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Flux balance analysis

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https://www.readbyqxmd.com/read/28453682/distributedfba-jl-high-level-high-performance-flux-balance-analysis-in-julia
#1
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...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28444480/model-based-biotechnological-potential-analysis-of-kluyveromyces-marxianus-central-metabolism
#2
A Pentjuss, E Stalidzans, J Liepins, A Kokina, J Martynova, P Zikmanis, I Mozga, R Scherbaka, H Hartman, M G Poolman, D A Fell, A Vigants
The non-conventional yeast Kluyveromyces marxianus is an emerging industrial producer for many biotechnological processes. Here, we show the application of a biomass-linked stoichiometric model of central metabolism that is experimentally validated, and mass and charge balanced for assessing the carbon conversion efficiency of wild type and modified K. marxianus. Pairs of substrates (lactose, glucose, inulin, xylose) and products (ethanol, acetate, lactate, glycerol, ethyl acetate, succinate, glutamate, phenylethanol and phenylalanine) are examined by various modelling and optimisation methods...
April 25, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28444347/fluxomics-links-cellular-functional-analyses-to-whole-plant-phenotyping
#3
Christophe Salon, Jean-Christophe Avice, Sophie Colombié, Martine Dieuaide-Noubhani, Karine Gallardo, Christian Jeudy, Alain Ourry, Marion Prudent, Anne-Sophie Voisin, Dominique Rolin
Fluxes through metabolic pathways reflect the integration of genetic and metabolic regulations. While it is attractive to measure all the mRNAs (transcriptome), all the proteins (proteome), and a large number of the metabolites (metabolome) in a given cellular system, linking and integrating this information remains difficult. Measurement of metabolome-wide fluxes (termed the fluxome) provides an integrated functional output of the cell machinery and a better tool to link functional analyses to plant phenotyping...
April 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28432256/global-sensitivity-analysis-of-onguard-models-identifies-key-hubs-for-transport-interaction-in-stomatal-dynamics
#4
Silvere Rm Vialet-Chabrand, Adrian Hills, Yizhou Wang, Howard Griffiths, Virgilio Lew, Tracy Lawson, Mike R Blatt, Simon Rogers
The physical requirement for charge to balance across biological membranes means that transmembrane transport of each ionic species is inter-related, and manipulating solute flux through any one transporter will affect other transporters at the same membrane, often with unforeseen consequences. The OnGuard systems modelling platform has helped to resolve the mechanics of stomatal movements, uncovering previously unexpected behaviors of stomata. To date, however, the manual approach to exploring model parameter space has captured little formal information about the emergent connections between parameters that define the most interesting properties of the system as a whole...
April 21, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28429787/heat-temperature-and-clausius-inequality-in-a-model-for-active-brownian-particles
#5
Umberto Marini Bettolo Marconi, Andrea Puglisi, Claudio Maggi
Methods of stochastic thermodynamics and hydrodynamics are applied to a recently introduced model of active particles. The model consists of an overdamped particle subject to Gaussian coloured noise. Inspired by stochastic thermodynamics, we derive from the system's Fokker-Planck equation the average exchanges of heat and work with the active bath and the associated entropy production. We show that a Clausius inequality holds, with the local (non-uniform) temperature of the active bath replacing the uniform temperature usually encountered in equilibrium systems...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28420402/sser-species-specific-essential-reactions-database
#6
Abraham A Labena, Yuan-Nong Ye, Chuan Dong, Fa-Z Zhang, Feng-Biao Guo
BACKGROUND: Essential reactions are vital components of cellular networks. They are the foundations of synthetic biology and are potential candidate targets for antimetabolic drug design. Especially if a single reaction is catalyzed by multiple enzymes, then inhibiting the reaction would be a better option than targeting the enzymes or the corresponding enzyme-encoding gene. The existing databases such as BRENDA, BiGG, KEGG, Bio-models, Biosilico, and many others offer useful and comprehensive information on biochemical reactions...
April 19, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28419089/erroneous-energy-generating-cycles-in-published-genome-scale-metabolic-networks-identification-and-removal
#7
Claus Jonathan Fritzemeier, Daniel Hartleb, Balázs Szappanos, Balázs Papp, Martin J Lercher
Energy metabolism is central to cellular biology. Thus, genome-scale models of heterotrophic unicellular species must account appropriately for the utilization of external nutrients to synthesize energy metabolites such as ATP. However, metabolic models designed for flux-balance analysis (FBA) may contain thermodynamically impossible energy-generating cycles: without nutrient consumption, these models are still capable of charging energy metabolites (such as ADP→ATP or NADP+→NADPH). Here, we show that energy-generating cycles occur in over 85% of metabolic models without extensive manual curation, such as those contained in the ModelSEED and MetaNetX databases; in contrast, such cycles are rare in the manually curated models of the BiGG database...
