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genome scale metabolic modeling

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https://www.readbyqxmd.com/read/28338129/prediction-of-metabolic-fluxes-from-gene-expression-data-with-huber-penalty-convex-optimization-function
#1
Shao-Wu Zhang, Wang-Long Gou, Yan Li
As one of the critical parameters of a metabolic pathway, the metabolic flux in a metabolic network serves as an essential role in physiology and pathology. Constraint-based metabolic models are the widely used frameworks for predicting metabolic fluxes in genome-scale metabolic networks. Integrating the transcriptomic data into the constraint-based metabolic models can effectively predict context-specific fluxes across different conditions. However, these methods always need user-defined thresholds to identify the expression levels of metabolic genes or restrain the rate of biomass production, and the predictive results are sensitive to the thresholds...
March 24, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28334407/organismal-and-spatial-partitioning-of-energy-and-macronutrient-transformations-within-a-hypersaline-mat
#2
Jennifer M Mobberley, Stephen R Lindemann, Hans C Bernstein, James J Moran, Ryan S Renslow, Jerome Babauta, Dehong Hu, Haluk Beyenal, William C Nelson
Phototrophic mat communities are model ecosystems for studying energy cycling and elemental transformations because complete biogeochemical cycles occur over millimeter-to-centimeter scales. Characterization of energy and nutrient capture within hypersaline phototrophic mats has focused on specific processes and organisms, however little is known about community-wide distribution of and linkages between these processes. To investigate energy and macronutrient capture and flow through a structured community, the spatial and organismal distribution of metabolic functions within a compact hypersaline mat community from Hot Lake have been broadly elucidated through species-resolved metagenomics and geochemical, microbial diversity, and metabolic gradient measurements...
March 15, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28333921/bioenergetics-based-modeling-of-plasmodium-falciparum-metabolism-reveals-its-essential-genes-nutritional-requirements-and-thermodynamic-bottlenecks
#3
Anush Chiappino-Pepe, Stepan Tymoshenko, Meriç Ataman, Dominique Soldati-Favre, Vassily Hatzimanikatis
Novel antimalarial therapies are urgently needed for the fight against drug-resistant parasites. The metabolism of malaria parasites in infected cells is an attractive source of drug targets but is rather complex. Computational methods can handle this complexity and allow integrative analyses of cell metabolism. In this study, we present a genome-scale metabolic model (iPfa) of the deadliest malaria parasite, Plasmodium falciparum, and its thermodynamics-based flux analysis (TFA). Using previous absolute concentration data of the intraerythrocytic parasite, we applied TFA to iPfa and predicted up to 63 essential genes and 26 essential pairs of genes...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28325918/robust-analysis-of-fluxes-in-genome-scale-metabolic-pathways
#4
Michael MacGillivray, Amy Ko, Emily Gruber, Miranda Sawyer, Eivind Almaas, Allen Holder
Constraint-based optimization, such as flux balance analysis (FBA), has become a standard systems-biology computational method to study cellular metabolisms that are assumed to be in a steady state of optimal growth. The methods are based on optimization while assuming (i) equilibrium of a linear system of ordinary differential equations, and (ii) deterministic data. However, the steady-state assumption is biologically imperfect, and several key stoichiometric coefficients are experimentally inferred from situations of inherent variation...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28323032/metabolic-re-wiring-of-isogenic-breast-epithelial-cell-lines-following-epithelial-to-mesenchymal-transition
#5
Skarphedinn Halldorsson, Neha Rohatgi, Manuela Magnusdottir, Kumari Sonal Choudhary, Thorarinn Guðjónsson, Erik Knutsen, Anna Barkovskaya, Bylgja Hilmarsdottir, Maria Perander, Gunhild M Mælandsmo, Steinn Gudmundsson, Óttar Rolfsson
Epithelial to mesenchymal transition (EMT) has implications in tumor progression and metastasis. Metabolic alterations have been described in cancer development but studies focused on the metabolic re-wiring that takes place during EMT are still limited. We performed metabolomics profiling of a breast epithelial cell line and its EMT derived mesenchymal phenotype to create genome-scale metabolic models descriptive of both cell lines. Glycolysis and OXPHOS were higher in the epithelial phenotype while amino acid anaplerosis and fatty acid oxidation fueled the mesenchymal phenotype...
March 18, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28319856/systems-biology-solutions-for-biochemical-production-challenges
#6
REVIEW
Anne Sofie Lærke Hansen, Rebecca M Lennen, Nikolaus Sonnenschein, Markus J Herrgård
There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions...
March 16, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28303457/lipid-metabolism-and-potentials-of-biofuel-and-high-added-value-oil-production-in-red-algae
#7
REVIEW
Naoki Sato, Takashi Moriyama, Natsumi Mori, Masakazu Toyoshima
Biomass production is currently explored in microalgae, macroalgae and land plants. Microalgal biofuel development has been performed mostly in green algae. In the Japanese tradition, macrophytic red algae such as Pyropia yezoensis and Gelidium crinale have been utilized as food and industrial materials. Researches on the utilization of unicellular red microalgae such as Cyanidioschyzon merolae and Porphyridium purpureum started only quite recently. Red algae have relatively large plastid genomes harboring more than 200 protein-coding genes that support the biosynthetic capacity of the plastid...
