{"id":{"repo_id":"cambridge","oai_identifier":"oai:www.repository.cam.ac.uk:1810/293634"},"canonical_url":"https://search.dev.ndltd.org/etd/cambridge/oai:www.repository.cam.ac.uk:1810/293634","repository":{"repo_id":"cambridge","name":"Cambridge University","base_url":"https://api.repository.cam.ac.uk/server/oai/request"},"display":{"title":"On the coupling of noisy processes in biology to produce functional phenotypic variability","abstract":"Noise is ubiquitous in biology. Recent studies have demonstrated that both gene expression and physiological processes, such as growth, can be noisy. The cell-to-cell variation resulting from this stochasticity has been implicated in survival strategies for bacterial populations. However, it remains unclear how single cells couple gene expression with growth to implement these strategies. In this thesis we show how noisy expression of a key stress response regulator, RpoS, allows $\\textit{E. coli}$ to modulate its noisy growth dynamics to survive future adverse environments. We first demonstrate that single cells in bulk, exponential phase cultures have heterogeneous $\\textit{rpoS}$ expression. Combining microfluidics and time-lapse microscopy we reveal multi-generation RpoS activity pulses are responsible for this heterogeneity. We next show that RpoS and growth have stochastic dynamics and are anti-correlated. With a stochastic simulation of chemical reactions coupled to a deterministic cell growth model we show that a mutual inhibition loop between RpoS activity and growth rate is sufficient to capture the observed dynamics. We test our model by performing experimental perturbations and find good agreement between theory and experiment. Next, we demonstrate the functionality of this phenotypic variability by using the microfluidic platform to apply a short, intense period of oxidative stress. By tracking cells prior to the stress and testing for survival after the stress we reveal that $\\textit{E. coli}$ prepare for sudden stressful events by entering prolonged periods of slow growth mediated by RpoS. This dynamic phenotype is captured by the RpoS-growth feedback model. Our synthesis of noisy gene expression, growth, and survival paves the way for further exploration of functional phenotypic variability.","abstract_html":"Noise is ubiquitous in biology. Recent studies have demonstrated that both gene expression and physiological processes, such as growth, can be noisy. The cell-to-cell variation resulting from this stochasticity has been implicated in survival strategies for bacterial populations. However, it remains unclear how single cells couple gene expression with growth to implement these strategies. In this thesis we show how noisy expression of a key stress response regulator, RpoS, allows <span class=\"etd-inline-math\"><em>E. coli</em></span> to modulate its noisy growth dynamics to survive future adverse environments. We first demonstrate that single cells in bulk, exponential phase cultures have heterogeneous <span class=\"etd-inline-math\"><em>rpoS</em></span> expression. Combining microfluidics and time-lapse microscopy we reveal multi-generation RpoS activity pulses are responsible for this heterogeneity. We next show that RpoS and growth have stochastic dynamics and are anti-correlated. With a stochastic simulation of chemical reactions coupled to a deterministic cell growth model we show that a mutual inhibition loop between RpoS activity and growth rate is sufficient to capture the observed dynamics. We test our model by performing experimental perturbations and find good agreement between theory and experiment. Next, we demonstrate the functionality of this phenotypic variability by using the microfluidic platform to apply a short, intense period of oxidative stress. By tracking cells prior to the stress and testing for survival after the stress we reveal that <span class=\"etd-inline-math\"><em>E. coli</em></span> prepare for sudden stressful events by entering prolonged periods of slow growth mediated by RpoS. This dynamic phenotype is captured by the RpoS-growth feedback model. Our synthesis of noisy gene expression, growth, and survival paves the way for further exploration of functional phenotypic variability.","abstract_has_math":true,"creators":["Patange, Om"],"institution":"University of Cambridge","degree_name":"Doctor of Philosophy (PhD)","degree_level":"Doctoral","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Locke, James C.W."],"committee_chairs":[],"committee_members":[],"year":2019,"date_issued":"2019-07-19","date_published":"2019-07-19","updated_at":"2026-07-22T22:24:07Z","subjects":["noise","rpos","growth","stress response","e. coli","phenotypic heterogeneity","single-cell","time-lapse microscopy","quantitative biology","stochastic simulation","Gillespie algorithm","Mother Machine","microfluidic","bet-hedging","stochastic gene expression"],"languages":["en"],"rights":[],"rights_urls":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/6250c1d3-4966-47d1-ad6b-4d7b665f326c/download","https://creativecommons.org/licenses/by-nc-sa/4.0/"],"identifier_entries":[{"key":"dc:creator.authoridentifier","label":"Author Identifier","values":["0000000228106216"],"render_values":[{"text":"0000-0002-2810-6216","href":"https://orcid.org/0000-0002-2810-6216","code":true}]}]},"links":{"outbound_url":"https://doi.org/10.17863/CAM.40747","outbound_label":"DOI","outbound_source":"dc:identifier.doi"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Locke, James C.W."]},{"key":"dc:contributor.sponsor","label":"Sponsor","values":["I was generously supported by a PhD Scholarship from Microsoft Research. I also gratefully acknowledge the support provided by my supervisor, James Locke, whose group was supported by the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 338060, a fellowship from the Gatsby Foundation (GAT3272/GLC), and an award from the Human Frontier Science Programme (CDA00068/2012)."]