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Flux balance analysis

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https://www.readbyqxmd.com/read/28928003/learning-from-quantitative-data-to-understand-central-carbon-metabolism
#1
REVIEW
Fumio Matsuda, Yoshihiro Toya, Hiroshi Shimizu
Quantitative analysis of metabolism has been used to identify driver reactions occurring during cancer development and bottleneck reactions in the metabolic engineering of microorganisms. In this review, we compare the advantages and disadvantages of various metabolic analysis methods. We emphasize that metabolic flux analysis based on material balance is a critical method for quantitative investigations into cell metabolism. The absolute determination of metabolite concentration appears to be essential for evaluating the thermodynamic state of metabolism...
September 16, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28921534/exploring-cellular-behaviour-under-transient-gene-expression-and-its-impact-on-mab-productivity-and-fc-glycosylation
#2
Si Nga Sou, Ken Lee, Kalpana Nayyar, Karen M Polizzi, Christopher Sellick, Cleo Kontoravdi
Transient gene expression (TGE) is a methodology employed in bioprocessing for the fast provision of recombinant protein material. Mild hypothermia is often introduced to overcome the low yield typically achieved with TGE and improve specific protein productivity. It is therefore of interest to examine the impact of mild hypothermic temperatures on both the yield and quality of transiently-expressed proteins and the relationship to changes in cellular processes and metabolism. In this study, we focus on the ability of a Chinese hamster ovary cell line to galactosylate a recombinant monoclonal antibody (mAb) product...
September 16, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28886026/population-fba-predicts-metabolic-phenotypes-in-yeast
#3
Piyush Labhsetwar, Marcelo C R Melo, John A Cole, Zaida Luthey-Schulten
Using protein counts sampled from single cell proteomics distributions to constrain fluxes through a genome-scale model of metabolism, Population flux balance analysis (Population FBA) successfully described metabolic heterogeneity in a population of independent Escherichia coli cells growing in a defined medium. We extend the methodology to account for correlations in protein expression arising from the co-regulation of genes and apply it to study the growth of independent Saccharomyces cerevisiae cells in two different growth media...
September 8, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28881985/popfba-tackling-intratumour-heterogeneity-with-flux-balance-analysis
#4
Chiara Damiani, Marzia Di Filippo, Dario Pescini, Davide Maspero, Riccardo Colombo, Giancarlo Mauri
Motivation: Intratumour heterogeneity poses many challenges to the treatment of cancer. Unfortunately, the transcriptional and metabolic information retrieved by currently available computational and experimental techniques portrays the average behaviour of intermixed and heterogeneous cell subpopulations within a given tumour. Emerging single-cell genomic analyses are nonetheless unable to characterize the interactions among cancer subpopulations. In this study, we propose popFBA , an extension to classic Flux Balance Analysis, to explore how metabolic heterogeneity and cooperation phenomena affect the overall growth of cancer cell populations...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28873499/bioremediation-in-fractured-rock-2-mobilization-of-chloroethene-compounds-from-the-rock-matrix
#5
Allen M Shapiro, Claire R Tiedeman, Thomas E Imbrigiotta, Daniel J Goode, Paul A Hsieh, Pierre J Lacombe, Mary F DeFlaun, Scott R Drew, Gary P Curtis
A mass balance is formulated to evaluate the mobilization of chlorinated ethene compounds (CE) from the rock matrix of a fractured mudstone aquifer under pre- and postbioremediation conditions. The analysis relies on a sparse number of monitoring locations and is constrained by a detailed description of the groundwater flow regime. Groundwater flow modeling developed under the site characterization identified groundwater fluxes to formulate the CE mass balance in the rock volume exposed to the injected remediation amendments...
September 5, 2017: Ground Water
https://www.readbyqxmd.com/read/28868622/proliferation-inhibition-of-cisplatin-resistant-ovarian-cancer-cells-using-drugs-screened-by-integrating-a-metabolic-model-and-transcriptomic-data
#6
E Motamedian, E Taheri, F Bagheri
OBJECTIVES: If screening to find effective drugs is possible, the inhibition of proliferation using existing drugs can be a practical strategy to control the drug resistance of cancer. Development of a system-oriented strategy to find effective drugs was the main aim of this research. MATERIALS AND METHODS: An algorithm (transcriptional regulated flux balance analysis [TRFBA]) integrating a generic human metabolic model with transcriptomic data was used to identify genes affecting the growth of drug-resistant cancer cells...
