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genome scale metabolic modeling

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https://www.readbyqxmd.com/read/29322933/integrating-transcriptional-activity-in-genome-scale-models-of-metabolism
#1
Daniel Trejo Banos, Pauline Trébulle, Mohamed Elati
BACKGROUND: Genome-scale metabolic models provide an opportunity for rational approaches to studies of the different reactions taking place inside the cell. The integration of these models with gene regulatory networks is a hot topic in systems biology. The methods developed to date focus mostly on resolving the metabolic elements and use fairly straightforward approaches to assess the impact of genome expression on the metabolic phenotype. RESULTS: We present here a method for integrating the reverse engineering of gene regulatory networks into these metabolic models...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29318410/flux-analysis-of-inborn-errors-of-metabolism
#2
D-J Reijngoud
Patients with an inborn error of metabolism (IEM) are deficient of an enzyme involved in metabolism, and as a consequence metabolism reprograms itself to reach a new steady state. This new steady state underlies the clinical phenotype associated with the deficiency. Hence, we need to know the flux of metabolites through the different metabolic pathways in this new steady state of the reprogrammed metabolism. Stable isotope technology is best suited to study this. In this review the progress made in characterizing the altered metabolism will be presented...
January 9, 2018: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/29317285/wide-spread-whole-genome-duplications-contribute-to-genome-complexity-and-species-diversity-in-angiosperms
#3
Ren Ren, Haifeng Wang, Chunce Guo, Ning Zhang, Liping Zeng, Yamao Chen, Hong Ma, Ji Qi
Gene duplications (GDs) provide evolutionary potentials for generating novel functions, while polyploidization or whole genome duplication (WGD) doubles the chromosomes initially and results in hundreds to thousands of retained duplicates. WGDs are strongly supported by evidence commonly found in many species-rich lineages of eukaryotes, thus are considered as a major driving force in species diversification. We performed comparative genomic and phylogenomic analyses on 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms, to detect large-scale gene duplication events by survey of tens of thousands of gene family trees...
January 6, 2018: Molecular Plant
https://www.readbyqxmd.com/read/29316921/insights-into-metabolic-osmoadaptation-of-the-ectoines-producer-bacterium-chromohalobacter-salexigens-through-a-high-quality-genome-scale-metabolic-model
#4
Francine Piubeli, Manuel Salvador, Montserrat Argandoña, Joaquín J Nieto, Vicente Bernal, Jose M Pastor, Manuel Cánovas, Carmen Vargas
BACKGROUND: The halophilic bacterium Chromohalobacter salexigens is a natural producer of ectoines, compatible solutes with current and potential biotechnological applications. As production of ectoines is an osmoregulated process that draws away TCA intermediates, bacterial metabolism needs to be adapted to cope with salinity changes. To explore and use C. salexigens as cell factory for ectoine(s) production, a comprehensive knowledge at the systems level of its metabolism is essential...
January 9, 2018: Microbial Cell Factories
https://www.readbyqxmd.com/read/29307284/environmental-basis-of-primary-biliary-cholangitis
#5
Atsushi Tanaka, Patrick Sc Leung, M Eric Gershwin
Autoimmunity is a consequence of both genetic and environmental factors, occurring in genetically susceptible hosts with environmental triggers. While genome-wide association studies have revealed a number of susceptible genes contributing to etiology, the environmental triggers remain poorly understood. Primary biliary cholangitis, formally known as primary biliary cirrhosis, is considered a model autoimmune disease for which our group has extensively evaluated environmental factors involved in its etiology...
January 1, 2018: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/29304175/genome-scale-metabolic-models-as-tools-for-drug-design-and-personalized-medicine
#6
Vytautas Raškevičius, Valeryia Mikalayeva, Ieva Antanavičiūtė, Ieva Ceslevičienė, Vytenis Arvydas Skeberdis, Visvaldas Kairys, Sergio Bordel
In this work we aim to show how Genome Scale Metabolic Models (GSMMs) can be used as tools for drug design. By comparing the chemical structures of human metabolites (obtained using their KEGG indexes) and the compounds contained in the DrugBank database, we have observed that compounds showing Tanimoto scores higher than 0.9 with a metabolite, are 29.5 times more likely to bind the enzymes metabolizing the considered metabolite, than ligands chosen randomly. By using RNA-seq data to constrain a human GSMM it is possible to obtain an estimation of its distribution of metabolic fluxes and to quantify the effects of restraining the rate of chosen metabolic reactions (for example using a drug that inhibits the enzymes catalyzing the mentioned reactions)...
2018: PloS One
https://www.readbyqxmd.com/read/29300748/functional-interrogation-of-plasmodium-genus-metabolism-identifies-species-and-stage-specific-differences-in-nutrient-essentiality-and-drug-targeting
#7
Alyaa M Abdel-Haleem, Hooman Hefzi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori, Bernhard O Palsson, Nathan E Lewis, Neema Jamshidi
Several antimalarial drugs exist, but differences between life cycle stages among malaria species pose challenges for developing more effective therapies. To understand the diversity among stages and species, we reconstructed genome-scale models (GEMs) of metabolism for five life cycle stages and five species of Plasmodium spanning the blood, transmission, and mosquito stages. The stage-specific models of Plasmodium falciparum uncovered stage-dependent changes in central carbon metabolism and predicted potential targets that could affect several life cycle stages...
