nucleotide sequence" returned 3 results.
    • The third result is the paper titled "The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patient" that we are using for our project.
  • Prospective search in the ISI Web of Science/Knowledge database of genome sequence paper
    • How many articles does this article cite?
      • This article has 150 cited references.
    • How many articles cite this article?
      • This article is cited 128 times in Web of Science Core Collection, and 468 in All Databases.
    • Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
      • Based on the titles and abstracts of the papers that cite this article, some topics of research include: bacterial antimicrobial metal ion resistance, ffflux pump-mediated drug resistance, biofilm formation in Burkholderia, and the relationship between Burkholderia and Cystic Fibrosis.
    • Advanced Search Options:
      • We searched the key terms in the title fields of the papers, and then refined further using Web of Sciences refining search option.
      • Searching by the title was incredibly helpful to narrow down the number of results we had. That being said, having the refining search tool is a cool way to narrow down search results in a more open ended manner.

Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08

  • The link to the abstract from PubMed. http://www.ncbi.nlm.nih.gov/pubmed/18931103
  • The link to the full text of the article in PubMedCentral. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/
  • The link to the full text of the article (HTML format) from the publisher web site. http://jb.asm.org/content/191/1/261.long
  • The link to the full PDF version of the article from the publisher web site. http://jb.asm.org/content/191/1/261.full.pdf+html
  • Who owns the rights to the article? American Society for Microbiology
    • Does the journal own the copyright? Yes
    • Do the authors own the copyright? No
    • Do the authors own the rights under a Creative Commons license? No
    • Is the article available “Open Access”? Yes
  • What organization is the publisher of the article? What type of organization is it? American Society for Microbiology which is a scientific society
  • Is this article available in print or online only? It is both available in print and online.
  • Has LMU paid a subscription or other fee for your access to this article? No
  • How many articles does this article cite? It has 150 cited references.
  • How many articles cite this article? It is cited 128 times on all databases.
  • Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most papers are about antibiotic resistance and therapeutic strategies.

Find Microarray Paper

  • In ArrayExpress, filtered by organism Burkholderia cenocepacia, experiment type "rna assay", experiment type "array assay".
    • This search resulted in 24 results.
    • In order to find array data with articles, I systematically clicked through all of the experiments in my search results in order of highest to lowest replicates and looked for the experiments with a paper associated or linked.
    • Relevant Articles (found in ArrayExpress):
      1. Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. PLoS One, 8(3), e58943.
        • The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
        • The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
        • The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
          • Cannot find HTML format on publisher web site.
        • The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
        • Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
        • Does the journal own the copyright? Yes.
        • Do the authors own the copyright? No.
        • Do the authors own the rights under a Creative Commons license? Yes.
        • Is the article available “Open Access”? Yes.
        • What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
        • Is this article available in print or online only? Available in print and online.
        • Has LMU paid a subscription or other fee for your access to this article? No.
        • Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
        • What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
        • Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
        • How many articles does this article cite? This article has 34 cited references.
        • How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
        • Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.
      2. Mira, N. P., Madeira, A., Moreira, A. S., Coutinho, C. P., & Sá-Correia, I. (2011). Genomic expression analysis reveals strategies of Burkholderia cenocepacia to adapt to cystic fibrosis patients’ airways and antimicrobial therapy. PLoS One, 6(12), e28831.


Other Links

User Page: Anindita Varshneya
Class Page: BIOL/CMSI 367: Biological Databases, Fall 2015
Group Page: GÉNialOMICS

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