September 3, 2017: Cell Proliferation
https://www.readbyqxmd.com/read/28859811/engineering-escherichia-coli-for-poly-3-hydroxybutyrate-production-guided-by-genome-scale-metabolic-network-analysis
#7
Yangyang Zheng, Qianqian Yuan, Xiaoyan Yang, Hongwu Ma
Poly-(3-hydroxybutyrate) (P3HB) is a promising biodegradable plastic synthesized from acetyl-CoA. One important factor affecting the P3HB production cost is the P3HB yield. Through flux balance analysis of an extended genome-scale metabolic network of E. coli, we found that the introduction of non-oxidative glycolysis pathway (NOG), a previously reported pathway enabling complete carbon conservation, can increase the theoretical carbon yield from 67% to 89%, equivalent to the theoretical mass yield from 0.48g P3HB/g glucose to 0...
November 2017: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/28852058/key-glycolytic-branch-influences-mesocarp-oil-content-in-oil-palm
#8
Nurliyana Ruzlan, Yoke Sum Jaime Low, Wilonita Win, Noor Azizah Musa, Ai-Ling Ong, Fook-Tim Chew, David Appleton, Hirzun Mohd Yusof, Harikrishna Kulaveerasingam
The fructose-1,6-bisphosphate aldolase catalyzed glycolysis branch that forms dihydroxyacetone phosphate and glyceraldehyde-3-phosphate was identified as a key driver of increased oil synthesis in oil palm and was validated in Saccharomyces cerevisiae. Reduction in triose phosphate isomerase (TPI) activity in a yeast knockdown mutant resulted in 19% increase in lipid content, while yeast strains overexpressing oil palm fructose-1,6-bisphosphate aldolase (EgFBA) and glycerol-3-phosphate dehydrogenase (EgG3PDH) showed increased lipid content by 16% and 21%, respectively...
August 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28845460/integration-of-metabolomics-and-transcriptomics-reveals-a-complex-diet-of-mycobacterium-tuberculosis-during-early-macrophage-infection
#9
Michael Zimmermann, Maria Kogadeeva, Martin Gengenbacher, Gayle McEwen, Hans-Joachim Mollenkopf, Nicola Zamboni, Stefan Hugo Ernst Kaufmann, Uwe Sauer
Nutrient acquisition from the host environment is crucial for the survival of intracellular pathogens, but conceptual and technical challenges limit our knowledge of pathogen diets. To overcome some of these technical roadblocks, we exploited an experimentally accessible model for early infection of human macrophages by Mycobacterium tuberculosis, the etiological agent of tuberculosis, to study host-pathogen interactions with a multi-omics approach. We collected metabolomics and complete transcriptome RNA sequencing (dual RNA-seq) data of the infected macrophages, integrated them in a genome-wide reaction pair network, and identified metabolic subnetworks in host cells and M...
July 2017: MSystems
https://www.readbyqxmd.com/read/28820904/parametric-studies-of-metabolic-cooperativity-in-escherichia-coli-colonies-strain-and-geometric-confinement-effects
#10
Joseph R Peterson, John A Cole, Zaida Luthey-Schulten
Characterizing the complex spatial and temporal interactions among cells in a biological system (i.e. bacterial colony, microbiome, tissue, etc.) remains a challenge. Metabolic cooperativity in these systems can arise due to the subtle interplay between microenvironmental conditions and the cells' regulatory machinery, often involving cascades of intra- and extracellular signalling molecules. In the simplest of cases, as demonstrated in a recent study of the model organism Escherichia coli, metabolic cross-feeding can arise in monoclonal colonies of bacteria driven merely by spatial heterogeneity in the availability of growth substrates; namely, acetate, glucose and oxygen...
