Blitvak Week 10

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Week 10 Assignment

Used Resources

Keyword Searches

  • Pubmed was entered, on 11/5, and the keywords Burkholderia cenocepacia genome were utilized and a search was conducted; 150 records were found with these keywords and most of the results were related to Burkholderia cenocepacia genes and their characterization. The results seemed very broad and covered a wide variety of topics (the observed papers covered the purpose of certain genetic regions, the virulence of the bacteria, and protein characterization, among many other topics). A paper related to the sequencing of the entire genome of a Burkholderia cenocepacia strain was found on the second page of the search results (was result #21). The keyword sequence was added to the search, which now yielded 106 results. The results appeared to be very similar to the previous search (lots of topics were still covered, which appear to be related to the use of genome data). The same paper that was previously found, which announced the complete genome sequencing of a B. cenocepacia strain (H111), was found earlier. Reading through the genome sequence paper (titled "Genome Sequence of Burkholderia cenocepacia H111, a Cystic Fibrosis Airway Isolate"), the term Burkholderia cepacia complex was noticed (abbreviated BCC), which is a name of a group of bacteria (composed of at least 18 species) to which Burkholderia cenocepacia belongs. Using the search terms burkholderia cenocepacia genome sequence BCC led to 25 results (genome paper appeared as the second result); BCC was effective in filtering the results.
  • Google Scholar was entered, on 11/5, and the search query burkholderia cenocepacia sequenced genome was used, this search led to 16,400 results which were fairly similar to what was previously found using Pubmed; the vast majority of results, on the first couple of pages, appear to be papers related to B. cenocepacia genes (which used data from a genome paper). The second result was a paper detailing the full genome of the J2315 strain of B. cenocepacia (which is possibly the "model" strain for work related to the bacteria). Using the keywords burkholderia cenocepacia genome bcc cystic fibrosis led to 1,070 results, with the paper regarding the J2315 strain being the first result.
  • Web of Science was entered, on 11/8, and a search was conducted using the keywords Burkholderia cenocepacia genome via search by Topic; this search yielded 104 results (93 articles and 9 review papers out of the 104). Adding the keywords nucleotide sequence led to there being 8 results (genome paper on the J2315 strain was the first result).

Advanced Searches

  • Pubmed was entered on 11/9 and an advanced search was conducted using ((((genome[Title/Abstract]) AND burkholderia cenocepacia[Text Word]) AND J2315[Text Word])); it was decided that the strain of focus will be J2315 and, thus, J2315 was searched for through the use of the [Text Word] advanced search field. It was also determined that the word genome would go well with the [Title/Abstract] (it was thought that this will would make the results focus on genomes and genome-related experimental work). Burkholderia Cenocepacia was also used with the [Text Word] field. In the end, this advanced search led to 25 results, with one of the results being a genome paper on J2315 (the rest being research that, presumably, stemmed from that work).
  • Google Scholar was entered on 11/9 and an initial search was conducted with burkholderia cenocepacia genome j2315, this led to about 933 results with the top result being the genome paper of interest (The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients); the rest of the papers, as was previously seen, were related to work tied to the genome of the bacteria. The advanced search menu item was clicked (by pressing the arrow button to the right of the My Citations menu item) and the advanced search overlay popped up; I decided to work with the where my words occur section and I changed the setting to in the title of the article. Using the advanced search allintitle: burkholderia cenocepacia genome j2315, I found 7 results and the genome paper of choice was the top result.
  • Web of Science was entered on 11/9 and Basic Search was set to Advanced Search through the drop-down menu next to the Basic Search heading. I noticed that there was a little help section next to the search box which listed the Booleans and Field Tags that can be used. I decided to use the TS (topic), TI (title, and the AND boolean; I used TS=(burkholderia cenocepacia AND J2315 AND cystic fibrosis) AND TI=(genome) for my advanced search which led to 6 results, which included the genome paper of interest.

Prospective Search

  • Web of Science was entered on 11/9/15
  • Search was conducted by Title; The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients was used for the search
  • How many articles does this article cite: 150
  • How many articles cite this article: 128 (from Web of Science Core Collection), 468 (in All Databases)
  • Based on the titles and abstracts of the works that cited this article, it seems that the research has been focused upon factors related to the virulence and antibiotic resistance of B. cenocepacia. Much research is also related to the bacteria and its relationship with individuals with cystic fibrosis (treatment focused). Using the genome data, it seems that researchers are focusing on the biofilm forming/virulence properties of the bacteria (which are related to quorum sensing) and other characteristics that inhibit antibiotic action (such as the presence of efflux pump proteins that diminish the effects of an antibiotic).

Finding Microarray Papers

  • Database Used: ArrayExpress
  • Search was initially conducted by using these keywords: burkholderia cenocepacia j2315, this resulted in 20 experiments as the results.
  • In the Filter search results drop-down menu, By organism was set to "Burkholderia cenocepacia", By experiment type was set to "RNA assay" and "Array assay", By array was kept as "All arrays"; after setting the filters, the filter button was pressed. The results now represented 16 experiments; 14 out of 16 results appeared to be directly related with the J2315 strain. It was also noticed that 12 of the 16 data-sets had the same author, Andrea M. Sass.
  • Chosen Microarray dataset:
    • Accension: E-GEOD-15817
    • Data Title: Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics
  • Looking at the page for the data, it was found that the related paper is titled: Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics

Annotated Bibliography

  1. Holden, M. T., Seth-Smith, H. M., 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.
    • 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?sid=acd9ceae-4092-48fa-8b2e-44b6859a3653
    • Publisher Full Text (PDF): http://jb.asm.org/content/191/1/261.full.pdf+html
    • Copyright: © 2009, American Society for Microbiology (information found on PDF version of article); the article and the journal is delayed open access (available 6 months after publication)
    • Publisher: American Society for Microbiology (scientific society)
    • Availability: in print and online
    • Did LMU pay a fee for this article: No
    • How many articles does this article cite: 150
    • How many articles cite this article: 128 (from Web of Science Core Collection), 468 (in All Databases)
    • *Based on the titles and abstracts of the works that cited this article, it seems that the research has been focused upon factors related to the virulence and antibiotic resistance of B. cenocepacia. Much research is also related to the bacteria and its relationship with individuals with cystic fibrosis (treatment focused). Using the genome data, it seems that researchers are focusing on the biofilm forming/virulence properties of the bacteria (which are related to quorum sensing) and other characteristics that inhibit antibiotic action (such as the presence of efflux pump proteins that diminish the effects of an antibiotic).
  2. Yoder-Himes, D. R., Konstantinidis, K. T., & Tiedje, J. M. (2010). Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics. PLoS One, 5(1), e8724.

Brandon Litvak
BIOL 367, Fall 2015

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