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 40 for “"Metabolic Network"”.
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Metabolic network design and engineering in Escherichia coli
This thesis is a study of metabolic engineering to design and engineer novel metabolic networks with improved metabolic processes that can increase product yield and enhance cellular properties. The succinate synthesis pathways in E. coli were chosen as the model system for network design and …
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A Mathematical Model of a Denitrification Metabolic Network in Pseudomonas aeruginosa
… study focuses on a mathematical model of the metabolic network in Pseudomonas aeruginosa under denitrification and testable hypotheses generation using polynomial dynamical systems and stochastic discrete dynamical systems. Analysis of the long-term behavior of the system changing the …
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Metabolic network reconstruction and genome-scale model of butanol-producing strain clostridium beijerinckii ncimb 8052
… modifications. We present the first genome-scale metabolic model (iCM925) for C. beijerinckii, containing 925 genes, 938 reactions, and 881 metabolites. To build the model we employed a semi-automated procedure that integrated genome annotation information from KEGG, BioCyc, and The SEED, and …
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Quantifying the Intracellular Metabolic Network that Establishes the Simultaneous Utilization of Sugars and Aromatic Substrates in Pseudomonas putida KT2440
… a combination of 13C tracer experiments with metabolic flux analysis (MFA), I elucidated and quantified the discriminate metabolic routing of each substrate throughout central carbon metabolism. The results determined that glucose-derived carbon was primarily routed to the Entner-Doudoroff …
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Towards structure and dynamics of metabolic networks
… approaches to cover various aspects of metabolic network modelling, especially regarding the limited availability of detailed kinetic knowledge on reaction rates. It is shown that precise mathematical formulations of problems are needed i) to find appropriate and, if possible, efficient …
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Protein-protein interactions and metabolic pathways reconstruction of Caenorhabditis elegans
Metabolic networks are the collections of all cellular activities taking place in a living cell and all the relationships among biological elements of the cell including genes, proteins, enzymes, metabolites, and reactions. They provide a better understanding of cellular mechanisms and phenotypic …
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Systems biology approaches to the computational modelling of trypanothione metabolism in Trypanosoma brucei
… modelling approaches to the trypanothione metabolic network in the bloodstream form of Trypanosoma brucei, the parasite responsible for African Sleeping sickness. Trypanothione has previously been identified as an essential compound for parasitic protozoa, however the underlying metabolic …
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Development of 13C Fingerprint Tool and Its Application for Exploring Carbon and Energy Metabolism in Cyanobacterium Synechocystis sp. PCC 6803
… will provide guidelines for rational design of metabolic engineering strategies.</p><p>The emerging of multiple omics tools, e.g. genomics, transcriptomics, proteinomics, and metabolomics analysis, allowed the comprehensive determination of microbial metabolisms. This dissertation describes the …
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Evaluation of network inference algorithms and their effects on network analysis for the study of small metabolomic data sets
… evi- dence has recently mounted for the role of metabolic dysfunction in AD. Metabolomic data has therefore been increasingly used in AD studies. Metabolomic disease studies often suffer from small sample sizes and inflated false discovery rates. It is therefore of great importance to identify …
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A control-theoretic approach to dynamic optimization of metabolic networks
… of general control principles that underpin metabolic dynamics is an important part of systems analysis in biology. It has been long argued that many biological regulatory mechanisms have evolved so as to optimize cellular adaptation in response to external stimuli. In this thesis we use an …
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Extracting information from biological networks
… by the powerful abstraction of biological networks. This thesis examines several types of these networks and looks in detail at the kind of information their analysis can yield. The first part discusses protein interaction networks. We introduce a new algorithm for the pairwise alignment of …
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The dynamics of metabolic regulation
Cellular metabolism is a complex network of biochemical reactions, whose regulation enables living cells to cope with variable environments and perturbations. Since metabolic regulation occurs at multiple time scales and involves diverse molecular mechanisms, understanding and manipulating the …
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Computational Tools for Metabolic Modeling and Gene Duplication Analysis
… short timescales. We develop a novel method of network regression, AccliNet, based on the acclimation times, which takes into account prior knowledge of functional links between genes to improve the performance of the algorithm. The results obtained by AccliNet are compared with the performance …
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Evolutionary fingerprints in genome-scale networks
… The quest for evolutionary fingerprints in metabolic and gene-coexpression networks is the central topic of this cumulative thesis based on four published articles. An understanding of the actual origin of life will probably remain an insoluble problem. However, one can argue that after a …
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Machine learning methods for detecting structure in metabolic flow networks
Metabolic flow networks are large scale, mechanistic biological models with good predictive power. However, even when they provide good predictions, interpreting the meaning of their structure can be very difficult, especially for large networks which model entire organisms. This is an …
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Systems metabolic engineering through application of genome-scale metabolic flux modeling
Systems metabolic engineering has enabled systematic studying of microbes for modifying their genetic contents, analyzing their metabolism, and designing new capabilities. One of the most commonly used approaches in systems metabolic engineering involves genome-scale metabolic flux modeling. These …
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Methodologies and analysis of metabolic flux in mammalian systems
<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 …
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System analysis and metabolic engineering of biocatalytic reaction networks : application to indene bioconversion
Metabolic engineering is a science concerned with the improvement of cellular properties through the application of recombinant DNA technology. To this point, the field has frequently been limited to methodological issues pertaining to gene introduction, expression and control by way of molecular …
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Computer-assisted generation and curation of genome-scale metabolic models with case studies in the methanogen genus Methanosarcina
… to other methanogens): the diversity in metabolic capabilities for these organisms enables manipulations of methanogenesis pathways that would be lethal in other methanogens. Genetic manipulation tools have been valuable for identifying functions of individual enzymes and pathways in …
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