April 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28302587/transcriptomic-changes-in-cho-cells-after-adaptation-to-suspension-growth-in-protein-free-medium-analysed-by-a-species-specific-microarray
#8
Smriti Shridhar, Gerald Klanert, Norbert Auer, Inmaculada Hernandez-Lopez, Maciej M Kańduła, Matthias Hackl, Johannes Grillari, Nancy Stralis-Pavese, David P Kreil, Nicole Borth
Chinese Hamster Ovary (CHO) cells are the preferred cell line for production of biopharmaceuticals. These cells are capable to grow without serum supplementation, but drastic changes in their phenotype occur during adaptation to protein-free growth, which typically include the change to a suspension phenotype with reduced growth rate. A possible approach to understand this transformation, with the intention to counteract the reduction in growth by targeted supplementation of protein-free media, is gene expression profiling...
March 14, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28301739/systems-biology-of-metabolism
#9
Jens Nielsen
Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are described, and two different types of mathematical models used for studying metabolism are discussed: kinetic models and genome-scale metabolic models. The use of different omics technologies, including transcriptomics, proteomics, metabolomics, and fluxomics, for studying metabolism is presented...
March 8, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28300137/corrigendum-ecolicore2-a-reference-network-model-of-the-central-metabolism-of-escherichia-coli-and-relationships-to-its-genome-scale-parent-model
#10
Oliver Hädicke, Steffen Klamt
No abstract text is available yet for this article.
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28298424/richer-data-with-personalized-gems
#11
Miles A Miller
Personalized genome-scale metabolic models augment clinical hepatic steatosis data and motivate treatment based on glutathione repletion.
March 15, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28280499/deep-sequencing-of-suppression-subtractive-hybridisation-drought-and-recovery-libraries-of-the-non-model-crop-trifolium-repens-l
#12
Maciej Bisaga, Matthew Lowe, Matthew Hegarty, Michael Abberton, Adriana Ravagnani
White clover is a short-lived perennial whose persistence is greatly affected by abiotic stresses, particularly drought. The aim of this work was to characterize its molecular response to water deficit and recovery following re-hydration to identify targets for the breeding of tolerant varieties. We created a white clover reference transcriptome of 16,193 contigs by deep sequencing (mean base coverage 387x) four Suppression Subtractive Hybridization (SSH) libraries (a forward and a reverse library for each treatment) constructed from young leaf tissue of white clover at the onset of the response to drought and recovery...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28273479/systems-biology-of-metabolism-a-driver-for-developing-personalized-and-precision-medicine
#13
REVIEW
Jens Nielsen
Systems biology uses mathematical models to analyze large datasets and simulate system behavior. It enables integrative analysis of different types of data and can thereby provide new insight into complex biological systems. Here will be discussed the challenges of using systems medicine for advancing the development of personalized and precision medicine to treat metabolic diseases like insulin resistance, obesity, NAFLD, NASH, and cancer. It will be illustrated how the concept of genome-scale metabolic models can be used for integrative analysis of big data with the objective of identifying novel biomarkers that are foundational for personalized and precision medicine...
March 7, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28268592/a-multiscale-model-based-analysis-of-the-multi-tissue-interplay-underlying-blood-glucose-regulation-in-type-i-diabetes
#14
Federico Wadehn, Stephan Schaller, Thomas Eissing, Markus Krauss, Lars Kupfer
A multiscale model for blood glucose regulation in diabetes type I patients is constructed by integrating detailed metabolic network models for fat, liver and muscle cells into a whole body physiologically-based pharmacokinetic/pharmacodynamic (pBPK/PD) model. The blood glucose regulation PBPK/PD model simulates the distribution and metabolization of glucose, insulin and glucagon on an organ and whole body level. The genome-scale metabolic networks in contrast describe intracellular reactions. The developed multiscale model is fitted to insulin, glucagon and glucose measurements of a 48h clinical trial featuring 6 subjects and is subsequently used to simulate (in silico) the influence of geneknockouts and drug-induced enzyme inhibitions on whole body blood glucose levels...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28266498/reconstruction-of-the-metabolic-network-of-pseudomonas-aeruginosa-to-interrogate-virulence-factor-synthesis
#15
Jennifer A Bartell, Anna S Blazier, Phillip Yen, Juliane C Thøgersen, Lars Jelsbak, Joanna B Goldberg, Jason A Papin
Virulence-linked pathways in opportunistic pathogens are putative therapeutic targets that may be associated with less potential for resistance than targets in growth-essential pathways. However, efficacy of virulence-linked targets may be affected by the contribution of virulence-related genes to metabolism. We evaluate the complex interrelationships between growth and virulence-linked pathways using a genome-scale metabolic network reconstruction of Pseudomonas aeruginosa strain PA14 and an updated, expanded reconstruction of P...
