Biofilm formation is a common lifestyle adapted by bacteria and fungi in response to various environmental stresses. Bacterial and fungal biofilms adhering to medical devices convey resistance to antibiotics or biocides, causing high rates of clinical infections. Microorganisms are protected from harsh environmental conditions by reduced stress penetration through the complex biofilm architecture with distinct patterns. Although the molecular regulations of surface patterning have been well characterized in bacteria, the mechanisms underlying the complex pattern formation in eukaryotic biofilms remain unclear.
This dissertation aims to investigate the salient features of robust colony expansion in yeast biofilms and the processes driving the complex pattern development. Various salient features of Saccharomyces cerevisiae colony expansion, such as of the change of size, shape, and surface pattern properties were analyzed quantitatively for various combinations of agar and sugar concentrations. I found that the size and irregularity of the FLO11 expressing colony, and wavelength of the pattern were all monotonically decreasing with agar density. These trends were consistent regardless of sugar sources. Using a mathematical model, I also demonstrated that the differential expansion pattern between the center and the edge of the colony due to the spatial differences in glucose concentration affected the convexity of the expansion curve.
I found that pattern formation in S. cerevisiae was not caused by localized cell death as in Bacillus subtilis biofilms. Using quantitative measurement and physical models, I found that the surface pattern of S. cerevisiae was consistent with hierarchical wrinkling, determined by the physicochemical properties and thickness of the layered structures of the yeast biofilm and the viscoelastic agar. Furthermore, I found that two-dimensional expansion conferred a competitive advantage for FLO11 sectors during head-to-head competition with flo11Δ cells. Overall these results suggested that two-dimensionality of expansion conveyed by FLO11 directs rapid colony expansion with high irregularity at the rim, hierarchical wrinkling pattern, and competitive advantage during head-to-head competition.
","abstract_html":"<p>Biofilm formation is a common lifestyle adapted by bacteria and fungi in response to various environmental stresses. Bacterial and fungal biofilms adhering to medical devices convey resistance to antibiotics or biocides, causing high rates of clinical infections. Microorganisms are protected from harsh environmental conditions by reduced stress penetration through the complex biofilm architecture with distinct patterns. Although the molecular regulations of surface patterning have been well characterized in bacteria, the mechanisms underlying the complex pattern formation in eukaryotic biofilms remain unclear.</p> <p>This dissertation aims to investigate the salient features of robust colony expansion in yeast biofilms and the processes driving the complex pattern development. Various salient features of <em>Saccharomyces cerevisiae </em>colony expansion, such as of the change of size, shape, and surface pattern properties were analyzed quantitatively for various combinations of agar and sugar concentrations. I found that the size and irregularity of the <em>FLO11 </em>expressing colony, and wavelength of the pattern were all monotonically decreasing with agar density. These trends were consistent regardless of sugar sources. Using a mathematical model, I also demonstrated that the differential expansion pattern between the center and the edge of the colony due to the spatial differences in glucose concentration affected the convexity of the expansion curve.</p> <p>I found that pattern formation in <em>S. cerevisiae</em> was not caused by localized cell death as in <em>Bacillus subtilis</em> biofilms<em>.</em> Using quantitative measurement and physical models, I found that the surface pattern of <em>S. cerevisiae</em> was consistent with hierarchical wrinkling, determined by the physicochemical properties and thickness of the layered structures of the yeast biofilm and the viscoelastic agar. Furthermore, I found that<em> </em>two-dimensional expansion conferred a competitive advantage for <em>FLO11 </em>sectors during head-to-head competition with <em>flo11Δ </em>cells. Overall these results suggested that two-dimensionality of expansion conveyed by <em>FLO11 </em>directs rapid colony expansion with high irregularity at the rim, hierarchical wrinkling pattern, and competitive advantage during head-to-head competition.</p>","abstract_has_math":false,"creators":["CHEN, LIN"],"institution":null,"degree_name":"Doctor of Philosophy (PhD)","degree_level":"Dissertation (PhD)","degree_discipline":null,"degree_department":null,"school":null,"contributors":["Gábor Balázsi","Yi Xu","Krešimir Josić"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2014,"date_issued":"2014-12-01T08:00:00Z","date_published":"2014-12-01T08:00:00Z","updated_at":"2026-07-24T05:50:02Z","subjects":["FLO11","Pattern Formation","Hierarchical Wrinkling","Competition","Medicine and Health Sciences","Other Life Sciences","Other Microbiology","Systems Biology"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://digitalcommons.library.tmc.edu/utgsbs_dissertations/524","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Gábor Balázsi","Yi Xu","Krešimir Josić"]},{"key":"dc:creator","label":"Author","values":["CHEN, LIN"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2015-11-14T08:00:00Z"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation (PhD)"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["FLO11","Pattern Formation","Hierarchical Wrinkling","Competition","Medicine and Health Sciences","Other Life Sciences","Other Microbiology","Systems Biology"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://digitalcommons.library.tmc.edu/utgsbs_dissertations/524"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Biofilm formation is a common lifestyle adapted by bacteria and fungi in response to various environmental stresses. Bacterial and fungal biofilms adhering to medical devices convey resistance to antibiotics or biocides, causing high rates of clinical infections. Microorganisms are protected from harsh environmental conditions by reduced stress penetration through the complex biofilm architecture with distinct patterns. Although the molecular regulations of surface patterning have been well characterized in bacteria, the mechanisms underlying the complex pattern formation in eukaryotic biofilms remain unclear.
