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genome scale metabolic modeling

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https://www.readbyqxmd.com/read/28649430/predicting-growth-of-the-healthy-infant-using-a-genome-scale-metabolic-model
#1
Avlant Nilsson, Adil Mardinoglu, Jens Nielsen
An estimated 165 million children globally have stunted growth, and extensive growth data are available. Genome scale metabolic models allow the simulation of molecular flux over each metabolic enzyme, and are well adapted to analyze biological systems. We used a human genome scale metabolic model to simulate the mechanisms of growth and integrate data about breast-milk intake and composition with the infant's biomass and energy expenditure of major organs. The model predicted daily metabolic fluxes from birth to age 6 months, and accurately reproduced standard growth curves and changes in body composition...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28649285/introduction-of-the-diagene-study-clinical-characteristics-pathophysiology-and-determinants-of-vascular-complications-of-type-2-diabetes
#2
Thijs T W van Herpt, Roosmarijn F H Lemmers, Mandy van Hoek, Janneke G Langendonk, Ronald J Erdtsieck, Bert Bravenboer, Annelies Lucas, Monique T Mulder, Harm R Haak, Aloysius G Lieverse, Eric J G Sijbrands
BACKGROUND: Type 2 diabetes is a major healthcare problem. Glucose-, lipid-, and blood pressure-lowering strategies decrease the risk of micro- and macrovascular complications. However, a substantial residual risk remains. To unravel the etiology of type 2 diabetes and its complications, large-scale, well-phenotyped studies with prospective follow-up are needed. This is the goal of the DiaGene study. In this manuscript, we describe the design and baseline characteristics of the study...
2017: Diabetology & Metabolic Syndrome
https://www.readbyqxmd.com/read/28648476/constraint-based-metabolic-modelling-of-marine-microbes-and-communities
#3
REVIEW
Marco Fondi, Renato Fani
Constraint-based metabolic modelling (CBMM) consists in the use of computational methods and tools to perform genome-scale simulations and predict metabolic features at the whole cellular level. This approach is rapidly expanding in microbiology, as it combines reliable predictive abilities with conceptually and technically simple frameworks. Among the possible outcomes of CBMM, the capability to i) guide a focused planning of metabolic engineering experiments and ii) provide a system-level understanding of (single or community-level) microbial metabolic circuits also represent primary aims in present-day marine microbiology...
June 22, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28644920/genome-scale-metabolic-models-applied-to-human-health-and-disease
#4
REVIEW
Daniel J Cook, Jens Nielsen
Advances in genome sequencing, high throughput measurement of gene and protein expression levels, data accessibility, and computational power have allowed genome-scale metabolic models (GEMs) to become a useful tool for understanding metabolic alterations associated with many different diseases. Despite the proven utility of GEMs, researchers confront multiple challenges in the use of GEMs, their application to human health and disease, and their construction and simulation in an organ-specific and disease-specific manner...
June 23, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28639622/growth-coupled-overproduction-is-feasible-for-almost-all-metabolites-in-five-major-production-organisms
#5
Axel von Kamp, Steffen Klamt
Computational modelling of metabolic networks has become an established procedure in the metabolic engineering of production strains. One key principle that is frequently used to guide the rational design of microbial cell factories is the stoichiometric coupling of growth and product synthesis, which makes production of the desired compound obligatory for growth. Here we show that the coupling of growth and production is feasible under appropriate conditions for almost all metabolites in genome-scale metabolic models of five major production organisms...
June 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28611042/competition-between-dna-methylation-nucleotide-synthesis-and-anti-oxidation-in-cancer-versus-normal-tissues
#6
Sha Cao, Xiwen Zhu, Chi Zhang, Hong Qian, Heinz-Bernd Schuttler, Jian-Ping Gong, Ying Xu
Global DNA hypomethylation occurs in many cancer types but there is no explanation for its differential occurance or possible impact on cancer cell physiology. Here we address these issues with a computational study of genome-scale DNA methylation in 16 cancer types. Specifically, we identified (1) a possible determinant for global DNA methylation in cancer cells, and (2) a relationship between levels of DNA methylation, nucleotide synthesis and intracellular oxidative stress in cells. We developed a system of kinetic equations to capture the metabolic relations among DNA methylation, nucleotide synthesis, and anti-oxidative stress response, including their competitions for methyl and sulfur groups, based on known information about one-carbon metabolism and trans-sulfuration pathways...
