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Snapshot of iron response in Shewanella oneidensis by gene network reconstruction Emily Simso and Ronald Legaspi Departments of Biology and Computer Science.

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Presentation on theme: "Snapshot of iron response in Shewanella oneidensis by gene network reconstruction Emily Simso and Ronald Legaspi Departments of Biology and Computer Science."— Presentation transcript:

1 Snapshot of iron response in Shewanella oneidensis by gene network reconstruction Emily Simso and Ronald Legaspi Departments of Biology and Computer Science Loyola Marymount University November 17, 2015

2 Overview Defining necessary vocabulary The significance of Shewanella oneidensis as a model organism Experimental design for the study Studying iron depletion in an anaerobic state Analyzing results through figures and tables Discussion and significance of results, contextualized with other organisms

3 Overview Defining necessary vocabulary The significance of Shewanella oneidensis as a model organism Experimental design for the study Studying iron depletion in an anaerobic state Analyzing results through figures and tables Discussion and significance of results, contextualized with other organisms

4 Defining necessary vocabulary Iron chelator Induced Repressed Repletion Depletion Up-regulated Down-regulated Aerobic Anaerobic

5 Overview Defining necessary vocabulary The significance of Shewanella oneidensis as a model organism Experimental design for the study Studying iron depletion in an anaerobic state Analyzing results through figures and tables Discussion and significance of results, contextualized with other organisms

6 The significance of Shewanella oneidensis as a model organism -S. oneidensis is a pathogen to both fish and humans -Iron-regulated metabolisms are often needed for virulent organisms  Vibrio cholerae  Bacillus cereus -Could be used to remediate U.S. Department of Energy’s uranium-contaminated sites due to grouping of transcriptional regulators

7 Overview Defining necessary vocabulary The significance of Shewanella oneidensis as a model organism Experimental design for the study Studying iron depletion in an anaerobic state Analyzing results through figures and tables Discussion and significance of results, contextualized with other organisms

8 Experimental design for the study

9 Overview Defining necessary vocabulary The significance of Shewanella oneidensis as a model organism Experimental design for the study Studying iron depletion in an anaerobic state Analyzing results through figures and tables Discussion and significance of results, contextualized with other organisms

10 Studying iron depletion in an anaerobic state

11 Overview Defining necessary vocabulary The significance of Shewanella oneidensis as a model organism Experimental design for the study Studying iron depletion in an anaerobic state Analyzing results through figures and tables Discussion and significance of results, contextualized with other organisms

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15 Three major modules in gene co-expression network

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22 Overview Defining necessary vocabulary The significance of Shewanella oneidensis as a model organism Experimental design for the study Studying iron depletion in an anaerobic state Analyzing results through figures and tables Discussion and significance of results, contextualized with other organisms

23 Anaerobic energy metabolism model New role of Crp Lack of oxidative stress Fur-independent results Rapid uptake of iron in S. oneidensis

24 References Biology Online. N.p., 27 May 2009. Web. 15 Nov. 2015.. 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, 131. http://doi.org/10.1186/1471-2164-10-131

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