This dissertation aims to investigate the salient features of robust colony expansion in yeast biofilms and the processes driving the complex pattern development. Various salient features of Saccharomyces cerevisiae colony expansion, such as of the change of size, shape, and surface pattern properties were analyzed quantitatively for various combinations of agar and sugar concentrations. I found that the size and irregularity of the FLO11 expressing colony, and wavelength of the pattern were all monotonically decreasing with agar density. These trends were consistent regardless of sugar sources. Using a mathematical model, I also demonstrated that the differential expansion pattern between the center and the edge of the colony due to the spatial differences in glucose concentration affected the convexity of the expansion curve.
I found that pattern formation in S. cerevisiae was not caused by localized cell death as in Bacillus subtilis biofilms. Using quantitative measurement and physical models, I found that the surface pattern of S. cerevisiae was consistent with hierarchical wrinkling, determined by the physicochemical properties and thickness of the layered structures of the yeast biofilm and the viscoelastic agar. Furthermore, I found that two-dimensional expansion conferred a competitive advantage for FLO11 sectors during head-to-head competition with flo11Δ cells. Overall these results suggested that two-dimensionality of expansion conveyed by FLO11 directs rapid colony expansion with high irregularity at the rim, hierarchical wrinkling pattern, and competitive advantage during head-to-head competition.
"]},{"key":"dc:title","label":"Title","values":["Quantitative Analysis and Imaging-Based Insights Into The Characteristics and Mechanisms of Yeast Pattern Formation"]}]}],"canonical_facts":{"dc:contributor":["Gábor Balázsi","Yi Xu","Krešimir Josić"],"dc:creator":["CHEN, LIN"],"dc:date.available":["2015-11-14T08:00:00Z"],"dc:description.abstract":["Biofilm formation is a common lifestyle adapted by bacteria and fungi in response to various environmental stresses. Bacterial and fungal biofilms adhering to medical devices convey resistance to antibiotics or biocides, causing high rates of clinical infections. Microorganisms are protected from harsh environmental conditions by reduced stress penetration through the complex biofilm architecture with distinct patterns. Although the molecular regulations of surface patterning have been well characterized in bacteria, the mechanisms underlying the complex pattern formation in eukaryotic biofilms remain unclear.
This dissertation aims to investigate the salient features of robust colony expansion in yeast biofilms and the processes driving the complex pattern development. Various salient features of Saccharomyces cerevisiae colony expansion, such as of the change of size, shape, and surface pattern properties were analyzed quantitatively for various combinations of agar and sugar concentrations. I found that the size and irregularity of the FLO11 expressing colony, and wavelength of the pattern were all monotonically decreasing with agar density. These trends were consistent regardless of sugar sources. Using a mathematical model, I also demonstrated that the differential expansion pattern between the center and the edge of the colony due to the spatial differences in glucose concentration affected the convexity of the expansion curve.
I found that pattern formation in S. cerevisiae was not caused by localized cell death as in Bacillus subtilis biofilms. Using quantitative measurement and physical models, I found that the surface pattern of S. cerevisiae was consistent with hierarchical wrinkling, determined by the physicochemical properties and thickness of the layered structures of the yeast biofilm and the viscoelastic agar. Furthermore, I found that two-dimensional expansion conferred a competitive advantage for FLO11 sectors during head-to-head competition with flo11Δ cells. Overall these results suggested that two-dimensionality of expansion conveyed by FLO11 directs rapid colony expansion with high irregularity at the rim, hierarchical wrinkling pattern, and competitive advantage during head-to-head competition.
"],"dc:identifier":["https://digitalcommons.library.tmc.edu/utgsbs_dissertations/524"],"dc:subject":["FLO11","Pattern Formation","Hierarchical Wrinkling","Competition","Medicine and Health Sciences","Other Life Sciences","Other Microbiology","Systems Biology"],"dc:title":["Quantitative Analysis and Imaging-Based Insights Into The Characteristics and Mechanisms of Yeast Pattern Formation"],"thesis:degree_level":["Dissertation (PhD)"],"thesis:degree_name":["Doctor of Philosophy (PhD)"]},"updated_at":"2026-07-24T05:50:02Z"}