Msaeedi23 Week 10

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Annotated Bibliography of Genomics Papers for your Species

For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.

  • On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search.
  • On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography. Specifically, you need to search the literature/biological databases for the following:
    1. The journal article which describes the results of the whole genome sequencing for your species. (Note that you will be giving a journal club presentation on this article for your Week 11 assignment.)
      • Use a keyword search for each of these databases/tools and answer the following: 
PubMed

<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4463544/> 

What original keyword(s) did you use?  How many results did you get?
  • Searched for "bordetella pertussis" and it produced 9183 results. 
Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
  • Searched for "complete genome bordetella pertussis" and received 2129 results. 
Google Scholar

<http://www.nature.com/ng/journal/v35/n1/abs/ng1227.html> 

What original keyword(s) did you use?  How many results did you get?
  • I searched "bordetella pertussis" and received 69,400 results. 
Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
  • In adding "genome sequence" to my search I was able to narrow down the search results much more. I ended up receiving almost a third of the results at 20,300.
Web of Science

<http://apps.webofknowledge.com/full_record.do?product=WOS&search_mode=GeneralSearch&qid=2&SID=3Elv4Vzh4mOAmjyCxBn&page=1&doc=7> 

What original keyword(s) did you use?  How many results did you get?
  • In the initial search I conducted, I searched for "bordetella pertussis" and received 34,588 results.
Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
  • I narrowed the search down by searching for "complete genome bordetella pertussis" which significantly narrowed the results down to 52.
        • Remember, microarray data is not centrally located on the web. Some major sources are:
      • On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

Annotated Bibliography

Genome Sequencing Paper:

King, A. J., van Gorkom, T., Pennings, J. L., van der Heide, H. G., He, Q., Diavatopoulos, D., … Mooi, F. R. (2010). Correction: Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains. BMC Genomics, 11, 196. http://doi.org/10.1186/1471-2164-11-196

Microarray Papers:

Nakamura, M. M., Liew, S.-Y., Cummings, C. A., Brinig, M. M., Dieterich, C., & Relman, D. A. (2006). Growth Phase- and Nutrient Limitation-Associated Transcript Abundance Regulation in Bordetella pertussis . Infection and Immunity, 74(10), 5537–5548. http://doi.org/10.1128/IAI.00781-06

  1. What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
    • Changes in the complete "transcriptional profile" of Bordetella Pertussis was tested using two distinct strains, to determine responses in respective growth phases-lag, log, stationary- and to specific nutrient limitations. GMT-1 and Tohama I were the wild-type clinical isolates used as the control in the experiment. Tahoma I Sc3 mutants were grown from the wild type strain and selected for Bvg+. This is a phase locked mutant derived from a single substitution in bvgS.
  2. Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
    • Tahoma I and Tahoma I Sc3 mutants were plated into 12 separate plates, six of each. Microarray data from previous research analyzing GMT 1 was used to compare transcriptional differences observed in distinct bacterial phases under differing nutrient limitations for both the mutant and wild-type strain.

Mahrad Saeedi

Class Whoopers Team Page
Assignment Links
Individual Journals
Shared Journals
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