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Revealing Microbial Responses to Environmental Dynamics: Developing Methods for Analysis and Visualization of Complex Sequence Datasets.

Abstract The greatest barrier to understanding how life interacts with its environment is the complexity in which biology operates. In this work, I present experimental designs, analysis methods, and visualization techniques to overcome the challenges of deciphering complex biological datasets. First, I examine an iron limitation transcriptome of Synechocystis sp. PCC 6803 using a new methodology. Until now, iron limitation in experiments of Synechocystis sp. PCC 6803 gene expression has been achieved through media chelation. Notably, chelation also reduces the bioavailability of other metals, whereas naturally occurring low iron settings likely result from a lack of iron influx and not as a result of chelation. The overall metabolic trends of previ... (more)
Created Date 2017
Contributor Kellom, Matthew (Author) / Raymond, Jason (Advisor) / Anbar, Ariel (Committee member) / Elser, James (Committee member) / Shock, Everett (Committee member) / Walker, Sara (Committee member) / Arizona State University (Publisher)
Subject Bioinformatics / Bioinformatics / Clustering / Microbiology / Phylogenetics / Transcriptomics / Visualization
Type Doctoral Dissertation
Extent 173 pages
Language English
Reuse Permissions All Rights Reserved
Note Doctoral Dissertation Geological Sciences 2017
Collaborating Institutions Graduate College / ASU Library
Additional Formats MODS / OAI Dublin Core / RIS

  Full Text
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Description Dissertation/Thesis
102.2 KB application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
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Description Chapter 2 Excel file of transcriptome responses
4.7 KB application/zip
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Description Chapter 2 Perl scripts
14.1 KB text/x-perl
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Description Chapter 3 Cluster Aggregation Perl script
974.9 KB application/pdf
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Description Chapter 4 Example of the top-down clustering method used to construct dendritic heat maps
77.1 MB application/zip
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Description Chapter 4Perl scripts and dendritic heat map images
70.2 MB application/zip
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Description Chapter 4 Perl scripts and dendritic heat map images