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Flux balance analysis

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https://www.readbyqxmd.com/read/28107392/upon-accounting-for-the-impact-of-isoenzyme-loss-gene-deletion-costs-anticorrelate-with-their-evolutionary-rates
#1
Christopher Jacobs, Luke Lambourne, Yu Xia, Daniel Segrè
System-level metabolic network models enable the computation of growth and metabolic phenotypes from an organism's genome. In particular, flux balance approaches have been used to estimate the contribution of individual metabolic genes to organismal fitness, offering the opportunity to test whether such contributions carry information about the evolutionary pressure on the corresponding genes. Previous failure to identify the expected negative correlation between such computed gene-loss cost and sequence-derived evolutionary rates in Saccharomyces cerevisiae has been ascribed to a real biological gap between a gene's fitness contribution to an organism "here and now" and the same gene's historical importance as evidenced by its accumulated mutations over millions of years of evolution...
2017: PloS One
https://www.readbyqxmd.com/read/28103880/the-use-of-genome-scale-metabolic-network-reconstruction-to-predict-fluxes-and-equilibrium-composition-of-n-fixing-versus-c-fixing-cells-in-a-diazotrophic-cyanobacterium-trichodesmium-erythraeum
#2
Joseph J Gardner, Nanette R Boyle
BACKGROUND: Computational, genome based predictions of organism phenotypes has enhanced the ability to investigate the biological phenomena that help organisms survive and respond to their environments. In this study, we have created the first genome-scale metabolic network reconstruction of the nitrogen fixing cyanobacterium T. erythraeum and used genome-scale modeling approaches to investigate carbon and nitrogen fluxes as well as growth and equilibrium population composition. RESULTS: We created a genome-scale reconstruction of T...
January 19, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28093405/distributedfba-jl-high-level-high-performance-flux-balance-analysis-in-julia
#3
Laurent Heirendt, Ines Thiele, Ronan M T Fleming
MOTIVATION: Flux balance analysis, and its variants, are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. RESULTS: DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes...
January 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28088694/metabolic-network-modeling-with-model-organisms
#4
REVIEW
L Safak Yilmaz, Albertha Jm Walhout
Flux balance analysis (FBA) with genome-scale metabolic network models (GSMNM) allows systems level predictions of metabolism in a variety of organisms. Different types of predictions with different accuracy levels can be made depending on the applied experimental constraints ranging from measurement of exchange fluxes to the integration of gene expression data. Metabolic network modeling with model organisms has pioneered method development in this field. In addition, model organism GSMNMs are useful for basic understanding of metabolism, and in the case of animal models, for the study of metabolic human diseases...
January 12, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28081159/osmoregulation-in-the-halophilic-bacterium-halomonas-elongata-a-case-study-for-integrative-systems-biology
#5
Viktoria Kindzierski, Silvia Raschke, Nicole Knabe, Frank Siedler, Beatrix Scheffer, Katharina Pflüger-Grau, Friedhelm Pfeiffer, Dieter Oesterhelt, Alberto Marin-Sanguino, Hans-Jörg Kunte
Halophilic bacteria use a variety of osmoregulatory methods, such as the accumulation of one or more compatible solutes. The wide diversity of compounds that can act as compatible solute complicates the task of understanding the different strategies that halophilic bacteria use to cope with salt. This is specially challenging when attempting to go beyond the pathway that produces a certain compatible solute towards an understanding of how the metabolic network as a whole addresses the problem. Metabolic reconstruction based on genomic data together with Flux Balance Analysis (FBA) is a promising tool to gain insight into this problem...
