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dc.contributor.advisorBaliga, Nitin Sen_US
dc.contributor.authorBeer, Karlyn Doraldyneen_US
dc.date.accessioned2014-02-24T18:26:43Z
dc.date.issued2014-02-24
dc.date.submitted2013en_US
dc.identifier.otherBeer_washington_0250E_12435.pdfen_US
dc.identifier.urihttp://hdl.handle.net/1773/25099
dc.descriptionThesis (Ph.D.)--University of Washington, 2013en_US
dc.description.abstractAlthough microbial adaptation to new environments has been studied extensively in laboratory evolution experiments, less is understood about how natural strains adapt to new, constant laboratory conditions after transitioning to become model organisms. In this dissertation, I took a cross-sectional approach to query the osmotolerance repertoire of a decades-old model halophilic archaeon compared with recently isolated conspecific natural isolates. Using growth rate reaction norms and whole genome sequencing, I found that fitness is highly variable across gradients in total salinity and ion composition for both laboratory and natural strains. Although we expected divergent reaction norms and genome sequences to support evidence of specialization in the model organism, both the model and natural isolates shared similar growth patterns across conditions and shared >95% sequence similarity. In the following chapters, I characterize the hypersaline environment in the Great Salt Lake, quantify osmotolerance phenotypes across three gradients in salinity, and I explore gene expression signatures across an ion composition gradient in H. salinarum NRC-1. I close by comparing fitness profiles and genome sequences of the model and natural strains, and I address the unexpected similarity among strains, even after eliminating contamination as an explanation. Ultimately, despite at least 50 years of evolutionary opportunity between the lab and natural isolates, we find that osmotolerance phenotypes and nucleotide sequence is largely maintained in the laboratory, and that a decades-old model organism remains a relevant study organism for microbial-environmental response.en_US
dc.format.mimetypeapplication/pdfen_US
dc.language.isoen_USen_US
dc.relation.haspartBioscreen_Staging_Karlyn_101111_RUN_16media_4culture.pkg; other; Method file for Hamilton Microlab Star liquid handling robot -16media x 4 culture.en_US
dc.relation.haspartBioscreen_Staging_Karlyn_120811_RUN_15media_4culture.pkg; other; Method file for Hamilton Microlab Star liquid handling robot -15media x 4 culture.en_US
dc.relation.haspartGCAFupdate_042012.zip; code/script; Growth Curve Analysis R package scripts for extracting parameters from Bioscreen growth curve data.en_US
dc.relation.haspartSalinityRatios_II_GCAF_v2.R; code/script; Analysis and statistics using growth curve parameters from GCAF package.en_US
dc.relation.haspartSalinityII_stats_plots.R; code/script; Global analysis of all growth curves using output of SalinityRatios_II_GCAF_v2.R.en_US
dc.relation.haspartGSL_imitation_GCAF.R; code/script; GCAF analysis of the Great Salt Lake imitation media series.en_US
dc.relation.haspartEvap_Mratio_diffs.R; code/script; Script for comparing compositional data and mapping Great Salt Lake salinities onto media compositions.en_US
dc.relation.haspartSalODvsCts_ImageAnalysis.R; code/script; Analysis of ImageJ cell size/morphology microscopy data.en_US
dc.relation.haspartSalArrays_expt4_analysis.R; code/script; Whole-genome array analysis of H. salinarum in 10 different salinity media.en_US
dc.relation.haspartDefense_kb_20130828.pptx; presentation; Defense seminar slides, including the halobacteria video.en_US
dc.rightsCopyright is held by the individual authors.en_US
dc.subjectArchaea; halobacterium; Osmotolerance; plasticity; Salinity; Systems biologyen_US
dc.subject.otherMicrobiologyen_US
dc.subject.otherMolecular biologyen_US
dc.subject.otherBioinformaticsen_US
dc.subject.othermolecular and cellular biologyen_US
dc.titlePhenotypic and genomic stability in a halophilic model organismen_US
dc.typeThesisen_US
dc.embargo.termsDelay release for 2 years -- then make Open Accessen_US
dc.embargo.lift2016-02-14T18:26:43Z


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