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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
Copyright
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
  Chapter2_Supplemental_File_S1.xlsx
102.2 KB application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
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Description Chapter 2 Excel file of transcriptome responses
  Chapter2_Supplemental_File_S2.zip
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Description Chapter 2 Perl scripts
  Chapter3_Supplemental_File_1.pl
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Description Chapter 3 Cluster Aggregation Perl script
  Chapter4_Supplemental_File_S1.pdf
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Description Chapter 4 Example of the top-down clustering method used to construct dendritic heat maps
  Chapter4_Supplemental_File_S2.zip
77.1 MB application/zip
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Description Chapter 4Perl scripts and dendritic heat map images
  Chapter4_Supplemental_File_S3.zip
70.2 MB application/zip
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Description Chapter 4 Perl scripts and dendritic heat map images