Difference between revisions of "Taur.vil Week 10"
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| − | [[ | + | [[Week_10| Week 10]] Individual Journal |
| + | ==My Papers== | ||
| + | ===Reference Paper=== | ||
| + | Title: Genome of the Bacterium Streptococcus pneumoniae Strain R6 | ||
| + | :By Hoskins et al. (2001) | ||
| + | :[http://jb.asm.org/content/183/19/5709.full link] | ||
| + | :[[Media: R6_Reference_Genome_Paper.pdf|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: [http://iai.asm.org/cgi/content/full/80/9/3268] | ||
| + | :PDF: [[Media:Article1.pdf|Article1.pdf]] | ||
| + | :Data at: [http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=305&action=view&l=a] | ||
| + | :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: [http://www.sciencedirect.com/science/article/pii/S037811190900184X] | ||
| + | :PDF: Not available (under copyright). May be downloaded directly from the link above. | ||
| + | :Data at: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12607] | ||
| + | :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== | ==Lab Journal== | ||
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#Searched within results for microarray (56 results) | #Searched within results for microarray (56 results) | ||
#Selected the third option Title: "Identification of Genes That Contribute to the Pathogenesis of Invasive Pneumococcal Disease by In Vivo Transcriptomic Analysis" ([http://apps.webofknowledge.com/full_record.do?product=WOS&search_mode=Refine&qid=4&SID=4FpPeeam4xp5wvHIYs3&page=1&doc=3 link]) | #Selected the third option Title: "Identification of Genes That Contribute to the Pathogenesis of Invasive Pneumococcal Disease by In Vivo Transcriptomic Analysis" ([http://apps.webofknowledge.com/full_record.do?product=WOS&search_mode=Refine&qid=4&SID=4FpPeeam4xp5wvHIYs3&page=1&doc=3 link]) | ||
| − | #*Clicked on links, found in [http://www.ncbi.nlm.nih.gov/pmc/?cmd=Search&term=22778095%5Bpmid%5D PubMed Central], and downloaded [[Media:Article1.pdf|pdf]]. The full article is also available online on [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418729/?report=classic PubMed Central] and the [http://iai.asm.org/cgi/content/full/80/9/3268 Journal of Infection and Immunology]. The data is accessible at [http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=305&action=view&l=a]. | + | #*Clicked on links, found in [http://www.ncbi.nlm.nih.gov/pmc/?cmd=Search&term=22778095%5Bpmid%5D PubMed Central], and downloaded [[Media:Article1.pdf|pdf]]. The full article is also available online on [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418729/?report=classic PubMed Central] and the [http://iai.asm.org/cgi/content/full/80/9/3268 Journal of Infection and Immunology]. |
| − | + | #*The data is accessible at [http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=305&action=view&l=a]. | |
| − | + | #Went back to works citing the reference paper and restricted the search to "gene expression" and "transcription profiling" (8 results). | |
| − | - | + | #Selected a paper titled "Global transcription profiling and virulence potential of Streptococcus pneumoniae after serial passage". |
| − | + | #*Found journal link [http://www.sciencedirect.com/science/article/pii/S037811190900184X] on the LMU library links page and downloaded the pdf. The pdf is under copyright protection and can be found at [http://ac.els-cdn.com/S037811190900184X/1-s2.0-S037811190900184X-main.pdf?_tid=99f4bfc0-429c-11e3-aef1-00000aab0f01&acdnat=1383272791_5988b606730e935c9a89b816b6f73ef0]. | |
| − | + | #* The data is accessible at [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12607] and included 2 biological replicates per trial and four spot replicates. The GEO accession number is 12607. | |
| − | # | + | |
| + | ===Thoughts on Finding Papers=== | ||
| + | #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. | ||
| + | #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. | ||
Latest revision as of 22:19, 2 November 2013
Week 10 Individual Journal
Contents |
[edit] My Papers
[edit] Reference Paper
Title: Genome of the Bacterium Streptococcus pneumoniae Strain R6
- 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.
[edit] 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.
[edit] 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.
[edit] Lab Journal
[edit] Finding Reference Paper
- Used PubMed and searched "Streptococcus pneumoniae" & "whole genome" & sequence to find microarray papers
- With Kevin Meilak, found [5]
- In the paper, identified strain R6 (accession no. NC_003098) as the reference sequence
- Searched in UniProt for complete genome taxonomies containing Streptococcus pneumoniae and R6 (search results)
- Found corresponding link in PubMed (link) and followed links to the original paper (link, PDF)
[edit] Finding other papers
- In web of science, searched for "Streptococcus pneumoniae strain R6" under title and Hoskins in author to find the reference paper search
- Only the reference paper appeared, and looked at the times cited (412 results)
- Searched within results for microarray (56 results)
- 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].
- Went back to works citing the reference paper and restricted the search to "gene expression" and "transcription profiling" (8 results).
- Selected a paper titled "Global transcription profiling and virulence potential of Streptococcus pneumoniae after serial passage".
[edit] Thoughts on Finding Papers
- 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.
- 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.
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