June 13, 2017: Cancer Research
https://www.readbyqxmd.com/read/28600895/metabolic-modeling-of-energy-balances-in-mycoplasma-hyopneumoniae-shows-that-pyruvate-addition-increases-growth-rate
#7
Tjerko Kamminga, Simen-Jan Slagman, Jetta J E Bijlsma, Vitor A P Martins Dos Santos, Maria Suarez-Diez, Peter J Schaap
Mycoplasma hyopneumoniae is cultured on large-scale to produce antigen for inactivated whole-cell vaccines against respiratory disease in pigs. However, the fastidious nutrient requirements of this minimal bacterium and the low growth rate make it challenging to reach sufficient biomass yield for antigen production. In this study, we sequenced the genome of M. hyopneumoniae strain 11 and constructed a high quality constraint-based genome-scale metabolic model of 284 chemical reactions and 298 metabolites. We validated the model with time-series data of duplicate fermentation cultures to aim for an integrated model describing the dynamic profiles measured in fermentations...
June 10, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28598965/metabolic-network-segmentation-a-probabilistic-graphical-modeling-approach-to-identify-the-sites-and-sequential-order-of-metabolic-regulation-from-non-targeted-metabolomics-data
#8
Andreas Kuehne, Urs Mayr, Daniel C Sévin, Manfred Claassen, Nicola Zamboni
In recent years, the number of large-scale metabolomics studies on various cellular processes in different organisms has increased drastically. However, it remains a major challenge to perform a systematic identification of mechanistic regulatory events that mediate the observed changes in metabolite levels, due to complex interdependencies within metabolic networks. We present the metabolic network segmentation (MNS) algorithm, a probabilistic graphical modeling approach that enables genome-scale, automated prediction of regulated metabolic reactions from differential or serial metabolomics data...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28592500/epistatic-networks-jointly-influence-phenotypes-related-to-metabolic-disease-and-gene-expression-in-diversity-outbred-mice
#9
Anna L Tyler, Bo Ji, Daniel M Gatti, Steven C Munger, Gary A Churchill, Karen L Svenson, Gregory W Carter
Genetic studies of multidimensional phenotypes can potentially link genetic variation, gene expression, and physiological data to create multi-scale models of complex traits. The challenge of reducing these data to specific hypotheses has become increasingly acute with the advent of genome-scale data resources. Multi-parent populations derived from model organisms provide a resource for developing methods to understand this complexity. In this study, we simultaneously modeled body composition, serum biomarkers, and liver transcript abundances from 474 Diversity Outbred mice...
June 2017: Genetics
https://www.readbyqxmd.com/read/28571567/clostridium-butyricum-maximizes-growth-while-minimizing-enzyme-usage-and-atp-production-metabolic-flux-distribution-of-a-strain-cultured-in-glycerol
#10
Luis Miguel Serrano-Bermúdez, Andrés Fernando González Barrios, Costas D Maranas, Dolly Montoya
BACKGROUND: The increase in glycerol obtained as a byproduct of biodiesel has encouraged the production of new industrial products, such as 1,3-propanediol (PDO), using biotechnological transformation via bacteria like Clostridium butyricum. However, despite the increasing role of Clostridium butyricum as a bio-production platform, its metabolism remains poorly modeled. RESULTS: We reconstructed iCbu641, the first genome-scale metabolic (GSM) model of a PDO producer Clostridium strain, which included 641 genes, 365 enzymes, 891 reactions, and 701 metabolites...
