Rlegaspi Week 11

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Shewanella oneidensis

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Journal Club Preparation: Microarray Paper

Bibliographic Information of Microarray Paper

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.

Experimental Design of the Study

Purpose: Examining the iron response of Shewanella oneidensis through the depletion and repletion of iron. Sample: Wild-type Shewanella oneidensis MR-1 (grown to mid-log phase, diluted in LB medium) Treatment: Iron chelator 2,2'-dipyridyl diluted in water to 80, 160, 240, and 320 micro-molar concentrations (Iron chelator depletes iron) Biological treatments - all of the studies were done in triplicates 3 samples per treatment Number of chips: 12 (3 samples x 4 treatments = 12) Dye swaps - Undetermined

Defining Unfamiliar Biological Terms

  1. Proteobacterium: comprise one of the largest divisions within prokaryotes and account for the vast majority of the known Gram-negative bacteria; great biological significance as it includes a large number of known human, animal and plant pathogens
  2. Methanogenesis: Bacterial conversion of methanogenic substrates [acetate, formate, hydrogen, carbon dioxide] into methane and carbon dioxide
  3. Ferric Uptake Regulator: a transcription factor which utilizes Fe(2+) as a corepressor and represses siderophore synthesis in pathogens
  4. RT-PCR (reverse transcriptase-PCR): a reaction applied when the target sequence is RNA, such as viral RNA or messenger RNA. Reverse transcriptase that copies DNA from an RNA template is present in the first round.
  5. Cytochrome: any of a class of hemoproteins, widely distributed in animal and plant tissues, whose main function is electron transport using the heme prosthetic group; distinguished according to their prosthetic groups
  6. Palindromic: In molecular biology, a self-complementary nucleic acid sequence; a sequence identical to its complementary strand, if both are "read" in the same 5' to 3' direction, or inverted repeating sequences running in opposite directions (for example, 5'-AGTTGA-3') on either side of an axis of symmetry
  7. Mutagenesis: act of mutating by deleting or changing the nucleotide sequence
  8. Spectrophotometric quantification: The determination of the structure or quantity of substances by measuring their capacity to absorb light of various wavelengths
  9. Chi square test: a statistical method of assessing the significance of a difference, as when the data from two or more samples is represented by a discrete number
  10. Hybridization: The process of forming a double stranded nucleic acid from joining two complementary strands of DNA (or RNA).

Article Outline

Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser to see the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.

    • What is the importance or significance of this work (i.e., your species)?
    • What were the methods used in the study?
    • Briefly state the result shown in each of the figures and tables.
    • How do the results of this study compare to the results of previous studies (See Discussion).
    • For the microarray paper (GenMAPP Users only), include the following:
      1. Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
      2. Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
      3. Construct a flow chart that illustrates the above.

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Ron Legaspi
BIOL 367, Fall 2015

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