2017: PloS One
https://www.readbyqxmd.com/read/28073473/how-rising-co2-and-global-warming-may-stimulate-harmful-cyanobacterial-blooms
#6
REVIEW
Petra M Visser, Jolanda M H Verspagen, Giovanni Sandrini, Lucas J Stal, Hans C P Matthijs, Timothy W Davis, Hans W Paerl, Jef Huisman
Climate change is likely to stimulate the development of harmful cyanobacterial blooms in eutrophic waters, with negative consequences for water quality of many lakes, reservoirs and brackish ecosystems across the globe. In addition to effects of temperature and eutrophication, recent research has shed new light on the possible implications of rising atmospheric CO2 concentrations. Depletion of dissolved CO2 by dense cyanobacterial blooms creates a concentration gradient across the air-water interface. A steeper gradient at elevated atmospheric CO2 concentrations will lead to a greater influx of CO2, which can be intercepted by surface-dwelling blooms, thus intensifying cyanobacterial blooms in eutrophic waters...
April 2016: Harmful Algae
https://www.readbyqxmd.com/read/28065897/trfba-an-algorithm-to-integrate-genome-scale-metabolic-and-transcriptional-regulatory-networks-with-incorporation-of-expression-data
#7
Ehsan Motamedian, Maryam Mohammadi, Seyed Abbas Shojaosadati, Mona Heydari
MOTIVATION: Integration of different biological networks and data-types has been a major challenge in systems biology. The present study introduces the transcriptional regulated flux balance analysis (TRFBA) algorithm that integrates transcriptional regulatory and metabolic models using a set of expression data for various perturbations. RESULTS: TRFBA considers the expression levels of genes as a new continuous variable and introduces two new linear constraints...
January 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28053665/improved-growth-rate-in-clostridium-thermocellum-hydrogenase-mutant-via-perturbed-sulfur-metabolism
#8
Ranjita Biswas, Charlotte M Wilson, Richard J Giannone, Dawn M Klingeman, Thomas Rydzak, Manesh B Shah, Robert L Hettich, Steven D Brown, Adam M Guss
BACKGROUND: Metabolic engineering is a commonly used approach to develop organisms for an industrial function, but engineering aimed at improving one phenotype can negatively impact other phenotypes. This lack of robustness can prove problematic. Cellulolytic bacterium Clostridium thermocellum is able to rapidly ferment cellulose to ethanol and other products. Recently, genes involved in H2 production, including the hydrogenase maturase hydG and NiFe hydrogenase ech, were deleted from the chromosome of C...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28042698/geochemically-distinct-carbon-isotope-distributions-in-allochromatium-vinosum-dsm-180-t-grown-photoautotrophically-and-photoheterotrophically
#9
T Tang, W Mohr, S R Sattin, D R Rogers, P R Girguis, A Pearson
Anoxygenic, photosynthetic bacteria are common at redox boundaries. They are of interest in microbial ecology and geosciences through their role in linking the carbon, sulfur, and iron cycles, yet much remains unknown about how their flexible carbon metabolism-permitting either autotrophic or heterotrophic growth-is recorded in the bulk sedimentary and lipid biomarker records. Here, we investigated patterns of carbon isotope fractionation in a model photosynthetic sulfur-oxidizing bacterium, Allochromatium vinosum DSM180(T) ...
January 1, 2017: Geobiology
https://www.readbyqxmd.com/read/28031032/metabolic-model-of-central-carbon-and-energy-metabolisms-of-growing-arabidopsis-thaliana-in-relation-to-sucrose-translocation
#10
Maksim Zakhartsev, Irina Medvedeva, Yury Orlov, Ilya Akberdin, Olga Krebs, Waltraud X Schulze
BACKGROUND: Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of these metabolic and underlying regulatory processes allow a detailed understanding of carbon distribution within the plant and the formation of associated phenotypic traits. Sucrose translocation from 'source' tissues (e.g. mesophyll) to 'sink' tissues (e.g. root) is tightly bound to the proton gradient across the membranes. The plant sucrose transporters are grouped into efflux exporters (SWEET family) and proton-symport importers (SUC, STP families)...