June 1, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28557990/on-the-effects-of-alternative-optima-in-context-specific-metabolic-model-predictions
#11
Semidán Robaina-Estévez, Zoran Nikoloski
The integration of experimental data into genome-scale metabolic models can greatly improve flux predictions. This is achieved by restricting predictions to a more realistic context-specific domain, like a particular cell or tissue type. Several computational approaches to integrate data have been proposed-generally obtaining context-specific (sub)models or flux distributions. However, these approaches may lead to a multitude of equally valid but potentially different models or flux distributions, due to possible alternative optima in the underlying optimization problems...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28546903/comprehensive-reconstruction-and-evaluation-of-pichia-pastoris-genome-scale-metabolic-model-that-accounts-for-1243-orfs
#12
Rui Ye, Mingzhi Huang, Hongzhong Lu, Jiangchao Qian, Weilu Lin, Ju Chu, Yingping Zhuang, Siliang Zhang
BACKGROUND: Pichia pastoris is one of the most important cell factories for production of industrial enzymes and heterogenous proteins. The genome-scale metabolic model of high quality is crucial for comprehensive understanding of the P. pastoris metabolism. METHODS: In this paper, we upgraded P. pastoris genome-scale metabolic model based on the combination of latest genome annotations and literatures. Then the performance of the new model was evaluated using the Cobra Toolbox v2...
2017: Bioresources and Bioprocessing
https://www.readbyqxmd.com/read/28544881/mammalian-systems-biotechnology-reveals-global-cellular-adaptations-in-a-recombinant-cho-cell-line
#13
Faraaz Noor Khan Yusufi, Meiyappan Lakshmanan, Ying Swan Ho, Bernard Liat Wen Loo, Pramila Ariyaratne, Yuansheng Yang, Say Kong Ng, Tessa Rui Min Tan, Hock Chuan Yeo, Hsueh Lee Lim, Sze Wai Ng, Ai Ping Hiu, Chung Ping Chow, Corrine Wan, Shuwen Chen, Gavin Teo, Gao Song, Ju Xin Chin, Xiaoan Ruan, Ken Wing Kin Sung, Wei-Shou Hu, Miranda Gek Sim Yap, Muriel Bardor, Niranjan Nagarajan, Dong-Yup Lee
Effective development of host cells for therapeutic protein production is hampered by the poor characterization of cellular transfection. Here, we employed a multi-omics-based systems biotechnology approach to elucidate the genotypic and phenotypic differences between a wild-type and recombinant antibody-producing Chinese hamster ovary (CHO) cell line. At the genomic level, we observed extensive rearrangements in specific targeted loci linked to transgene integration sites. Transcriptional re-wiring of DNA damage repair and cellular metabolism in the antibody producer, via changes in gene copy numbers, was also detected...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28530276/focus-a-metaheuristic-algorithm-for-computing-knockouts-from-genome-scale-models-for-strain-optimization
#14
Sarma Mutturi
Although handful tools are available for constraint-based flux analysis to generate knockout strains, most of these are either based on bilevel-MIP or its modifications. However, metaheuristic approaches that are known for their flexibility and scalability have been less studied. Moreover, in the existing tools, sectioning of search space to find optimal knocks has not been considered. Herein, a novel computational procedure, termed as FOCuS (Flower-pOllination coupled Clonal Selection algorithm), was developed to find the optimal reaction knockouts from a metabolic network to maximize the production of specific metabolites...