2017: PloS One
https://www.readbyqxmd.com/read/28819232/ensemble-of-thermostatically-controlled-loads-statistical-physics-approach
#11
Michael Chertkov, Vladimir Chernyak
Thermostatically controlled loads, e.g., air conditioners and heaters, are by far the most widespread consumers of electricity. Normally the devices are calibrated to provide the so-called bang-bang control - changing from on to off, and vice versa, depending on temperature. We considered aggregation of a large group of similar devices into a statistical ensemble, where the devices operate following the same dynamics, subject to stochastic perturbations and randomized, Poisson on/off switching policy. Using theoretical and computational tools of statistical physics, we analyzed how the ensemble relaxes to a stationary distribution and established a relationship between the relaxation and the statistics of the probability flux associated with devices' cycling in the mixed (discrete, switch on/off, and continuous temperature) phase space...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28798305/revealing-extracellular-electron-transfer-mediated-parasitism-energetic-considerations
#12
Roman Moscoviz, Clément Flayac, Elie Desmond-Le Quéméner, Eric Trably, Nicolas Bernet
Extracellular electron transfer (EET) is a mechanism that allows energetic coupling between two microorganisms or between a microorganism and an electrode surface. EET is either supported by direct physical contacts or mediated by electron shuttles. So far, studies dealing with interspecies EET (so-called IET) have mainly focused on possible syntrophic interactions between microorganisms favoured by this mechanism. In this article, the case of fermentative bacteria receiving extracellular electrons while fermenting a substrate is considered...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28767679/compartmentalized-metabolic-network-reconstruction-of-microbial-communities-to-determine-the-effect-of-agricultural-intervention-on-soils
#13
María Camila Alvarez-Silva, Astrid Catalina Álvarez-Yela, Fabio Gómez-Cano, María Mercedes Zambrano, Johana Husserl, Giovanna Danies, Silvia Restrepo, Andrés Fernando González-Barrios
Soil microbial communities are responsible for a wide range of ecological processes and have an important economic impact in agriculture. Determining the metabolic processes performed by microbial communities is crucial for understanding and managing ecosystem properties. Metagenomic approaches allow the elucidation of the main metabolic processes that determine the performance of microbial communities under different environmental conditions and perturbations. Here we present the first compartmentalized metabolic reconstruction at a metagenomics scale of a microbial ecosystem...
2017: PloS One
https://www.readbyqxmd.com/read/28759793/modelling-recovery-of-ammonium-from-urine-by-electro-concentration-in-a-3-chamber-cell
#14
Emma Thompson Brewster, Johannes Jermakka, Stefano Freguia, Damien J Batstone
Electro-concentration enables treatment and nutrient recovery from source-separated urine, and is a potential technology for on-site treatment using a 3 compartment configuration that has anode, cathode and middle concentrate compartments. There is a particular focus on driving concentration towards the precipitation threshold in the concentrate compartment to generate solid ammonium salts, including ammonium bicarbonate. To evaluate controlling mechanisms and the feasibility of achieving high concentrations, a dynamic mechanistic model was developed and validated using experiments with synthetic urine...
July 20, 2017: Water Research
https://www.readbyqxmd.com/read/28754360/glycosylation-flux-analysis-reveals-dynamic-changes-of-intracellular-glycosylation-flux-distribution-in-chinese-hamster-ovary-fed-batch-cultures
#15
Sandro Hutter, Thomas K Villiger, David Brühlmann, Matthieu Stettler, Hervé Broly, Miroslav Soos, Rudiyanto Gunawan
N-linked glycosylation of proteins has both functional and structural significance. Importantly, the glycan structure of a therapeutic protein influences its efficacy, pharmacokinetics, pharmacodynamics and immunogenicity. In this work, we developed glycosylation flux analysis (GFA) for predicting intracellular production and consumption rates (fluxes) of glycoforms, and applied this analysis to CHO fed-batch immunoglobulin G (IgG) production using two different media compositions, with and without additional manganese feeding...
