Global ETD Search
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Showing 1 to 11 of 11 for “"Metabolic reconstruction"”.
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An updated genome scale metabolic reconstruction of methanosarcina barkeri
… barkeri genome was published in 2006 after the metabolic reconstruction of M. barkeri, iAF692, was published. The iAF692 reconstruction preformed the first large scale simulations of an Archaea. Since the publication of iAF692, a deeper understanding of Archaea biology has shed light on …
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Genome scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A
… constructed and manually curated a genome-scale metabolic model, iMB744, accounting for 744 of the 4540 predicted protein coding genes (16%) in the M. acetivorans genome. The reconstruction effort has identified key knowledge gaps and differences in the peripheral metabolism and central …
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Elucidating microbial interactions, adaptations, and evolution under extreme environmental conditions in modern microbial mats from Shark Bay, Western Australia
… protection from harsh environmental conditions. Metabolic reconstruction of poorly-characterized members of the rare biosphere is then used to i) determine the functional role of these bacteria within the pustular mat community for the first time and ii) infer the adaptational mechanisms for …
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Modeling cellular metabolism in multiple scales
… our description of physiological variability in metabolic phenotypes of yeast, we improved the Population FBA method to dynamically constrain a genome-wide metabolic reconstruction of S. cerevisiae using comprehensive proteomics and microarray data sets. Moreover, a genetic algorithm approach was …
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Genomic Diversity of Magnetotactic Bacteria from Underexplored Extreme Aquatic Habitats
Magnetotactic bacteria (MTB) are metabolically versatile prokaryotes characterised by their ability to biomineralise intracellular magnetic nanocrystals within organelles called magnetosomes. These organelles assist MTB to align with geomagnetic field lines using magnetotaxis, thereby facilitating …
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Genomic Diversity of Magnetotactic Bacteria from Underexplored Extreme Aquatic Habitats
Magnetotactic bacteria (MTB) are metabolically versatile prokaryotes characterised by their ability to biomineralise intracellular magnetic nanocrystals within organelles called magnetosomes. These organelles assist MTB to align with geomagnetic field lines using magnetotaxis, thereby facilitating …
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Bioinformatic and biological analysis of DNA methylation in the human genome
… of systems biology were used to study the metabolic effects of different expression level of imprinted genes. The greatest perturbation in the metabolic reconstruction occurred when differential expression of the ATP10A gene was simulated. The simulated effects of differential expression on …
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Identifying and modeling perturbed networks in cancer through statistical and constraint-based analysis
… for identifying biomolecular pathways (e.g., metabolic or signaling) that are perturbed in disease data. I used this method (described in Chapter 4) to identify differentially regulated and variably expressed pathways in a number of human diseases, and later investigated behavior-associated …
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Metabolic heterogeneity in microbial populations
… how variability in the copy numbers of metabolic enzymes affects how individual cells extract nourishment from their environment and grow. We model independent microbial cells, each with their own set of enzyme copy numbers sampled from experimental distributions, and use flux balance …
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Integrating manual and automated metabolic engineering methods
Made available in DSpace on 2016-07-07T20:27:15Z (GMT). No. of bitstreams: 4 RICHARDS-DISSERTATION-2016.pdf: 3860821 bytes, checksum: cbaf30718ce7594d7f76859b49a220de (MD5) Richards_Matthew.docx: 2576729 bytes, checksum: e2a1076a288d7d31c646df244282d03a (MD5) LICENSE.txt: 4213 bytes, checksum: …
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Characterizing and analyzing disease-related omics data using network modeling approaches
… information related to biochemical processes and metabolic networks involving metabolites. Metabolomics data can give an instantaneous snapshot of the current state of the cell and thus offers a distinct view of the effects of diet, drugs and disease on the model organism. The third part of my …