May 22, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28527885/maintenance-of-atp-homeostasis-triggers-metabolic-shifts-in-gas-fermenting-acetogens
#15
Kaspar Valgepea, Renato de Souza Pinto Lemgruber, Kieran Meaghan, Robin William Palfreyman, Tanus Abdalla, Björn Daniel Heijstra, James Bruce Behrendorff, Ryan Tappel, Michael Köpke, Séan Dennis Simpson, Lars Keld Nielsen, Esteban Marcellin
Acetogens are promising cell factories for producing fuels and chemicals from waste feedstocks via gas fermentation, but quantitative characterization of carbon, energy, and redox metabolism is required to guide their rational metabolic engineering. Here, we explore acetogen gas fermentation using physiological, metabolomics, and transcriptomics data for Clostridium autoethanogenum steady-state chemostat cultures grown on syngas at various gas-liquid mass transfer rates. We observe that C. autoethanogenum shifts from acetate to ethanol production to maintain ATP homeostasis at higher biomass concentrations but reaches a limit at a molar acetate/ethanol ratio of ∼1...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28520105/large-scale-computational-models-of-liver-metabolism-how-far-from-the-clinics
#16
REVIEW
Tanja Cvitanović, Matthias C Reichert, Miha Moškon, Miha Mraz, Frank Lammert, Damjana Rozman
Understanding the dynamics of human liver metabolism is fundamental for effective diagnosis and treatment of liver diseases in general and the metabolism of drugs in particular. This knowledge can be obtained with systems biology/medicine approaches that account for the complexity of hepatic responses and their systemic consequences in other organs. Computational modelling can reveal hidden principles of the system by classification of individual components, analysing their interactions and simulating the effects that are difficult to investigate experimentally...
May 18, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28511646/emergence-of-microbial-diversity-due-to-cross-feeding-interactions-in-a-spatial-model-of-gut-microbial-metabolism
#17
Milan J A van Hoek, Roeland M H Merks
BACKGROUND: The human gut contains approximately 10(14) bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down nutrient sources that our own digestive enzymes cannot handle, including complex polysaccharides, producing short chain fatty acids and additional metabolites, e.g., vitamin K. Microbial diversity is important for colonic health: Changes in the composition of the microbiota have been associated with inflammatory bowel disease, diabetes, obesity and Crohn's disease, and make the microbiota more vulnerable to infestation by harmful species, e...
May 16, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28509388/proteomic-explorations-of-autism-spectrum-disorder
#18
Nicholas Szoko, Adam J McShane, Marvin R Natowicz
Proteomics, the large-scale study of protein expression in cells and tissues, is a powerful tool to study the biology of clinical conditions and has provided significant insights in many experimental systems. Herein, we review the basics of proteomic methodology and discuss challenges in using proteomic approaches to study autism. Unlike other experimental approaches, such as genomic approaches, there have been few large-scale studies of proteins in tissues from persons with autism. Most of the proteomic studies on autism used blood or other peripheral tissues; few studies used brain tissue...
May 16, 2017: Autism Research: Official Journal of the International Society for Autism Research
https://www.readbyqxmd.com/read/28505184/steadycom-predicting-microbial-abundances-while-ensuring-community-stability
#19
Siu Hung Joshua Chan, Margaret N Simons, Costas D Maranas
Genome-scale metabolic modeling has become widespread for analyzing microbial metabolism. Extending this established paradigm to more complex microbial communities is emerging as a promising way to unravel the interactions and biochemical repertoire of these omnipresent systems. While several modeling techniques have been developed for microbial communities, little emphasis has been placed on the need to impose a time-averaged constant growth rate across all members for a community to ensure co-existence and stability...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28469704/development-of-a-core-clostridium-thermocellum-kinetic-metabolic-model-consistent-with-multiple-genetic-perturbations
#20
Satyakam Dash, Ali Khodayari, Jilai Zhou, Evert K Holwerda, Daniel G Olson, Lee R Lynd, Costas D Maranas
BACKGROUND: Clostridium thermocellum is a Gram-positive anaerobe with the ability to hydrolyze and metabolize cellulose into biofuels such as ethanol, making it an attractive candidate for consolidated bioprocessing (CBP). At present, metabolic engineering in C. thermocellum is hindered due to the incomplete description of its metabolic repertoire and regulation within a predictive metabolic model. Genome-scale metabolic (GSM) models augmented with kinetic models of metabolism have been shown to be effective at recapitulating perturbed metabolic phenotypes...
2017: Biotechnology for Biofuels
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