Emilysimso Week 10

In Class Notes - what you need for annotated bibliography

1. Genome Sequence paper - find the best one (not for a subspecies)
2. Microarray data paper - data that will be analyzed
3. 1-2 papers per group member on species (will rank on group page on which to focus on)\

Electronic lab notebook - details the search for these papers

Individual page - annotate bibliography

Teams page - copy genome paper and create ranked list

Use APA style to cite, make sure to translate into wiki text

DOI = primary ID for an article (digital object identifier)

Genome Sequence Paper

PubMed

• First keyword search: Shewanella Oneidensis genome sequence, 128 results from PubMed
• Second search: Shewanella Oneidensis in Genome, there were 5 publications
• Advanced search: Shewanella Oneidensis genome (in Title/Abstract section), 3 results

Google Scholar

• First search: Shewanella Oneidensis genome sequence, 7,450 results
• Second search: Shewanella Oneidensis complete genome sequence, 6,460 results
  • Removed patents, had 6,220 results
  • Searched for papers since 2011, got 2,950 results

Web of Science

• First search: Shewanella Oneidensis genome, 441 results
  • Refined by selecting just articles, got 262 results

Chosen Paper Information

• APA citation: Heidelberg, J. F., Paulsen, I. T., Nelson, K. E., Gaidos, E. J., Nelson, W. C., Read, T. D., ... & Fraser, C. M. (2002). Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis. Nature biotechnology, 20(11), 1118-1123.
• PubMed abstract
• PubMedCentral article:
• Full text from publisher website
• PDF file from publisher website
• Article rights: copyright owned by publisher
• Publishing organization of article: Nature Publishing Group, which is for profit
• Print or online only: online only
• Has LMU paid subscription: no

Microarray Paper

• Browsed all of ArrayExpress
• Filtered search results: Shewanella oneidensis, RNA assay, Array assay, All arrays
  • Had 20 experiments
  • Look for transcription profiling by array
  • Want a large assay number
• Results seemed to be relevant to what we were searching for

Chosen Paper

• Paper ID: E-GEOD-15334

• The complete bibliographic reference in the APA style
  • Yang, Y., Harris, D. P., Luo, F., Xiong, W., Joachimiak, M., Wu, L., ... & Zhou, J. (2009). Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. BMC genomics, 10(1), 131.
• The link to the abstract from PubMed.
• The link to the full text of the article in PubMedCentral
• The link to the full text of the article (HTML format) from the publisher web site.
• The link to the full PDF version of the article from the publisher web site.
• Who owns the rights to the article?
  • The article is Open Access and the authors own the rights under a Creative Commons license.
• What organization is the publisher of the article? What type of organization is it?
  • BMC Genomics is the publisher, which is a scientific society
• Is this article available in print or online only?
  • It is online only
• Has LMU paid a subscription or other fee for your access to this article?
  • No
• How many articles does this article cite?
  • This paper sites 48 other articles
• How many articles cite this article?
  • 3
    • Roles of UndA and MtrC of Shewanella putrefaciens W3-18-1 in iron reduction
    • Global transcriptional response of Caulobacter crescentus to iron availability
    • Molecular ecological network analysis
• Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
  • This article has mostly been used to look at the iron response of other strains or organisms. It may have been used for comparison's sake or to modify the original methodology to fit the new experiment.
• Link to microarray data
  • Found it on ArrayExpress
  • This contains the raw data that we will use for our research
• What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
  • Strains of Shewanella oneidensis were put under iron depletion and repletion conditions. The control would be a regular strain of the organism, while the treatments would be either increasing or decreasing the iron levels.
• Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
  • 4 biological replicates of each treatment condition were performed

Weekly Assignment Information

User: Emilysimso

Assignments

• Week 1
• Week 2
• Week 3
• Week 4
• Week 5
• Week 6
• Week 7
• Week 8
• Week 9
• Week 10
• Week 11
• Week 12
• Week 13
• Week 14
• Week 15

Individual Journal Entries

• Emilysimso Week 2
• Emilysimso Week 3
• Emilysimso Week 4
• Emilysimso Week 5
• Emilysimso Week 6
• Emilysimso Week 7
• Emilysimso Week 8
• Emilysimso Week 9
• Emilysimso Week 10
• Emilysimso Week 11
• Emilysimso Week 12
• Emilysimso Week 13
• Emilysimso Week 14
• Emilysimso Week 15

Class Journal Entries

• Class Journal Week 1
• Class Journal Week 2
• Class Journal Week 3
• Class Journal Week 4
• Class Journal Week 5
• Class Journal Week 6
• Class Journal Week 7
• Class Journal Week 8
• Class Journal Week 9
• Class Journal Week 10
• Class Journal Week 11
• Class Journal Week 12
• Class Journal Week 13
• Class Journal Week 14
• Class Journal Week 15

Group Project

Heavy Metal HaterZ