Show simple item record

dc.contributor.advisorChairperson, Graduate Committee: Brendan Mumeyen
dc.contributor.authorSalinas Duron, Danielen
dc.description.abstractChanges in cellular metabolism can be deduced from how they affect the measurable metabolites in cell samples. We provide methods to compute metabolic reaction rates from changes in measurable metabolites over time. The methods provided are intended to overcome technical challenges, such as the inapplicability of a steady state assumption, heterogeneity of samples from different donors, and the lack of targeted metabolomics data. Solutions to these challenges involve identifying metabolites constrained even under non-steady state, using components analysis to find the donor consensus, and using an integer linear program to solve a set cover variant designed to generate targeted data from untargeted data. The methods are applied on data derived from diseased articular cells. The results show that the reaction rates inferred from the incomplete data are biologically relevant, and that the minimal pathways captured ancillary processes that alternative approaches ignored. We conclude that, although the resulting rates and pathways are not conclusive, they provide useful guidance on experiments to pursue. On the experimental side, our findings have lead us to believe that osteoarthritic chondrocytes respond to compression by initiating protein synthesis, opening the possibility of physical therapy as a stimulus for cartilage regeneration.en
dc.publisherMontana State University - Bozeman, College of Engineeringen
dc.subject.lcshMicrobial metabolitesen
dc.subject.lcshMathematical optimizationen
dc.subject.lcshNP-complete problemsen
dc.titleNew methods in computation of reaction fluxes from metabolomics dataen
dc.rights.holderCopyright 2018 by Daniel Salinas Duronen, Graduate Committee: Ronald K. June II; Binhai Zhu; Brittany Fasy.en Science.en

Files in this item


This item appears in the following Collection(s)

Show simple item record

MSU uses DSpace software, copyright © 2002-2017  Duraspace. For library collections that are not accessible, we are committed to providing reasonable accommodations and timely access to users with disabilities. For assistance, please submit an accessibility request for library material.