Quantification of metabolic fluxes has broad applications in studying metabolic physiology. Isotope tracing with heavy labeled carbon (13C labeled metabolic flux analysis, 13C-MFA) is a promising strategy due to its ability to compute metabolic fluxes from isotope tracing profiles without relying on assumptions such as metabolic objectives or enzyme kinetic parameters. However, most current 13C-MFA methods have limitations on model scope, algorithmic efficacy and user interaction, especially given the availability of modern mass spectrometry-based metabolomics techniques and computational resources. In this study, a new 13C-MFA framework is developed, with emphasis on flux resolution in larger-sized metabolic network. Novel simulation methods of isotope tracing data are also used to guide algorithm development. The new MFA methodology has been applied to isotope-labeled cultured cancer cell line and isotope-infused mice. In cultured cancer cell line, the new MFA framework enabled the discovery of long-term interaction from one-carbon metabolism to pentose phosphate pathway and TCA cycle. In isotope-infused mice, the new MFA framework directly measured systemic glucose and lactate contribution to TCA cycle under physiological condition, which confirms the conventional knowledge that glucose is the main direct energy source in body. Taken together the new MFA methodology will offer unprecedented opportunities for expanding research in metabolic physiology.
","abstract_html":"<p>Quantification of metabolic fluxes has broad applications in studying metabolic physiology. Isotope tracing with heavy labeled carbon (13C labeled metabolic flux analysis, 13C-MFA) is a promising strategy due to its ability to compute metabolic fluxes from isotope tracing profiles without relying on assumptions such as metabolic objectives or enzyme kinetic parameters. However, most current 13C-MFA methods have limitations on model scope, algorithmic efficacy and user interaction, especially given the availability of modern mass spectrometry-based metabolomics techniques and computational resources. In this study, a new 13C-MFA framework is developed, with emphasis on flux resolution in larger-sized metabolic network. Novel simulation methods of isotope tracing data are also used to guide algorithm development. The new MFA methodology has been applied to isotope-labeled cultured cancer cell line and isotope-infused mice. In cultured cancer cell line, the new MFA framework enabled the discovery of long-term interaction from one-carbon metabolism to pentose phosphate pathway and TCA cycle. In isotope-infused mice, the new MFA framework directly measured systemic glucose and lactate contribution to TCA cycle under physiological condition, which confirms the conventional knowledge that glucose is the main direct energy source in body. Taken together the new MFA methodology will offer unprecedented opportunities for expanding research in metabolic physiology.</p>","abstract_has_math":false,"creators":["Liu, Shiyu"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Locasale, Jason"],"committee_chairs":[],"committee_members":[],"year":2021,"date_issued":"2021","date_published":"2021","updated_at":"2026-07-24T02:07:03Z","subjects":["Bioinformatics","Computer science","Biology","13C-MFA","algorithm","flux analysis","methodology"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/10161/24405","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Locasale, Jason"]},{"key":"dc:creator","label":"Author","values":["Liu, Shiyu"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2022-02-11T21:39:04Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2022-02-11T21:39:04Z"]},{"key":"dc:date.issued","label":"Date","values":["2021"]},{"key":"dc:type","label":"Dc Type","values":["Dissertation"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Bioinformatics","Computer science","Biology","13C-MFA","algorithm","flux analysis","methodology"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/10161/24405"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Quantification of metabolic fluxes has broad applications in studying metabolic physiology. Isotope tracing with heavy labeled carbon (13C labeled metabolic flux analysis, 13C-MFA) is a promising strategy due to its ability to compute metabolic fluxes from isotope tracing profiles without relying on assumptions such as metabolic objectives or enzyme kinetic parameters. However, most current 13C-MFA methods have limitations on model scope, algorithmic efficacy and user interaction, especially given the availability of modern mass spectrometry-based metabolomics techniques and computational resources. In this study, a new 13C-MFA framework is developed, with emphasis on flux resolution in larger-sized metabolic network. Novel simulation methods of isotope tracing data are also used to guide algorithm development. The new MFA methodology has been applied to isotope-labeled cultured cancer cell line and isotope-infused mice. In cultured cancer cell line, the new MFA framework enabled the discovery of long-term interaction from one-carbon metabolism to pentose phosphate pathway and TCA cycle. In isotope-infused mice, the new MFA framework directly measured systemic glucose and lactate contribution to TCA cycle under physiological condition, which confirms the conventional knowledge that glucose is the main direct energy source in body. Taken together the new MFA methodology will offer unprecedented opportunities for expanding research in metabolic physiology.
"]},{"key":"dc:title","label":"Title","values":["Methodologies and analysis of metabolic flux in mammalian systems"]}]}],"canonical_facts":{"dc:contributor.advisor":["Locasale, Jason"],"dc:creator":["Liu, Shiyu"],"dc:date.accessioned":["2022-02-11T21:39:04Z"],"dc:date.available":["2022-02-11T21:39:04Z"],"dc:date.issued":["2021"],"dc:description.abstract":["Quantification of metabolic fluxes has broad applications in studying metabolic physiology. Isotope tracing with heavy labeled carbon (13C labeled metabolic flux analysis, 13C-MFA) is a promising strategy due to its ability to compute metabolic fluxes from isotope tracing profiles without relying on assumptions such as metabolic objectives or enzyme kinetic parameters. However, most current 13C-MFA methods have limitations on model scope, algorithmic efficacy and user interaction, especially given the availability of modern mass spectrometry-based metabolomics techniques and computational resources. In this study, a new 13C-MFA framework is developed, with emphasis on flux resolution in larger-sized metabolic network. Novel simulation methods of isotope tracing data are also used to guide algorithm development. The new MFA methodology has been applied to isotope-labeled cultured cancer cell line and isotope-infused mice. In cultured cancer cell line, the new MFA framework enabled the discovery of long-term interaction from one-carbon metabolism to pentose phosphate pathway and TCA cycle. In isotope-infused mice, the new MFA framework directly measured systemic glucose and lactate contribution to TCA cycle under physiological condition, which confirms the conventional knowledge that glucose is the main direct energy source in body. Taken together the new MFA methodology will offer unprecedented opportunities for expanding research in metabolic physiology.
"],"dc:identifier.uri":["https://hdl.handle.net/10161/24405"],"dc:subject":["Bioinformatics","Computer science","Biology","13C-MFA","algorithm","flux analysis","methodology"],"dc:title":["Methodologies and analysis of metabolic flux in mammalian systems"],"dc:type":["Dissertation"]},"updated_at":"2026-07-24T02:07:03Z"}