Difference between revisions of "Jkuroda Week 10"

Latest revision as of 04:58, 9 November 2015

Annotated Bibliography of Genomics Papers for Shewanella oneidensis

• Use a keyword search for each of these databases/tools and answer the following:
  • PubMed
    • What original keyword(s) did you use? How many results did you get?
      • "Shewanella oneidensis"
      • 793 results.
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • (("shewanella"[MeSH Terms] OR "shewanella"[All Fields]) AND oneidensis[All Fields]) AND ("2010/11/07"[PDat] : "2015/11/05"[PDat] AND English[lang])
      • 387 results
  • Google Scholar
    • What original keyword(s) did you use? How many results did you get?
      • "Shewanella oneidensis"
      • 13,200 results
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • "Shewanella oneidensis genomics" since 2014
      • 1,430 results
  • Web of Science
    • What original keyword(s) did you use? How many results did you get?
      • "Shewanella oneidensis"
      • 6,383 results
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • TOPIC: (Shewanella oneidensis) Refined by: LANGUAGES: ( ENGLISH ) AND RESEARCH DOMAINS: ( SCIENCE TECHNOLOGY ) AND LANGUAGES: ( ENGLISH ) AND RESEARCH AREAS: ( BIOCHEMISTRY MOLECULAR BIOLOGY OR MICROBIOLOGY OR GENETICS HEREDITY OR BIOTECHNOLOGY APPLIED MICROBIOLOGY OR SCIENCE TECHNOLOGY OTHER TOPICS OR ENVIRONMENTAL SCIENCES ECOLOGY OR CHEMISTRY OR CELL BIOLOGY )
      • 5,835 results

Microarray Paper

• Used ArrayExpress and searched for relevant microarray papers using filters.
• Wanted to find papers with bigger assay numbers so I sorted by that column.
• Among our group members we decided which papers to focus on.
• I chose E-GEOD-21044 - delta-arcS versus wild-type

Bibliographic Entry

• APA: Lassak J, Henche AL, Binnenkade L, Thormann KM. (2010). ArcS is the cognate sensor kinase in an atypical Arc system of Shewanella oneidensis MR-1. Applied and Environmental Microbiology, 76(10), 3263-3274.
• PubMed
• PMC
• Full Text
• PDF Version
• The American Society for Microbiology owns the copyright. The article is not open-access.
• The publisher is the American Society for Microbiology. It is a scientific society.
• This article is available in the printed and on-line journals.
• LMU has not paid for my access.
• This article has 76 citations.
• According to the Web of Science, this article is cited by 35 other articles.
• Looking at the titles of the other articles, it seems like most research has been focused on a two-component system present in shewanella oneidensis as well as anaerobic and aerobic respiration.
• Raw microarray data
• Processed microarray data
• The experiment looked to find more information about the Arc two-component system of shewanella oneidensis by shifting oxygen levels. The treatment in the experiment was the changing levels of oxygen. The control were strains of shewanella oneidensis MR-1 wild type cells.
• Expression profiles of three independent replicates of Shewanella oneidensis MR-1 delta-arcS were compared to three independent replicates of Shewanella oneidensis MR-1 wild type cells.

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