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Flux balance analysis

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https://www.readbyqxmd.com/read/28798305/revealing-extracellular-electron-transfer-mediated-parasitism-energetic-considerations
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
Jovan M Tadić, Anna M Michalak, Laura T Iraci, Velibor Ilic, Sébastien C Biraud, Daniel R Feldman, Thaopaul V 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...
July 20, 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
#8
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
#9
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
https://www.readbyqxmd.com/read/28715411/a-curated-genome-scale-metabolic-model-of-bordetella-pertussis-metabolism
#10
Nick Fyson, Jerry King, Thomas Belcher, Andrew Preston, Caroline Colijn
The Gram-negative bacterium Bordetella pertussis is the causative agent of whooping cough, a serious respiratory infection causing hundreds of thousands of deaths annually worldwide. There are effective vaccines, but their production requires growing large quantities of B. pertussis. Unfortunately, B. pertussis has relatively slow growth in culture, with low biomass yields and variable growth characteristics. B. pertussis also requires a relatively expensive growth medium. We present a new, curated flux balance analysis-based model of B...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28710856/quantitative-intracellular-flux-modeling-and-applications-in-biotherapeutic-development-and-production-using-cho-cell-cultures
#11
REVIEW
Zhuangrong Huang, Dong-Yup Lee, Seongkyu Yoon
Chinese hamster ovary (CHO) cells have been widely used for producing many recombinant therapeutic proteins. Constraint-based modeling, such as flux balance analysis (FBA) and metabolic flux analysis (MFA), has been developing rapidly for the quantification of intracellular metabolic flux distribution at a systematic level. Such methods would produce detailed maps of flows through metabolic networks, which contribute significantly to better understanding of metabolism in cells. Although these approaches have been extensively established in microbial systems, their application to mammalian cells is sparse...
July 15, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28690597/close-to-the-edge-growth-restrained-by-the-nad-p-h-atp-formation-flux-ratio
#12
Ed W J van Niel, Basti Bergdahl, Bärbel Hahn-Hägerdal
Most fermentative microorganisms grow well-under anaerobic conditions managing a balanced redox and appropriate energy metabolism, but a few species do exist in which cells have to cope with inadequate energy recovery or capture and/or redox balancing. Two cases of these species, i.e., the metabolically engineered Saccharomyces cerevisiae enabling it to ferment xylose and Lactobacillus reuteri fermenting glucose via the phosphoketolase pathway, are here used to introduce a quantification parameter to capture what limits the growth rate of these microorganisms under anaerobic conditions...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28686599/flux-balance-analysis-predicts-warburg-like-effects-of-mouse-hepatocyte-deficient-in-mir-122a
#13
Hua-Qing Wu, Mei-Ling Cheng, Jin-Mei Lai, Hsuan-Hui Wu, Meng-Chun Chen, Wen-Huan Liu, Wu-Hsiung Wu, Peter Mu-Hsin Chang, Chi-Ying F Huang, Ann-Ping Tsou, Ming-Shi Shiao, Feng-Sheng Wang
The liver is a vital organ involving in various major metabolic functions in human body. MicroRNA-122 (miR-122) plays an important role in the regulation of liver metabolism, but its intrinsic physiological functions require further clarification. This study integrated the genome-scale metabolic model of hepatocytes and mouse experimental data with germline deletion of Mir122a (Mir122a-/-) to infer Warburg-like effects. Elevated expression of MiR-122a target genes in Mir122a-/-mice, especially those encoding for metabolic enzymes, was applied to analyze the flux distributions of the genome-scale metabolic model in normal and deficient states...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28680442/perspectives-and-challenges-in-microbial-communities-metabolic-modeling
#14
Emanuele Bosi, Giovanni Bacci, Alessio Mengoni, Marco Fondi
Bacteria have evolved to efficiently interact each other, forming complex entities known as microbial communities. These "super-organisms" play a central role in maintaining the health of their eukaryotic hosts and in the cycling of elements like carbon and nitrogen. However, despite their crucial importance, the mechanisms that influence the functioning of microbial communities and their relationship with environmental perturbations are obscure. The study of microbial communities was boosted by tremendous advances in sequencing technologies, and in particular by the possibility to determine genomic sequences of bacteria directly from environmental samples...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28670341/integrated-analysis-of-transcriptome-and-metabolites-reveals-an-essential-role-of-metabolic-flux-in-starch-accumulation-under-nitrogen-starvation-in-duckweed
