This thesis studies the two fundamental mechanisms of bacterial evolution — horizontal gene transfer and spontaneous mutation, in the bacterium Escherichia coli through novel experimental assays and mathematical simulations. First, I will develop a growth assay utilizing the quantitative polymerase chain reaction (qPCR) to provide real-time enumeration of genetic marker abundance within bacterial populations. Second, I will focus on horizontal gene transfer in E. coli occurring through a process called conjugation. By fitting the qPCR data to a resource limited, logistic growth model, I will obtain estimated values of several key parameters governing the dynamics of DNA transfer through conjugation under two different conditions: i) in the absence of selection; ii) in the presence of negative selection pressure — bacteriophage infection. Last, I will investigate spontaneous mutation through qPCR assay of competition between wild-type and mutator phenotype E. coli. Mutator phenotype has an elevated mutation rate due to defects in DNA proofreading and repairing system. By introducing antibiotic selective pressure, I will examine the fixation probability of mutators competing with wild-type in novel environment. I also will utilize simulations to study the impact of three parameters on the fixation probability.
","abstract_html":"<p>This thesis studies the two fundamental mechanisms of bacterial evolution — horizontal gene transfer and spontaneous mutation, in the bacterium <em>Escherichia coli</em> through novel experimental assays and mathematical simulations. First, I will develop a growth assay utilizing the quantitative polymerase chain reaction (qPCR) to provide real-time enumeration of genetic marker abundance within bacterial populations. Second, I will focus on horizontal gene transfer in <em>E. coli</em> occurring through a process called conjugation. By fitting the qPCR data to a resource limited, logistic growth model, I will obtain estimated values of several key parameters governing the dynamics of DNA transfer through conjugation under two different conditions: i) in the absence of selection; ii) in the presence of negative selection pressure — bacteriophage infection. Last, I will investigate spontaneous mutation through qPCR assay of competition between wild-type and mutator phenotype <em>E. coli</em>. Mutator phenotype has an elevated mutation rate due to defects in DNA proofreading and repairing system. By introducing antibiotic selective pressure, I will examine the fixation probability of mutators competing with wild-type in novel environment. I also will utilize simulations to study the impact of three parameters on the fixation probability. </p>","abstract_has_math":false,"creators":["Wan, Zhenmao"],"institution":"The Graduate School and University Center of The City University of New York","degree_name":"Doctor of Philosophy","degree_level":"Doctoral","degree_discipline":"Physics","degree_department":null,"school":null,"contributors":[],"advisors":["Mark Hillery"],"committee_chairs":[],"committee_members":[],"year":2014,"date_issued":"2014-02-01T08:00:00Z","date_published":"2014-02-01T08:00:00Z","updated_at":"2026-07-24T02:00:26Z","subjects":["Biology","Biophysics","Physics","Bacterial Evolution","Horizontal Gene Transfer","Population Dynamics","Spontaneous Mutation"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://academicworks.cuny.edu/gc_etds/125","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Mark Hillery"]},{"key":"dc:creator","label":"Author","values":["Wan, Zhenmao"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2001-01-01T08:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Physics"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Doctoral"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Doctor of Philosophy"]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["The Graduate School and University Center of The City University of New York"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Biology","Biophysics","Physics","Bacterial Evolution","Horizontal Gene Transfer","Population Dynamics","Spontaneous Mutation"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://academicworks.cuny.edu/gc_etds/125"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["This thesis studies the two fundamental mechanisms of bacterial evolution — horizontal gene transfer and spontaneous mutation, in the bacterium Escherichia coli through novel experimental assays and mathematical simulations. First, I will develop a growth assay utilizing the quantitative polymerase chain reaction (qPCR) to provide real-time enumeration of genetic marker abundance within bacterial populations. Second, I will focus on horizontal gene transfer in E. coli occurring through a process called conjugation. By fitting the qPCR data to a resource limited, logistic growth model, I will obtain estimated values of several key parameters governing the dynamics of DNA transfer through conjugation under two different conditions: i) in the absence of selection; ii) in the presence of negative selection pressure — bacteriophage infection. Last, I will investigate spontaneous mutation through qPCR assay of competition between wild-type and mutator phenotype E. coli. Mutator phenotype has an elevated mutation rate due to defects in DNA proofreading and repairing system. By introducing antibiotic selective pressure, I will examine the fixation probability of mutators competing with wild-type in novel environment. I also will utilize simulations to study the impact of three parameters on the fixation probability.
"]},{"key":"dc:title","label":"Title","values":["An experimental investigation into the mechanisms of bacterial evolution"]}]}],"canonical_facts":{"dc:contributor.advisor":["Mark Hillery"],"dc:creator":["Wan, Zhenmao"],"dc:date.available":["2001-01-01T08:00:00Z"],"dc:description.abstract":["This thesis studies the two fundamental mechanisms of bacterial evolution — horizontal gene transfer and spontaneous mutation, in the bacterium Escherichia coli through novel experimental assays and mathematical simulations. First, I will develop a growth assay utilizing the quantitative polymerase chain reaction (qPCR) to provide real-time enumeration of genetic marker abundance within bacterial populations. Second, I will focus on horizontal gene transfer in E. coli occurring through a process called conjugation. By fitting the qPCR data to a resource limited, logistic growth model, I will obtain estimated values of several key parameters governing the dynamics of DNA transfer through conjugation under two different conditions: i) in the absence of selection; ii) in the presence of negative selection pressure — bacteriophage infection. Last, I will investigate spontaneous mutation through qPCR assay of competition between wild-type and mutator phenotype E. coli. Mutator phenotype has an elevated mutation rate due to defects in DNA proofreading and repairing system. By introducing antibiotic selective pressure, I will examine the fixation probability of mutators competing with wild-type in novel environment. I also will utilize simulations to study the impact of three parameters on the fixation probability.
"],"dc:identifier":["https://academicworks.cuny.edu/gc_etds/125"],"dc:subject":["Biology","Biophysics","Physics","Bacterial Evolution","Horizontal Gene Transfer","Population Dynamics","Spontaneous Mutation"],"dc:title":["An experimental investigation into the mechanisms of bacterial evolution"],"thesis:degree_discipline":["Physics"],"thesis:degree_level":["Doctoral"],"thesis:degree_name":["Doctor of Philosophy"],"thesis:institution_name":["The Graduate School and University Center of The City University of New York"]},"updated_at":"2026-07-24T02:00:26Z"}