March 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/28263984/managing-uncertainty-in-metabolic-network-structure-and-improving-predictions-using-ensemblefba
#16
Matthew B Biggs, Jason A Papin
Genome-scale metabolic network reconstructions (GENREs) are repositories of knowledge about the metabolic processes that occur in an organism. GENREs have been used to discover and interpret metabolic functions, and to engineer novel network structures. A major barrier preventing more widespread use of GENREs, particularly to study non-model organisms, is the extensive time required to produce a high-quality GENRE. Many automated approaches have been developed which reduce this time requirement, but automatically-reconstructed draft GENREs still require curation before useful predictions can be made...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28258322/metabolic-engineering-of-synechocystis-sp-pcc-6803-for-enhanced-ethanol-production-based-on-flux-balance-analysis
#17
Katsunori Yoshikawa, Yoshihiro Toya, Hiroshi Shimizu
Synechocystis sp. PCC 6803 is an attractive host for bio-ethanol production due to its ability to directly convert atmospheric carbon dioxide into ethanol using photosystems. To enhance ethanol production in Synechocystis sp. PCC 6803, metabolic engineering was performed based on in silico simulations, using the genome-scale metabolic model. Comprehensive reaction knockout simulations by flux balance analysis predicted that the knockout of NAD(P)H dehydrogenase enhanced ethanol production under photoautotrophic conditions, where ammonium is the nitrogen source...
March 3, 2017: Bioprocess and Biosystems Engineering
https://www.readbyqxmd.com/read/28255832/analysing-algorithms-and-data-sources-for-the-tissue-specific-reconstruction-of-liver-healthy-and-cancer-cells
#18
Jorge Ferreira, Sara Correia, Miguel Rocha
Genome-Scale Metabolic Models (GSMMs), mathematical representations of the cell metabolism in different organisms including humans, are resourceful tools to simulate metabolic phenotypes and understand associated diseases, such as obesity, diabetes and cancer. In the last years, different algorithms have been developed to generate tissue-specific metabolic models that simulate different phenotypes for distinct cell types. Hepatocyte cells are one of the main sites of metabolic conversions, mainly due to their diverse physiological functions...
March 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28254760/personal-model-assisted-identification-of-nad-and%C3%A2-glutathione-metabolism-as-intervention-target-in-nafld
#19
Adil Mardinoglu, Elias Bjornson, Cheng Zhang, Martina Klevstig, Sanni Söderlund, Marcus Ståhlman, Martin Adiels, Antti Hakkarainen, Nina Lundbom, Murat Kilicarslan, Björn M Hallström, Jesper Lundbom, Bruno Vergès, Peter Hugh R Barrett, Gerald F Watts, Mireille J Serlie, Jens Nielsen, Mathias Uhlén, Ulf Smith, Hanns-Ulrich Marschall, Marja-Riitta Taskinen, Jan Boren
To elucidate the molecular mechanisms underlying non-alcoholic fatty liver disease (NAFLD), we recruited 86 subjects with varying degrees of hepatic steatosis (HS). We obtained experimental data on lipoprotein fluxes and used these individual measurements as personalized constraints of a hepatocyte genome-scale metabolic model to investigate metabolic differences in liver, taking into account its interactions with other tissues. Our systems level analysis predicted an altered demand for NAD(+) and glutathione (GSH) in subjects with high HS Our analysis and metabolomic measurements showed that plasma levels of glycine, serine, and associated metabolites are negatively correlated with HS, suggesting that these GSH metabolism precursors might be limiting...
March 2, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28249569/unity-in-defence-honeybee-workers-exhibit-conserved-molecular-responses-to-diverse-pathogens
#20
Vincent Doublet, Yvonne Poeschl, Andreas Gogol-Döring, Cédric Alaux, Desiderato Annoscia, Christian Aurori, Seth M Barribeau, Oscar C Bedoya-Reina, Mark J F Brown, James C Bull, Michelle L Flenniken, David A Galbraith, Elke Genersch, Sebastian Gisder, Ivo Grosse, Holly L Holt, Dan Hultmark, H Michael G Lattorff, Yves Le Conte, Fabio Manfredini, Dino P McMahon, Robin F A Moritz, Francesco Nazzi, Elina L Niño, Katja Nowick, Ronald P van Rij, Robert J Paxton, Christina M Grozinger
BACKGROUND: Organisms typically face infection by diverse pathogens, and hosts are thought to have developed specific responses to each type of pathogen they encounter. The advent of transcriptomics now makes it possible to test this hypothesis and compare host gene expression responses to multiple pathogens at a genome-wide scale. Here, we performed a meta-analysis of multiple published and new transcriptomes using a newly developed bioinformatics approach that filters genes based on their expression profile across datasets...
March 2, 2017: BMC Genomics
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