December 28, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28025701/flux-control-based-design-of-furfural-resistance-strains-of-saccharomyces-cerevisiae-for-lignocellulosic-biorefinery
#11
Pornkamol Unrean
We have previously developed a dynamic flux balance analysis of Saccharomyces cerevisiae for elucidation of genome-wide flux response to furfural perturbation (Unrean and Franzen, Biotechnol J 10(8):1248-1258, 2015). Herein, the dynamic flux distributions were analyzed by flux control analysis to identify target overexpressed genes for improved yeast robustness against furfural. The flux control coefficient (FCC) identified overexpressing isocitrate dehydrogenase (IDH1), a rate-controlling flux for ethanol fermentation, and dicarboxylate carrier (DIC1), a limiting flux for cell growth, as keys of furfural-resistance phenotype...
December 26, 2016: Bioprocess and Biosystems Engineering
https://www.readbyqxmd.com/read/28012908/flux-balance-analysis-of-photoautotrophic-metabolism-uncovering-new-biological-details-of-subsystems-involved-in-cyanobacterial-photosynthesis
#12
Xiao Qian, Min Kyung Kim, G Kenchappa Kumaraswamy, Ananya Agarwal, Desmond S Lun, G Charles Dismukes
We have constructed and experimentally tested a comprehensive genome-scale model of photoautotrophic growth, denoted iSyp821, for the cyanobacterium Synechococcus sp. PCC 7002. iSyp821 incorporates a variable biomass objective function (vBOF), in which stoichiometries of the major biomass components vary according to light intensity. The vBOF was constrained to fit the measured cellular carbohydrate/protein content under different light intensities. iSyp821 provides rigorous agreement with experimentally measured cell growth rates and inorganic carbon uptake rates as a function of light intensity...
December 21, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28007998/pathological-glutamatergic-neurotransmission-in-gilles-de-la-tourette-syndrome
#13
Ahmad Seif Kanaan, Sarah Gerasch, Isabel García-García, Leonie Lampe, André Pampel, Alfred Anwander, Jamie Near, Harald E Möller, Kirsten Müller-Vahl
Gilles de la Tourette syndrome is a hereditary, neuropsychiatric movement disorder with reported abnormalities in the neurotransmission of dopamine and γ-aminobutyric acid (GABA). Spatially focalized alterations in excitatory, inhibitory and modulatory neurochemical ratios within specific functional subdivisions of the basal ganglia, may lead to the expression of diverse motor and non-motor features as manifested in Gilles de la Tourette syndrome. Current treatment strategies are often unsatisfactory thus provoking the need for further elucidation of the underlying pathophysiology...
January 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/27998937/improving-flux-predictions-by-integrating-data-from-multiple-strains
#14
Matthew R Long, Jennifer L Reed
MOTIVATION: Incorporating experimental data into constraint-based models can improve the quality and accuracy of their metabolic flux predictions. Unfortunately, routinely and easily measured experimental data such as growth rates, extracellular fluxes, transcriptomics, and even proteomics are not always sufficient to significantly improve metabolic flux predictions. RESULTS: We developed a new method (called REPPS) for incorporating experimental measurements of growth rates and extracellular fluxes from a set of perturbed reference strains (RSs) and a parental strain (PS) to substantially improve the predicted flux distribution of the parental strain...
December 20, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27996047/a-genome-scale-escherichia-coli-kinetic-metabolic-model-k-ecoli457-satisfying-flux-data-for-multiple-mutant-strains
#15
Ali Khodayari, Costas D Maranas
Kinetic models of metabolism at a genome scale that faithfully recapitulate the effect of multiple genetic interventions would be transformative in our ability to reliably design novel overproducing microbial strains. Here, we introduce k-ecoli457, a genome-scale kinetic model of Escherichia coli metabolism that satisfies fluxomic data for wild-type and 25 mutant strains under different substrates and growth conditions. The k-ecoli457 model contains 457 model reactions, 337 metabolites and 295 substrate-level regulatory interactions...
