Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 22 for “"flux balance analysis"”.
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Simulation, sensitivity analysis, and optimization of bioprocesses using dynamic flux balance analysis
… generated using highthroughput DNA sequencing. Flux balance analysis (FBA) is a modeling framework that incorporates this new information into mathematical models of microbial communities. With FBA, growth and exchange flux predictions are made by solving linear programs (LPs) that are …
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Systems metabolic engineering of Arabidopsis for increased cellulose production
… years. Using sophisticated algorithms, such as flux balance analysis, OptKnock, and OptForce, we can predict flux distributions and design metabolic engineering strategies at a greater efficiency. The caveat of these current methods is the accuracy of the predictions. We proposed using flux …
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Genome scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A
… metabolism between methanogenic species. Using flux balance analysis, the model quantitatively predicts wild type phenotypes and is 96% accurate in knockout lethality predictions compared to currently available experimental data. Flux balance analysis was used to probe the mechanisms and …
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Development and Application of Fluxomics Tools for Analyzing Metabolisms in Non-Model Microorganisms
… transcriptomics, proteinomics and metabolomics analysis of microbial metabolism, fluxomics tools can measure and simulate the in vivo enzymatic reactions as direct readouts of microbial metabolism. This dissertation develops and applies broad-scope tools in metabolic flux analysis to investigate …
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Computational Modeling of Planktonic and Biofilm Metabolism
… approaches (e.g., transcriptomics and proteomics analysis). However, these approaches are limited to provide the direct description of intracellular metabolism (e.g., metabolic fluxes) of microorganisms. Therefore, in this study, I have applied computational modeling approaches (i.e., 13C assisted …
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Systems metabolic engineering through application of genome-scale metabolic flux modeling
… engineering involves genome-scale metabolic flux modeling. These models allow generation of predictions of the global metabolic flux distribution in the metabolic network of organisms, in silico. With the current advances in genome sequencing technologies and the global demand for bio-based …
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Metabolic Changes in Astrocytes Following Traumatic Brain Injury
… study was to improve and validate a previous flux balance analysis model of astrocyte metabolism developed by Martín-Jiménez et al. to study the effects of environmental changes, specifically hypoxia and acidosis, on astrocytes following TBI [6]. To do this, updated metabolic reaction …
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Genome Scale Metabolic Modelling of Arabidopsis thaliana and Chlamydomonas reinhardtii
… make such change possible were identified using flux balance analysis. The analysis demonstrated a complementary role of SBPase and FBPase in the Calvin cycle and further proposed a novel role of transaldolase in daytime metabolism under knockout conditions. Both models, were used to investigate …
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Biological Circuit Design via BioCAD Tools
… and for local or global search; (ii) Sensitivity Analysis, for evaluating the importance of the parameters by ranking them according to their influence on the model; (iii) Robustness Analysis, for estimating the global and local fragility and robustness of optimal synthetic circuits; (iv) …
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Computational methods for integrating metabolomics data with metabolic engineering strain design
The genome-scale analysis of cellular metabolites, “metabolomics”, provides data ideal for applications in metabolic engineering. However, many of the computational tools for strain design are built around Flux Balance Analysis (FBA) and were developed using assumptions that preclude direct …
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Characterization and genome-scale metabolic modeling of catechol-degrading Pseudomonas fluorescens isolated from a petroleum hydrocarbon-impacted site
… proton transport chain has a P/O ratio of 11/8. Flux balance analysis (FBA) was performed to simulate the whole-cell metabolic flow. The simulation results suggested the β-ketoadipate pathway is involved in catechol metabolism by P. fluorescens while the uptake of oxygen is mandatory for cleavage …
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Computational Labeling, Partitioning, and Balancing of Molecular Networks
… computational models to label, partition, and balance molecular networks using modern machine learning techniques. (1) Due to the incompleteness of protein functional annotation, we develop AptRank, an adaptive PageRank model for protein function prediction on bilayer networks. By integrating …
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Strategies for engineering microbial communities
… precursors. I combined experimental data and flux balance analysis (FBA) to test our capacity to predict metabolic interactions between the two organisms, and explored a proof-of-concept method to monitor the growth dynamics of this coculture. I next explored the possibility of generalizing …
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Metabolic influences on ageing in Caenorhabditis elegans: A time series multi-omics and metabolic modelling study
… known to be metabolic and relate to managing the balance of energy availability to optimise resource usage and survival during times of scarcity. The model organism Caenorhabditis elegans, a small transparent nematode worm that ordinarily lives in the soil and eats bacteria, is one of the most …
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Development of Steady-State and Dynamic Flux Models for Broad-Scope Microbial Metabolism Analysis
<p>Flux analysis techniques, including flux balance analysis (FBA) and 13C-metabolic flux analysis (MFA), can characterize carbon and energy flows through a cells metabolic network. By employing both 13C-labeling experiments and nonlinear programming, 13C-MFA provides a rigorous way of examining …
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Model-guided Analysis of Plant Metabolism and Design of Metabolic Engineering Strategies
… method is constraint-based metabolic flux modeling. This is performed using genome-scale metabolic models (GEMs) that are a collection of biochemical reactions, derived from a genome's annotation. This type of flux modeling enables prediction of net metabolite conversion rates …
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Systematic and combinatorial approaches for metabolic engineering of optimal yeast strains to produce fuels and chemicals
… xylitol production demonstrated a redox imbalance problem due to NAD+ shortage without respiration. Two separate strategies were effective for alleviating the redox imbalance problem and further improving ethanol fermentation from xylose in the respiration-deficient evolved strain: (i) …
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Modelling metabolic landscapes in human naive and primed embryonic stem cells
… variability on the metabolism of the cells. Analysis of these modelling results shows that PCA of all reaction fluxes reveals clear differences between naive and primed cells, but interestingly also reveals subgroups within each cell type which exhibit different metabolic landscapes, which …
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Computational modelling of the glycinergic synapse
… of different types of CNS cells was developed. Flux Balance Analysis (FBA) methods were applied to the model in order to establish the most likely pathways of glycine and ATP production across dierent CNS cell types, suggesting the compartmentalization of the serine/glycine metabolism in CNS …
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Metabolic heterogeneity in microbial populations
… sampled from experimental distributions, and use flux balance analysis (FBA) to compute the optimal way that each cell can use its metabolic pathways—an approach we dubbed Population FBA. We find that enzyme variability gives rise to a wide distribution of growth rates, and several metabolic …
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