#15
Changjiang Yu, Xiaowen Zhao, Guang Qi, Zetao Bai, Yu Wang, Shumin Wang, Yubin Ma, Qian Liu, Ruibo Hu, Gongke Zhou
BACKGROUND: Duckweed is considered a promising source of energy due to its high starch content and rapid growth rate. Starch accumulation in duckweed involves complex processes that depend on the balanced expression of genes controlled by various environmental and endogenous factors. Previous studies showed that nitrogen starvation induces a global stress response and results in the accumulation of starch in duckweed. However, relatively little is known about the mechanisms underlying the regulation of starch accumulation under conditions of nitrogen starvation...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28606738/engineering-high-level-production-of-fatty-alcohols-by-saccharomyces-cerevisiae-from-lignocellulosic-feedstocks
#16
Leo d'Espaux, Amit Ghosh, Weerawat Runguphan, Maren Wehrs, Feng Xu, Oliver Konzock, Ishaan Dev, Melissa Nhan, Jennifer Gin, Amanda Reider Apel, Christopher J Petzold, Seema Singh, Blake A Simmons, Aindrila Mukhopadhyay, Héctor García Martín, Jay D Keasling
Fatty alcohols in the C12-C18 range are used in personal care products, lubricants, and potentially biofuels. These compounds can be produced from the fatty acid pathway by a fatty acid reductase (FAR), yet yields from the preferred industrial host Saccharomyces cerevisiae remain under 2% of the theoretical maximum from glucose. Here we improved titer and yield of fatty alcohols using an approach involving quantitative analysis of protein levels and metabolic flux, engineering enzyme level and localization, pull-push-block engineering of carbon flux, and cofactor balancing...
July 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28606124/remodeling-adipose-tissue-through-in-silico-modulation-of-fat-storage-for-the-prevention-of-type-2-diabetes
#17
Thierry Chénard, Frédéric Guénard, Marie-Claude Vohl, André Carpentier, André Tchernof, Rafael J Najmanovich
BACKGROUND: Type 2 diabetes is one of the leading non-infectious diseases worldwide and closely relates to excess adipose tissue accumulation as seen in obesity. Specifically, hypertrophic expansion of adipose tissues is related to increased cardiometabolic risk leading to type 2 diabetes. Studying mechanisms underlying adipocyte hypertrophy could lead to the identification of potential targets for the treatment of these conditions. RESULTS: We present iTC1390adip, a highly curated metabolic network of the human adipocyte presenting various improvements over the previously published iAdipocytes1809...
June 12, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28600876/rerouting-of-carbon-flux-in-a-glycogen-mutant-of-cyanobacteria-assessed-via-isotopically-non-stationary-13-c-metabolic-flux-analysis
#18
John I Hendry, Charulata Prasannan, Fangfang Ma, K Benedikt Möllers, Damini Jaiswal, Madhuri Digmurti, Doug K Allen, Niels-Ulrik Frigaard, Santanu Dasgupta, Pramod P Wangikar
Cyanobacteria, which constitute a quantitatively dominant phylum, have attracted attention in biofuel applications due to favorable physiological characteristics, high photosynthetic efficiency and amenability to genetic manipulations. However, quantitative aspects of cyanobacterial metabolism have received limited attention. In the present study, we have performed isotopically non-stationary (13) C metabolic flux analysis (INST-(13) C-MFA) to analyze rerouting of carbon in a glycogen synthase deficient mutant strain (glgA-I glgA-II) of the model cyanobacterium Synechococcus sp...
June 10, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28573283/the-effect-of-global-transcriptional-regulators-on-the-anaerobic-fermentative-metabolism-of-escherichia-coli
#19
Manika Kargeti, K V Venkatesh
Global transcription factors are known to regulate the anaerobic growth of Escherichia coli on glucose. These transcription factors help the organism to sense oxygen and accordingly regulate the synthesis of mixed acid producing enzymes. Five global transcription factors, namely ArcA, Fnr, IhfA-B, Crp and Fis, are known to play an important role in the growth phenotype of the organism in the transition from anaerobic to aerobic conditions. The effect of deletion of most of these global transcription factors on the growth phenotype has not been characterized under strict anaerobic fermentation conditions...
June 27, 2017: Molecular BioSystems
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
#20
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
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