Differential gene expression by two strains of Escherichia coli (K12 and an environmental isolate) in response to temperature and nutrient stress using microarrays

dc.contributor.authorWetherell, Charmaine
dc.contributor.supervisorRoy, Real
dc.date.accessioned2010-06-02T20:40:56Z
dc.date.available2010-06-02T20:40:56Z
dc.date.copyright2009en
dc.date.issued2010-06-02T20:40:56Z
dc.degree.departmentDept. of Biologyen
dc.degree.levelMaster of Science M.Sc.en
dc.description.abstractIn this study we evaluated the use of microarray technology in Bacterial Source Tracking (BST), with the intent of identifying candidate genes to be used to differentiate between closely related strains of Escherichia coli. We anticipate that genes differentially expressed in response to stress by both a laboratory strain and environmental isolate could be used as marker genes on a microarray in BST. Using microarrays we characterized the transcriptional response of E. coli K12 MG1655 (K12), maintained for about 80 years in an artificial environment versus E. coli 43(C)-4A or E43, a strain recently isolated from the natural environment. The responses were to a temperature decrease from 37°C to 21°C, and to growth in a diluted LB broth (dLB). Overall we found that there were more genes differentially expressed between the strains than either strain's response to the stresses. At the 4-fold threshold, at reduced temperature there were only 26 genes differentially regulated by K12 and 9 by E43, respectively. In K12 the functions of some differentially expressed genes were linked to the general stress response and biofilm formation. A few genes differentially expressed by E43 were involved in the stress response. Similarly, in response to dLB there were 46 and 11 genes differentially expressed by K12 and E43 respectively. While it appeared that genes differentially expressed by K12 were involved in dealing with nutrient deficiencies, the genes differentially expressed by E43 did not show a similar pattern. Of these genes, none were obvious candidate genes for a microarray to be used in BST. However, we did find that 169, 286 and 254 genes were differentially expressed between K12 and E43 at 37°C, 21°C, and in dLB, respectively. Many of these genes were differentially expressed under all 3 growth conditions. Several of the genes differentially expressed between the strains were in the O-antigen-lipopolysaccharide gene family and are genes that could potentially be used on a microarray in BST. We found that E43, isolated from the natural environment, did not respond to the growth conditions in the same way as the model strain, E. coli K12, indicating that strains of E. coli isolated from the natural environment may not be identical to the model strain K12. It is suggested that other strains isolated from the natural environment be investigated. Such studies could also reveal genes differentially expressed between the strains that could be used on a microarray for use in BST.en
dc.identifier.urihttp://hdl.handle.net/1828/2836
dc.languageEnglisheng
dc.language.isoenen
dc.rightsAvailable to the World Wide Weben
dc.subjectEscherichia colien
dc.subjectDrinking wateren
dc.subjectContaminationen
dc.subject.lcshUVic Subject Index::Sciences and Engineering::Biologyen
dc.titleDifferential gene expression by two strains of Escherichia coli (K12 and an environmental isolate) in response to temperature and nutrient stress using microarraysen
dc.typeThesisen

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