Blitvak Week 10

Annotated Bibliography

Used Resources

• Pubmed
• Google Scholar
• Web of Science

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)

Title/Abstract field would be useful with the word genome since this would, it was hoped,

TS=(burkholderia cenocepacia AND J2315 AND cystic fibrosis) AND TI=(genome) Timespan=2000-2015 Search language=Auto

Transcription profiling by array of tobramycin tolerance in Burkholderia cenocepacia J2315 biofilms Transcription profiling by array of Burkholderia cenocepacia J2315 was exposed to heat stress and to stress form reactive oxygen species

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Brandon Litvak
BIOL 367, Fall 2015

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