Kevin Wyllie Week 10

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Finding the Genome Paper for Burkholderia cenocepacia

Due to microarray data availability, we chose to use the J2315 strain.

PubMed

  • Search terms
    • The following queries, without any filters, returned the shown number of results.
      1. "Burkholderia cenocepacia" - 550 results
      2. "Burkholderia cenocepacia J2315 genome" - 37 results
      3. "Burkholderia cenocepacia J2315 genome sequence" - 24 results
  • Filters and advanced searches
    • Using query 2, after selecting "Advanced search" and "Title/Abstract" from the drop-down menu, the search returned 6 results.
    • I sorted by publication date and scrolled to the bottom of the list.
      • The earliest article in the list does refer to B. cencocepacia J2315's genome but does not include it.
      • I attempted to find the original genome paper through this paper's citations, but using a ctrl-F search for "genome" shows that none of the cited articles even have "genome" in their titles.

Google Scholar

  • Search terms
    • The following queries, without any filters, returned the shown number of results.
      1. "Burkholderia cenocepacia" - 21,500 results
      2. "Burkholderia cenocepacia J2315 genome" - 932 results
      3. "Burkholderia cenocepacia J2315 genome sequence" - 883 results
  • Filters and advanced searches
    • Using queries 2 and 3 (without filters), the desired article, "The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients" was actually the first article in the list (see below for full citation).
    • Using query 2, unchecking "include patents" reduced the number of results to 908.
    • Using query 2 Opening the advanced search page and changing "where my words occur" from "anywhere in the article" to "in the title of the article" reduced the number of results to 7.

Web of Science

  • Search terms
    • The following queries, without any filters, returned the shown number of results.
      1. "Burkholderia cenocepacia" - 1,185 results
      2. "Burkholderia cenocepacia J2315 genome" - 63 results
      3. "Burkholderia cenocepacia J2315 genome sequence" - 47 results
  • Filters and advanced searches
    • Using query 2, the number of results reduced to 4 when the following filters were applied.
      • "Title" was selected from dropdown bar, on the first page, next to the search bar.
      • After the search was conducted, these options were selected from the sidebar on the left.
        • "Research domains: SCIENCE TECHNOLOGY"
        • "Research areas: BIOCHEMISTRY MOLECULAR BIOLOGY"
        • "Document types: ARTICLE"
      • Arranging by "Publication date -- oldest to newest," the desired article is third from the top (the earlier two articles involve only specific locations in the genome).

Web of Science Citation Search

  • The following search terms were used.
    • Cited Title*: "burkholderia cenocepacia J2315 genome"
    • Cited Year(s): "2009"
  • The search returned three potential works
Kw assignment10 screenshot2.png
  • The results for the correct article are as follows.
    • This article has been cited 468 times across all databases, and 128 times within the Web of Science Core Collection.
    • This article cites 150 other articles.
Kw assignment10 screenshot.png
  • This organism's potential antibiotic resistance, as well as the mechanisms that mediate it, seem to be of interest to the scientific community. This is probably because Burkholderia cenocepacia is a known pathogen, commonly infecting cystic fibrosis patients.

Searching for Microarray Data using ArrayExpress

  • EBI ArrayExpress was used for this portion of the assignment.
  • The search term used was "burkholderia cenocepacia J2315," and the following filters were used (under "By experiment type" in the filter menu).
    • "RNA assays"
    • "Array assays"
  • The search returned 18 results.
  • Most/many of the results mention "transcriptional profiling," and most mention the treatment used in the title, both of which are desirable. Also, most use four or more assays.

Annotated Bibliography

Genome Paper

Holden, M. T. G. et al. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients. Journal of Bacteriology, 191(1), 261–277. doi: 10.1128/JB.01230-08

  • PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/18931103
  • PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/
  • Publisher Full Text (HTML): http://jb.asm.org/content/191/1/261.full
  • Publisher Full Text (PDF): http://jb.asm.org/content/191/1/261.full.pdf+html
  • Copyright: Journal of Bacteriology. Neither the article page nor ASM's "About ASM" page indicates whether or not they use OpenAccess, but they do refer to themselves as an "inclusive organization," so I would hope that they do.
  • Publisher: American Society for Microbiology, a scientific society.
  • Availability: In print, online.
  • Did LMU pay a fee for this article: Presumably, no. The article is available on PubMed.
  • This article has been cited 468 times across all databases, and 128 times within the Web of Science Core Collection.
  • This article cites 150 other articles.
  • This organism's potential antibiotic resistance, as well as the mechanisms that mediate it, seem to be of interest to the scientific community. This is probably because Burkholderia cenocepacia is a known pathogen, commonly infecting cystic fibrosis patients.

Microarray Paper

Sass, A., Marchbank, A., Tullis, E., LiPuma, J. J., & Mahenthiralingam, E. (2011) Spontaneous and evolutionary changes in the antibiotic resistance of Burkholderia cenocepacia observed by global gene expression analysis. BMC genomics, 12(1), 373. doi:10.1186/1471-2164-12-373

  • Transcriptomic analysis was performed using the following strains, after exposure to different antibiotics in the presence of an antibiotic potentiator:
    • Control: the wild-type J2315 strain
    • Treatment: mutant strains which showed antibiotic resistance
    • Treatment: ET12 outbreak isolates, described as "pan-resistant"
  • Three biological replicates were used for each experiment.
  • The raw data does not appear to be directly linked from the article itself. The supplement includes a summary spreadsheet, which only displays values for fold-changes that were statistically significant. However both the raw and processed data files are available on the ArrayExpress entry.
  • PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/21781329
  • PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155924/
  • Publisher Full Text (HTML): http://www.biomedcentral.com/1471-2164/12/373
  • Publisher Full Text (PDF): http://www.biomedcentral.com/content/pdf/1471-2164-12-373.pdf
  • Copyright: 2011 Sass et al; licensee BioMed Central Ltd. "This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited."
  • Publisher: BioMedCentral, respected Open Access organization.
  • Availability: Article does not initially appear to be available in print, however, BioMedCentral's website mentions that "high quality, bound reprints" can be purchased for any published article.
  • Did LMU pay a fee for this article: No - open access.
  • This article cites 64 other articles.
  • This article has been cited by 29 other articles (across all databases).
  • The scientific community seems to be particularly interested in this organism's antimicrobial resistance, probably because this is a known pathogen, particularly relevant in the context of cystic fibrosis.

Note: though there were ample entries for this organism in ArrayExpress, their corresponding articles could not be found, and were often not cited in ArrayExpress.


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