April 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28413845/carbon-uptake-by-mature-amazon-forests-has-mitigated-amazon-nations-carbon-emissions
#8
Oliver L Phillips, Roel J W Brienen
BACKGROUND: Several independent lines of evidence suggest that Amazon forests have provided a significant carbon sink service, and also that the Amazon carbon sink in intact, mature forests may now be threatened as a result of different processes. There has however been no work done to quantify non-land-use-change forest carbon fluxes on a national basis within Amazonia, or to place these national fluxes and their possible changes in the context of the major anthropogenic carbon fluxes in the region...
December 2017: Carbon Balance and Management
https://www.readbyqxmd.com/read/28412970/membrane-potential-independent-transport-of-nh3-in-the-absence-of-ammonium-permeases-in-saccharomyces-cerevisiae
#9
Hugo F Cueto-Rojas, Nicholas Milne, Ward van Helmond, Mervin M Pieterse, Antonius J A van Maris, Jean-Marc Daran, S Aljoscha Wahl
BACKGROUND: Microbial production of nitrogen containing compounds requires a high uptake flux and assimilation of the N-source (commonly ammonium), which is generally coupled with ATP consumption and negatively influences the product yield. In the industrial workhorse Saccharomyces cerevisiae, ammonium (NH4(+)) uptake is facilitated by ammonium permeases (Mep1, Mep2 and Mep3), which transport the NH4(+) ion, resulting in ATP expenditure to maintain the intracellular charge balance and pH by proton export using the plasma membrane-bound H(+)-ATPase...
April 17, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28411229/a-comprehensive-analysis-of-myocardial-substrate-preference-emphasizes-the-need-for-a-synchronized-fluxomic-metabolomic-research-design
#10
Mukundan Ragavan, Alexander Kirpich, Xiaorong Fu, Shawn C Burgess, Lauren M McIntyre, Matthew E Merritt
The heart oxidizes fatty acids, carbohydrates and ketone bodies inside the citric acid cycle (CAC) to generate the reducing equivalents needed for ATP production. Competition between these substrates makes it difficult to estimate the extent of pyruvate oxidation. Previously, hyperpolarized pyruvate detected propionate mediated activation of carbohydrate oxidation, even in the presence of acetate. In this report, the optimal concentration of propionate for activation of glucose oxidation is measured in mouse hearts perfused in Langendorff mode...
April 14, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28410570/natural-selection-drove-metabolic-specialization-of-the-chromatophore-in-paulinella-chromatophora
#11
Cecilio Valadez-Cano, Roberto Olivares-Hernández, Osbaldo Resendis-Antonio, Alexander DeLuna, Luis Delaye
BACKGROUND: Genome degradation of host-restricted mutualistic endosymbionts has been attributed to inactivating mutations and genetic drift while genes coding for host-relevant functions are conserved by purifying selection. Unlike their free-living relatives, the metabolism of mutualistic endosymbionts and endosymbiont-originated organelles is specialized in the production of metabolites which are released to the host. This specialization suggests that natural selection crafted these metabolic adaptations...
April 14, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28406903/from-elementary-flux-modes-to-elementary-flux-vectors-metabolic-pathway-analysis-with-arbitrary-linear-flux-constraints
#12
REVIEW
Steffen Klamt, Georg Regensburger, Matthias P Gerstl, Christian Jungreuthmayer, Stefan Schuster, Radhakrishnan Mahadevan, Jürgen Zanghellini, Stefan Müller
Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic pathways and have become an established tool for constraint-based modeling and metabolic network analysis. EFMs are characteristic (support-minimal) vectors of the flux cone that contains all feasible steady-state flux vectors of a given metabolic network. EFMs account for (homogeneous) linear constraints arising from reaction irreversibilities and the assumption of steady state; however, other (inhomogeneous) linear constraints, such as minimal and maximal reaction rates frequently used by other constraint-based techniques (such as flux balance analysis [FBA]), cannot be directly integrated...
April 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28401266/dynamic-flux-balance-analysis-with-nonlinear-objective-function
#13
Xiao Zhao, Stephan Noack, Wolfgang Wiechert, Eric von Lieres
Dynamic flux balance analysis (DFBA) extends flux balance analysis and enables the combined simulation of both intracellular and extracellular environments of microbial cultivation processes. A DFBA model contains two coupled parts, a dynamic part at the upper level (extracellular environment) and an optimization part at the lower level (intracellular environment). Both parts are coupled through substrate uptake and product secretion rates. This work proposes a Karush-Kuhn-Tucker condition based solution approach for DFBA models, which have a nonlinear objective function in the lower-level part...
April 11, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28400330/metabolomics-driven-approach-to-solving-a-coa-imbalance-for-improved-1-butanol-production-in-escherichia-coli
#14
Toshiyuki Ohtake, Sammy Pontrelli, Walter A Laviña, James C Liao, Sastia P Putri, Eiichiro Fukusaki
High titer 1-butanol production in Escherichia coli has previously been achieved by overexpression of a modified clostridial 1-butanol production pathway and subsequent deletion of native fermentation pathways. This strategy couples growth with production as 1-butanol pathway offers the only available terminal electron acceptors required for growth in anaerobic conditions. With further inclusion of other well-established metabolic engineering principles, a titer of 15g/L has been obtained. In achieving this titer, many currently existing strategies have been exhausted, and 1-butanol toxicity level has been surpassed...