January 4, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29300340/constraining-genome-scale-models-to-represent-the-bow-tie-structure-of-metabolism-for-13c-metabolic-flux-analysis
#8
Tyler W H Backman, David Ando, Jahnavi Singh, Jay D Keasling, Héctor García Martín
Determination of internal metabolic fluxes is crucial for fundamental and applied biology because they map how carbon and electrons flow through metabolism to enable cell function. 13 C Metabolic Flux Analysis ( 13 C MFA) and Two-Scale 13 C Metabolic Flux Analysis (2S- 13 C MFA) are two techniques used to determine such fluxes. Both operate on the simplifying approximation that metabolic flux from peripheral metabolism into central "core" carbon metabolism is minimal, and can be omitted when modeling isotopic labeling in core metabolism...
January 4, 2018: Metabolites
https://www.readbyqxmd.com/read/29282051/microbiota-dysbiosis-in-inflammatory-bowel-diseases-in-silico-investigation-of-the-oxygen-hypothesis
#9
Michael A Henson, Poonam Phalak
BACKGROUND: Inflammatory bowel diseases (IBD), which include ulcerative colitis and Crohn's disease, cause chronic inflammation of the digestive tract in approximately 1.6 million Americans. A signature of IBD is dysbiosis of the gut microbiota marked by a significant reduction of obligate anaerobes and a sharp increase in facultative anaerobes. Numerous experimental studies have shown that IBD is strongly correlated with a decrease of Faecalibacterium prausnitzii and an increase of Escherichia coli...
December 28, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29278837/advances-in-gap-filling-genome-scale-metabolic-models-and-model-driven-experiments-lead-to-novel-metabolic-discoveries
#10
REVIEW
Shu Pan, Jennifer L Reed
With rapid improvements in next-generation sequencing technologies, our knowledge about metabolism of many organisms is rapidly increasing. However, gaps in metabolic networks exist due to incomplete knowledge (e.g., missing reactions, unknown pathways, unannotated and misannotated genes, promiscuous enzymes, and underground metabolic pathways). In this review, we discuss recent advances in gap-filling algorithms based on genome-scale metabolic models and the importance of both high-throughput experiments and detailed biochemical characterization, which work in concert with in silico methods, to allow a more accurate and comprehensive understanding of metabolism...
December 23, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29276507/in-silico-analysis-of-the-small-molecule-content-of-outer-membrane-vesicles-produced-by-bacteroides-thetaiotaomicron-indicates-an-extensive-metabolic-link-between-microbe-and-host
#11
William A Bryant, Régis Stentz, Gwenaelle Le Gall, Michael J E Sternberg, Simon R Carding, Thomas Wilhelm
The interactions between the gut microbiota and its host are of central importance to the health of the host. Outer membrane vesicles (OMVs) are produced ubiquitously by Gram-negative bacteria including the gut commensal Bacteroides thetaiotaomicron. These vesicles can interact with the host in various ways but until now their complement of small molecules has not been investigated in this context. Using an untargeted high-coverage metabolomic approach we have measured the small molecule content of these vesicles in contrasting in vitro conditions to establish what role these metabolites could perform when packed into these vesicles...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29259305/genotypic-variability-based-genome-wide-association-study-identifies-non-additive-loci-hla-c-and-il12b-for-psoriasis
#12
Wen-Hua Wei, Jonathan Massey, Jane Worthington, Anne Barton, Richard B Warren
Genome-wide association studies (GWASs) have identified a number of loci for psoriasis but largely ignored non-additive effects. We report a genotypic variability-based GWAS (vGWAS) that can prioritize non-additive loci without requiring prior knowledge of interaction types or interacting factors in two steps, using a mixed model to partition dichotomous phenotypes into an additive component and non-additive environmental residuals on the liability scale and then the Levene's (Brown-Forsythe) test to assess equality of the residual variances across genotype groups genome widely...
December 19, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/29250098/reconstruction-of-oryza-sativa-indica-genome-scale-metabolic-model-and-its-responses-to-varying-rubisco-activity-light-intensity-and-enzymatic-cost-conditions
#13
Ankita Chatterjee, Benazir Huma, Rahul Shaw, Sudip Kundu
To combat decrease in rice productivity under different stresses, an understanding of rice metabolism is needed. Though there are different genome scale metabolic models (GSMs) of Oryza sativa japonica, no GSM with gene-protein-reaction association exist for Oryza sativa indica. Here, we report a GSM, OSI1136 of O.s. indica, which includes 3602 genes and 1136 metabolic reactions and transporters distributed across the cytosol, mitochondrion, peroxisome, and chloroplast compartments. Flux balance analysis of the model showed that for varying RuBisCO activity (Vc/Vo) (i) the activity of the chloroplastic malate valve increases to transport reducing equivalents out of the chloroplast under increased photorespiratory conditions and (ii) glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase can act as source of cytosolic ATP under decreased photorespiration...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29246152/linking-physiologically-based-pharmacokinetic-and-genome-scale-metabolic-networks-to-understand-estradiol-biology
#14
Joanna H Sier, Alfred E Thumser, Nick J Plant
BACKGROUND: Estrogen is a vital hormone that regulates many biological functions within the body. These include roles in the development of the secondary sexual organs in both sexes, plus uterine angiogenesis and proliferation during the menstrual cycle and pregnancy in women. The varied biological roles of estrogens in human health also make them a therapeutic target for contraception, mitigation of the adverse effects of the menopause, and treatment of estrogen-responsive tumours. In addition, endogenous (e...