December 20, 2016: Nature Communications
https://www.readbyqxmd.com/read/27992644/a-genome-scale-modeling-approach-to-quantify-biofilm-component-growth-of-salmonella-typhimurium
#16
Nicholas Ribaudo, Xianhua Li, Brett Davis, Thomas K Wood, Zuyi Jacky Huang
Salmonella typhimurium (S. typhimurium) is an extremely dangerous foodborne bacterium that infects both animal and human subjects, causing fatal diseases around the world. Salmonella's robust virulence, antibiotic-resistant nature, and capacity to survive under harsh conditions are largely due to its ability to form resilient biofilms. Multiple genome-scale metabolic models have been developed to study the complex and diverse nature of this organism's metabolism; however, none of these models fully integrated the reactions and mechanisms required to study the influence of biofilm formation...
January 2017: Journal of Food Science
https://www.readbyqxmd.com/read/27973728/nitrogen-removal-in-myriophyllum-aquaticum-wetland-microcosms-for-swine-wastewater-treatment-15-n-labelled-nitrogen-mass-balance-analysis
#17
Shunan Zhang, Feng Liu, Runlin Xiao, Yang He, Jinshui Wu
BACKGROUND: Ecological treatments are effective for treating agricultural wastewater. In this study, wetland microcosms vegetated with Myriophyllum aquaticum were designed for nitrogen (N) removal from two strengths of swine wastewater, and (15) N-labelled ammonium (NH4(+) -N) was added to evaluate the dominant NH4(+) -N removal pathway. RESULTS: The results showed that 98.8% of NH4(+) -N and 88.3% of TN (TN: 248.6 mg L(-1) ) were removed from low-strength swine wastewater (SW1) after an incubation of 21 days, with corresponding values for high-strength swine wastewater (SW2) being 99...
January 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/27939520/tapping-into-salmonella-typhimurium-lt2-genome-in-a-quest-to-explore-its-therapeutic-arsenal-a-metabolic-network-modeling-approach
#18
Kusum Mehla, Jayashree Ramana
S. typhimurium, the classical broad-host-range serovar is a widely distributed cause of food-borne illness. Escalating antibiotic resistance and potential of conjugal transmission to other pathogens attributable to its broad spectrum host specificities have aided S. typhimurium to emerge as a global health threat. To keep pace with ever evolving bacterial defenses, there is dire need to restock the antibiotic pipeline. Genome scale metabolic reconstructions present immense possibilities to decipher physiological properties of an organism using constraint-based methods The systems-level approaches of genome scale metabolic networks interrogation open up new avenues of drug target identification against deadly infectious diseases...
December 7, 2016: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/27939353/three-dimensional-diastolic-blood-flow-in-the-left-ventricle
#19
Seyed Saeid Khalafvand, Eddie Yin-Kwee Ng, Liang Zhong, Tin-Kan Hung
Three-dimensional blood flow in a human left ventricle is studied via a computational analysis with magnetic resonance imaging of the cardiac motion. Formation, growth and decay of vortices during the myocardial dilation are analyzed with flow patterns on various diametric planes. They are dominated by momentum transfer during flow acceleration and deceleration through the mitral orifice. The posterior and anterior vortices form an asymmetric annular vortex at the mitral orifice, providing a smooth transition for the rapid inflow to the ventricle...
January 4, 2017: Journal of Biomechanics
https://www.readbyqxmd.com/read/27911769/reductive-carboxylation-is-a-major-metabolic-pathway-in-the-retinal-pigment-epithelium
#20
Jianhai Du, Aya Yanagida, Kaitlen Knight, Abbi L Engel, Anh Huan Vo, Connor Jankowski, Martin Sadilek, Van Thi Bao Tran, Megan A Manson, Aravind Ramakrishnan, James B Hurley, Jennifer R Chao
The retinal pigment epithelium (RPE) is a monolayer of pigmented cells that requires an active metabolism to maintain outer retinal homeostasis and compensate for oxidative stress. Using (13)C metabolic flux analysis in human RPE cells, we found that RPE has an exceptionally high capacity for reductive carboxylation, a metabolic pathway that has recently garnered significant interest because of its role in cancer cell survival. The capacity for reductive carboxylation in RPE exceeds that of all other cells tested, including retina, neural tissue, glial cells, and a cancer cell line...
December 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
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