April 8, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28396843/clostridioides-difficile-630%C3%AE-erm-in-silico-and-in-vivo-quantitative-growth-and-extensive-polysaccharide-secretion
#15
Henning Dannheim, Sabine E Will, Dietmar Schomburg, Meina Neumann-Schaal
Antibiotic-associated infections with Clostridioides difficile are a severe and often lethal risk for hospitalized patients, and can also affect populations without these classical risk factors. For a rational design of therapeutical concepts, a better knowledge of the metabolism of the pathogen is crucial. Metabolic modeling can provide a simulation of quantitative growth and usage of metabolic pathways, leading to a deeper understanding of the organism. Here, we present an elaborate genome-scale metabolic model of C...
April 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28387366/elucidating-dynamic-metabolic-physiology-through-network-integration-of-quantitative-time-course-metabolomics
#16
Aarash Bordbar, James T Yurkovich, Giuseppe Paglia, Ottar Rolfsson, Ólafur E Sigurjónsson, Bernhard O Palsson
The increasing availability of metabolomics data necessitates novel methods for deeper data analysis and interpretation. We present a flux balance analysis method that allows for the computation of dynamic intracellular metabolic changes at the cellular scale through integration of time-course absolute quantitative metabolomics. This approach, termed "unsteady-state flux balance analysis" (uFBA), is applied to four cellular systems: three dynamic and one steady-state as a negative control. uFBA and FBA predictions are contrasted, and uFBA is found to be more accurate in predicting dynamic metabolic flux states for red blood cells, platelets, and Saccharomyces cerevisiae...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28382977/an-analytic-approximation-of-the-feasible-space-of-metabolic-networks
#17
Alfredo Braunstein, Anna Paola Muntoni, Andrea Pagnani
Assuming a steady-state condition within a cell, metabolic fluxes satisfy an underdetermined linear system of stoichiometric equations. Characterizing the space of fluxes that satisfy such equations along with given bounds (and possibly additional relevant constraints) is considered of utmost importance for the understanding of cellular metabolism. Extreme values for each individual flux can be computed with linear programming (as flux balance analysis), and their marginal distributions can be approximately computed with Monte Carlo sampling...
April 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/28381205/the-jbei-quantitative-metabolic-modeling-library-jqmm-a-python-library-for-modeling-microbial-metabolism
#18
Garrett W Birkel, Amit Ghosh, Vinay S Kumar, Daniel Weaver, David Ando, Tyler W H Backman, Adam P Arkin, Jay D Keasling, Héctor García Martín
BACKGROUND: Modeling of microbial metabolism is a topic of growing importance in biotechnology. Mathematical modeling helps provide a mechanistic understanding for the studied process, separating the main drivers from the circumstantial ones, bounding the outcomes of experiments and guiding engineering approaches. Among different modeling schemes, the quantification of intracellular metabolic fluxes (i.e. the rate of each reaction in cellular metabolism) is of particular interest for metabolic engineering because it describes how carbon and energy flow throughout the cell...
April 5, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28379541/resistance-to-apoptosis-and-autophagy-leads-to-enhanced-survival-in-sertoli-cells
#19
Ferial Aslani, Tim Sebastian, Miguel Keidel, Suada Fröhlich, Hans-Peter Elsässer, Hans-Christian Schuppe, Jörg Klug, Poornima Mahavadi, Monika Fijak, Martin Bergmann, Andreas Meinhardt, Sudhanshu Bhushan
STUDY QUESTION: What is the underlying mechanism of Sertoli cell (SC) resistance to cell death? SUMMARY ANSWER: High expression of pro-survival B cell lymphoma-2 (BCL2) proteins and inhibition of apoptosis and autophagy prolongs SC survival upon exposure to stress stimuli. WHAT IS KNOWN ALREADY: In human and in experimental models of orchitis, tolerogenic SC survive stress conditions, while germ cells undergo massive apoptosis. In general, non-dividing highly differentiated cells tend to resist stress conditions for a longer time by favoring activation of pro-survival mechanisms and inhibition of cell death pathways...
April 3, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/28365149/absolute-quantification-of-protein-and-mrna-abundances-demonstrate-variability-in-gene-specific-translation-efficiency-in-yeast
#20
Petri-Jaan Lahtvee, Benjamín J Sánchez, Agata Smialowska, Sergo Kasvandik, Ibrahim E Elsemman, Francesco Gatto, Jens Nielsen
Protein synthesis is the most energy-consuming process in a proliferating cell, and understanding what controls protein abundances represents a key question in biology and biotechnology. We quantified absolute abundances of 5,354 mRNAs and 2,198 proteins in Saccharomyces cerevisiae under ten environmental conditions and protein turnover for 1,384 proteins under a reference condition. The overall correlation between mRNA and protein abundances across all conditions was low (0.46), but for differentially expressed proteins (n = 202), the median mRNA-protein correlation was 0...
March 27, 2017: Cell Systems
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