},{"key":"dc:creator","label":"Author","values":["Patange, Om"]},{"key":"dc:creator.authoridentifier","label":"Author Identifier","values":["0000000228106216"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.issued","label":"Date","values":["2019-07-19"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Cambridge"]},{"key":"dc:relation.isreferencedby.uri","label":"Dc Relation Isreferencedby URI","values":["https://www.repository.cam.ac.uk/handle/1810/293634"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Doctoral"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["noise","rpos","growth","stress response","e. coli","phenotypic heterogeneity","single-cell","time-lapse microscopy","quantitative biology","stochastic simulation","Gillespie algorithm","Mother Machine","microfluidic","bet-hedging","stochastic gene expression"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/6250c1d3-4966-47d1-ad6b-4d7b665f326c/download","https://creativecommons.org/licenses/by-nc-sa/4.0/"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.doi","label":"DOI","values":["10.17863/CAM.40747"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/b2b96428-4d8f-4760-82a1-9776b1186929/download"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Noise is ubiquitous in biology. Recent studies have demonstrated that both gene expression and physiological processes, such as growth, can be noisy. The cell-to-cell variation resulting from this stochasticity has been implicated in survival strategies for bacterial populations. However, it remains unclear how single cells couple gene expression with growth to implement these strategies. In this thesis we show how noisy expression of a key stress response regulator, RpoS, allows $\\textit{E. coli}$ to modulate its noisy growth dynamics to survive future adverse environments. We first demonstrate that single cells in bulk, exponential phase cultures have heterogeneous $\\textit{rpoS}$ expression. Combining microfluidics and time-lapse microscopy we reveal multi-generation RpoS activity pulses are responsible for this heterogeneity. We next show that RpoS and growth have stochastic dynamics and are anti-correlated. With a stochastic simulation of chemical reactions coupled to a deterministic cell growth model we show that a mutual inhibition loop between RpoS activity and growth rate is sufficient to capture the observed dynamics. We test our model by performing experimental perturbations and find good agreement between theory and experiment. Next, we demonstrate the functionality of this phenotypic variability by using the microfluidic platform to apply a short, intense period of oxidative stress. By tracking cells prior to the stress and testing for survival after the stress we reveal that $\\textit{E. coli}$ prepare for sudden stressful events by entering prolonged periods of slow growth mediated by RpoS. This dynamic phenotype is captured by the RpoS-growth feedback model. Our synthesis of noisy gene expression, growth, and survival paves the way for further exploration of functional phenotypic variability."]},{"key":"dc:format.checksum.md5","label":"Dc Format Checksum Md5","values":["905d91b17df239b8a328fddbc609ec2b","87eda9de84448d1f82354d60eee3eb5f"]},{"key":"dc:title","label":"Title","values":["On the coupling of noisy processes in biology to produce functional phenotypic variability"]}]}],"canonical_facts":{"dc:contributor.advisor":["Locke, James C.W."],"dc:contributor.sponsor":["I was generously supported by a PhD Scholarship from Microsoft Research. I also gratefully acknowledge the support provided by my supervisor, James Locke, whose group was supported by the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 338060, a fellowship from the Gatsby Foundation (GAT3272/GLC), and an award from the Human Frontier Science Programme (CDA00068/2012)."],"dc:creator":["Patange, Om"],"dc:creator.authoridentifier":["0000000228106216"],"dc:date.issued":["2019-07-19"],"dc:description.abstract":["Noise is ubiquitous in biology. Recent studies have demonstrated that both gene expression and physiological processes, such as growth, can be noisy. The cell-to-cell variation resulting from this stochasticity has been implicated in survival strategies for bacterial populations. However, it remains unclear how single cells couple gene expression with growth to implement these strategies. In this thesis we show how noisy expression of a key stress response regulator, RpoS, allows $\\textit{E. coli}$ to modulate its noisy growth dynamics to survive future adverse environments. We first demonstrate that single cells in bulk, exponential phase cultures have heterogeneous $\\textit{rpoS}$ expression. Combining microfluidics and time-lapse microscopy we reveal multi-generation RpoS activity pulses are responsible for this heterogeneity. We next show that RpoS and growth have stochastic dynamics and are anti-correlated. With a stochastic simulation of chemical reactions coupled to a deterministic cell growth model we show that a mutual inhibition loop between RpoS activity and growth rate is sufficient to capture the observed dynamics. We test our model by performing experimental perturbations and find good agreement between theory and experiment. Next, we demonstrate the functionality of this phenotypic variability by using the microfluidic platform to apply a short, intense period of oxidative stress. By tracking cells prior to the stress and testing for survival after the stress we reveal that $\\textit{E. coli}$ prepare for sudden stressful events by entering prolonged periods of slow growth mediated by RpoS. This dynamic phenotype is captured by the RpoS-growth feedback model. Our synthesis of noisy gene expression, growth, and survival paves the way for further exploration of functional phenotypic variability."],"dc:format.checksum.md5":["905d91b17df239b8a328fddbc609ec2b","87eda9de84448d1f82354d60eee3eb5f"],"dc:identifier.doi":["10.17863/CAM.40747"],"dc:identifier.uri":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/b2b96428-4d8f-4760-82a1-9776b1186929/download"],"dc:language":["en"],"dc:publisher.institution":["University of Cambridge"],"dc:relation.isreferencedby.uri":["https://www.repository.cam.ac.uk/handle/1810/293634"],"dc:rights":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/6250c1d3-4966-47d1-ad6b-4d7b665f326c/download","https://creativecommons.org/licenses/by-nc-sa/4.0/"],"dc:subject":["noise","rpos","growth","stress response","e. coli","phenotypic heterogeneity","single-cell","time-lapse microscopy","quantitative biology","stochastic simulation","Gillespie algorithm","Mother Machine","microfluidic","bet-hedging","stochastic gene expression"],"dc:title":["On the coupling of noisy processes in biology to produce functional phenotypic variability"],"dc:type":["Thesis"],"dc:type.qualificationlevel":["Doctoral"],"dc:type.qualificationname":["Doctor of Philosophy (PhD)"]},"updated_at":"2026-07-22T22:24:07Z"}