July 25, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28745515/hydrology-of-the-north-klondike-river-carbon-export-water-balance-and-inter-annual-climate-influences-within-a-sub-alpine-permafrost-catchment
#16
Anthony Lapp, Ian Clark, Andrew Macumber, Tim Patterson
Arctic and sub-arctic watersheds are undergoing significant changes due to recent climate warming and degrading permafrost, engendering enhanced monitoring of arctic rivers. Smaller catchments provide understanding of discharge, solute flux and groundwater recharge at the process level that contributes to an understanding of how larger arctic watersheds are responding to climate change. The North Klondike River, located in west central Yukon, is a sub-alpine permafrost catchment, which maintains an active hydrological monitoring station with a record of >40 years...
July 26, 2017: Isotopes in Environmental and Health Studies
https://www.readbyqxmd.com/read/28742257/dynamic-carboniferous-tropical-forests-new-views-of-plant-function-and-potential-for-physiological-forcing-of-climate
#17
REVIEW
Jonathan P Wilson, Isabel P Montañez, Joseph D White, William A DiMichele, Jennifer C McElwain, Christopher J Poulsen, Michael T Hren
Contents 1333 I. 1334 II. 1335 III. 1339 IV. 1344 V. 1347 VI. 1347 1348 1348 References 1348 SUMMARY: The Carboniferous, the time of Earth's penultimate icehouse and widespread coal formation, was dominated by extinct lineages of early-diverging vascular plants. Studies of nearest living relatives of key Carboniferous plants suggest that their physiologies and growth forms differed substantially from most types of modern vegetation, particularly forests. It remains a matter of debate precisely how differently and to what degree these long-extinct plants influenced the environment...
September 2017: New Phytologist
https://www.readbyqxmd.com/read/28727429/elliptic-cylinder-airborne-sampling-and-geostatistical-mass-balance-approach-for-quantifying-local-greenhouse-gas-emissions
#18
Jovan M Tadić, Anna M Michalak, Laura Iraci, Velibor Ilić, Sébastien C Biraud, Daniel R Feldman, Thaopaul Bui, Matthew S Johnson, Max Loewenstein, Seongeun Jeong, Marc L Fischer, Emma L Yates, Ju-Mee Ryoo
In this study, we explore observational, experimental, methodological, and practical aspects of the flux quantification of greenhouse gases from local point sources by using in situ airborne observations, and suggest a series of conceptual changes to improve flux estimates. We address the major sources of uncertainty reported in previous studies by modifying (1) the shape of the typical flight path, (2) the modeling of covariance and anisotropy, and (3) the type of interpolation tools used. We show that a cylindrical flight profile offers considerable advantages compared to traditional profiles collected as curtains, although this new approach brings with it the need for a more comprehensive subsequent analysis...
August 8, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28725384/emissions-of-methane-from-northern-peatlands-a-review-of-management-impacts-and-implications-for-future-management-options
#19
REVIEW
Mohamed Abdalla, Astley Hastings, Jaak Truu, Mikk Espenberg, Ülo Mander, Pete Smith
Northern peatlands constitute a significant source of atmospheric methane (CH 4). However, management of undisturbed peatlands, as well as the restoration of disturbed peatlands, will alter the exchange of CH 4 with the atmosphere. The aim of this systematic review and meta-analysis was to collate and analyze published studies to improve our understanding of the factors that control CH 4 emissions and the impacts of management on the gas flux from northern (latitude 40° to 70°N) peatlands. The analysis includes a total of 87 studies reporting measurements of CH 4 emissions taken at 186 sites covering different countries, peatland types, and management systems...
October 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28724354/novel-plasmodium-falciparum-metabolic-network-reconstruction-identifies-shifts-associated-with-clinical-antimalarial-resistance
#20
Maureen A Carey, Jason A Papin, Jennifer L Guler
BACKGROUND: Malaria remains a major public health burden and resistance has emerged to every antimalarial on the market, including the frontline drug, artemisinin. Our limited understanding of Plasmodium biology hinders the elucidation of resistance mechanisms. In this regard, systems biology approaches can facilitate the integration of existing experimental knowledge and further understanding of these mechanisms. RESULTS: Here, we developed a novel genome-scale metabolic network reconstruction, iPfal17, of the asexual blood-stage P...
July 19, 2017: BMC Genomics
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