December 15, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29241534/integrating-extracellular-flux-measurements-and-genome-scale-modeling-reveals-differences-between-brown-and-white-adipocytes
#15
Alfred K Ramirez, Matthew D Lynes, Farnaz Shamsi, Ruidan Xue, Yu-Hua Tseng, C Ronald Kahn, Simon Kasif, Jonathan M Dreyfuss
White adipocytes are specialized for energy storage, whereas brown adipocytes are specialized for energy expenditure. Explicating this difference can help identify therapeutic targets for obesity. A common tool to assess metabolic differences between such cells is the Seahorse Extracellular Flux (XF) Analyzer, which measures oxygen consumption and media acidification in the presence of different substrates and perturbagens. Here, we integrate the Analyzer's metabolic profile from human white and brown adipocytes with a genome-scale metabolic model to predict flux differences across the metabolic map...
December 12, 2017: Cell Reports
https://www.readbyqxmd.com/read/29229946/find_tfsbp-find-thermodynamics-feasible-and-smallest-balanced-pathways-with-high-yield-from-large-scale-metabolic-networks
#16
Zixiang Xu, Jibin Sun, Qiaqing Wu, Dunming Zhu
Biologically meaningful metabolic pathways are important references in the design of industrial bacterium. At present, constraint-based method is the only way to model and simulate a genome-scale metabolic network under steady-state criteria. Due to the inadequate assumption of the relationship in gene-enzyme-reaction as one-to-one unique association, computational difficulty or ignoring the yield from substrate to product, previous pathway finding approaches can't be effectively applied to find out the high yield pathways that are mass balanced in stoichiometry...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29224928/association-of-rare-predicted-loss-of-function-variants-in-cellular-pathways-with-sub-phenotypes-in-age-related-macular-degeneration
#17
Alexandra Pietraszkiewicz, Freekje van Asten, Alan Kwong, Rinki Ratnapriya, Goncalo Abecasis, Anand Swaroop, Emily Y Chew
PURPOSE: To investigate the association of rare predicted loss-of-function (pLoF) variants within age-related macular degeneration (AMD) risk loci and AMD sub-phenotypes. DESIGN: Case-control study. PARTICIPANTS: Participants of AREDS, AREDS2, and Michigan Genomics Initiative. METHODS: Whole genome sequencing data were analyzed for rare pLoF variants (frequency <0.1%) in the regions of previously identified 52 independent risk variants known to be associated with AMD...
December 7, 2017: Ophthalmology
https://www.readbyqxmd.com/read/29222764/optimization-of-multi-omic-genome-scale-models-methodologies-hands-on-tutorial-and-perspectives
#18
Supreeta Vijayakumar, Max Conway, Pietro Lió, Claudio Angione
Genome-scale metabolic models are valuable tools for assessing the metabolic potential of living organisms. Being downstream of gene expression, metabolism is increasingly being used as an indicator of the phenotypic outcome for drugs and therapies. We here present a review of the principal methods used for constraint-based modelling in systems biology, and explore how the integration of multi-omic data can be used to improve phenotypic predictions of genome-scale metabolic models. We believe that the large-scale comparison of the metabolic response of an organism to different environmental conditions will be an important challenge for genome-scale models...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222763/designing-optimized-production-hosts-by-metabolic-modeling
#19
Christian Jungreuthmayer, Matthias P Gerstl, David A Peña Navarro, Michael Hanscho, David E Ruckerbauer, Jürgen Zanghellini
Many of the complex and expensive production steps in the chemical industry are readily available in living cells. In order to overcome the metabolic limits of these cells, the optimal genetic intervention strategies can be computed by the use of metabolic modeling. Elementary flux mode analysis (EFMA) is an ideal tool for this task, as it does not require defining a cellular objective function. We present two EFMA-based methods to optimize production hosts: (1) the standard approach that can only be used for small and medium scale metabolic networks and (2) the advanced dual system approach that can be utilized to directly compute intervention strategies in a genome-scale metabolic model...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222761/coupling-fluxes-enzymes-and-regulation-in-genome-scale-metabolic-models
#20
Paul A Jensen
Genome-scale models have expanded beyond their metabolic origins. Multiple modeling frameworks are required to combine metabolism with enzymatic networks, transcription, translation, and regulation. Mathematical programming offers a powerful set of tools for tackling these "multi-modality" models, although special attention must be paid to the connections between modeling types. This chapter reviews common methods for combining metabolic and discrete logical models into a single mathematical programming framework...
2018: Methods in Molecular Biology
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