Taur.vil Week 10

Week 10 Individual Journal

My Papers

Reference Paper

Title: Genome of the Bacterium Streptococcus pneumoniae Strain R6

By Hoskins et al. (2001)

link

PDF

Reference: Hoskins, J, Alborn, WE, Arnold, J, Blaszczak, LC, Burgett, S, DeHoff, BS, et al. (2001). Genome of the bacterium Streptococcus pneumoniae strain R6. Journal of Bacteriology, 183(19): 5709-5717.

1: Identification of Genes That Contribute to the Pathogenesis of Invasive Pneumococcal Disease by In Vivo Transcriptomic Analysis

Ogunniyi et al. 2012

Web Link: [1]

PDF: Article1.pdf

Data at: [2]

Experiment Performed: This paper compared the gene expression between pneumococci in virulent and non-virulent strains that had grown in the nasopharynx, lungs, and blood of mice.

Replicates: There were 3 biological replicates in this data set.

Reference: Ogunniyi, AD, Mahdi, LK, Trappetti, C, Verhoeven, N, Mermans, D, Van der Hoek, MB, et al. (2012). Identification of genes that contribute to the pathogenesis of invasive pneumococcal disease by in vivo transcriptomic analysis. Infection and Immunity, 80(9): 3268-3278.

2: Global transcription profiling and virulence potential of Streptococcus pneumoniae after serial passage

Pandya et al. 2009

Web Link: [3]

PDF: Not available (under copyright). May be downloaded directly from the link above.

Data at: [4]

Experiment Performed: In this experiment, they compared transcription profiles as virulent Streptococcus pneumoniae crossed from the nasopharynx into the blood. The control was transcription in the nasopharynx, the experimental condition transcription in the blood.

Replicates: For this paper there are 2 biological replicates and 4 spot replicates

Reference: Pandya, U, Sinha, M, Luxon, BA, Watson, DA, & Niesel, DW (2009). Global transcription profiling and virulence potential of Streptococcus pneumoniae after serial passage. Gene, 443(1): 22-31.

Lab Journal

Finding Reference Paper

1. Used PubMed and searched "Streptococcus pneumoniae" & "whole genome" & sequence to find microarray papers
2. With Kevin Meilak, found [5]
   • In the paper, identified strain R6 (accession no. NC_003098) as the reference sequence
3. Searched in UniProt for complete genome taxonomies containing Streptococcus pneumoniae and R6 (search results)
4. Found corresponding link in PubMed (link) and followed links to the original paper (link, PDF)

Finding other papers

1. In web of science, searched for "Streptococcus pneumoniae strain R6" under title and Hoskins in author to find the reference paper search
2. Only the reference paper appeared, and looked at the times cited (412 results)
3. Searched within results for microarray (56 results)
4. Selected the third option Title: "Identification of Genes That Contribute to the Pathogenesis of Invasive Pneumococcal Disease by In Vivo Transcriptomic Analysis" (link)
   • Clicked on links, found in PubMed Central, and downloaded pdf. The full article is also available online on PubMed Central and the Journal of Infection and Immunology.
   • The data is accessible at [6].
5. Went back to works citing the reference paper and restricted the search to "gene expression" and "transcription profiling" (8 results).
6. Selected a paper titled "Global transcription profiling and virulence potential of Streptococcus pneumoniae after serial passage".
   • Found journal link [7] on the LMU library links page and downloaded the pdf. The pdf is under copyright protection and can be found at [8].
   • The data is accessible at [9] and included 2 biological replicates per trial and four spot replicates. The GEO accession number is 12607.

Thoughts on Finding Papers

1. Looking at the articles citing the one I found, it appears most of the recent research has either been examining the specific genes of Stretococcus pneumoniae or in looking at changes in transcription that take place in virulent strains. There seems to be a very stron emphasis on how individual transcription factors regulate gene expression and what effect they have on bacterial phenotype.
2. During the process of finding papers, a lot of the ones on web of science seemed to not be very useful. However, by narrowing the search criteria, I was able to limit the total amount to a small number in which it was relatively easy to find useful papers. I am sure there are many more applicable papers available, they just did not appear near the top of my search criteria.

By Tauras Vilgalys

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