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Flux balance analysis

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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
#1
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/29308892/fate-of-cd-in-agricultural-soils-a-stable-isotope-approach-to-anthropogenic-impact-soil-formation-and-soil-plant-cycling
#2
Martin Imseng, Matthias Wiggenhauser, Armin Keller, Michael Müller, Mark Rehkämper, Katy Murphy, Katharina Kreissig, Emmanuel Frossard, Wolfgang Wilcke, Moritz Bigalke
The application of mineral phosphate fertilizers leads to an unintended Cd input into agricultural systems, which might affect soil fertility and quality of crops. The Cd fluxes at three arable sites in Switzerland were determined by a detailed analysis of all inputs (atmospheric deposition, mineral P fertilizers, manure and weathering) and outputs (seepage water, wheat and barley harvest) during one hydrological year. The most important inputs were mineral P fertilizers (0.49 to 0.57 g Cd ha-1 yr-1) and manure (0...
January 8, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29308297/force-fields-of-charged-particles-in-micro-nanofluidic-preconcentration-systems
#3
Lingyan Gong, Wei Ouyang, Zirui Li, Jongyoon Han
Electrokinetic concentration devices based on the ion concentration polarization (ICP) phenomenon have drawn much attention due to their simple setup, high enrichment factor, and easy integration with many subsequent processes, such as separation, reaction, and extraction etc. Despite significant progress in the experimental research, fundamental understanding and detailed modeling of the preconcentration systems is still lacking. The mechanism of the electrokinetic trapping of charged particles is currently limited to the force balance analysis between the electric force and fluid drag force in an over-simplified one-dimensional (1D) model, which misses many signatures of the actual system...
December 2017: AIP Advances
https://www.readbyqxmd.com/read/29302705/multi-scale-modeling-of-apc-and-formula-see-text-catenin-regulation-in-the-human-colonic-crypt
#4
Brooks Emerick, Gilberto Schleiniger, Bruce M Boman
Stem cell renewal and differentiation in the human colonic crypt are linked to the [Formula: see text]-catenin pathway. The spatial balance of Wnt factors in proliferative cells within the crypt maintain an appropriate level of cellular reproduction needed for normal crypt homeostasis. Mutational events at the gene level are responsible for deregulating the balance of Wnt factors along the crypt, causing an overpopulation of proliferative cells, a loss of structure of the crypt domain, and the initiation of colorectal carcinomas...
January 4, 2018: Journal of Mathematical Biology
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
#5
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/29235714/formate-hydrogenlyase-and-formate-secretion-ameliorate-h2-inhibition-in-the-hyperthermophilic-archaeon-thermococcus-paralvinellae
#6
Begüm D Topçuoğlu, Cem Meydan, Roberto Orellana, James F Holden
Some hyperthermophilic heterotrophs in the genus Thermococcus produce H2 in the absence of S° and have up to seven hydrogenases, but their combined physiological roles are unclear. Here, we show which hydrogenases in Thermococcus paralvinellae are affected by added H2 during growth without S°. Growth rates and steady-state cell concentrations decreased while formate production rates increased when T. paralvinallae was grown in a chemostat with 65 µM of added H2(aq) . Differential gene expression analysis using RNA-Seq showed consistent expression of six hydrogenase operons with and without added H2 ...
December 13, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29229856/global-biogeochemical-cycle-of-vanadium
#7
William H Schlesinger, Emily M Klein, Avner Vengosh
Synthesizing published data, we provide a quantitative summary of the global biogeochemical cycle of vanadium (V), including both human-derived and natural fluxes. Through mining of V ores (130 × 109 g V/y) and extraction and combustion of fossil fuels (600 × 109 g V/y), humans are the predominant force in the geochemical cycle of V at Earth's surface. Human emissions of V to the atmosphere are now likely to exceed background emissions by as much as a factor of 1.7, and, presumably, we have altered the deposition of V from the atmosphere by a similar amount...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29222762/dynamic-flux-balance-analysis-using-dfbalab
#8
Jose Alberto Gomez, Paul I Barton
Bioprocesses are of critical importance in several industries such as the food and pharmaceutical industries. Despite their importance and widespread application, bioprocess models remain rather simplistic and based on unstructured models. These simple models have limitations, making it very difficult to model complex bioprocesses. With dynamic flux balance analysis (DFBA) more comprehensive bioprocess models can be obtained. DFBA simulations are difficult to carry out because they result in dynamic systems with linear programs embedded...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222760/computational-prediction-of-synthetic-lethals-in-genome-scale-metabolic-models-using-fast-sl
#9
Karthik Raman, Aditya Pratapa, Omkar Mohite, Shankar Balachandran
In this chapter, we describe Fast-SL, an in silico approach to predict synthetic lethals in genome-scale metabolic models. Synthetic lethals are sets of genes or reactions where only the simultaneous removal of all genes or reactions in the set abolishes growth of an organism. In silico approaches to predict synthetic lethals are based on Flux Balance Analysis (FBA), a popular constraint-based analysis method based on linear programming. FBA has been shown to accurately predict the viability of various genome-scale metabolic models...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222748/analyzing-and-designing-cell-factories-with-optflux
#10
Paulo Vilaça, Paulo Maia, Hugo Giesteira, Isabel Rocha, Miguel Rocha
OptFlux was launched in 2010 as the first open-source and user-friendly platform containing all the major methods for performing metabolic engineering tasks in silico. Main features included the possibility of performing microbial strain simulations with widely used methods such as Flux Balance Analysis and strain design using Evolutionary Algorithms. Since then, OptFlux suffered a major re-factoring to improve its efficiency and reliability, while many features were added in the form of novel plug-ins, such as the BioVisualizer and the over/under expression plug-ins...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29212053/contaminant-back-diffusion-from-low-permeability-layers-as-affected-by-groundwater-velocity-a-laboratory-investigation-by-box-model-and-image-analysis
#11
Fabio Tatti, Marco Petrangeli Papini, Giuseppe Sappa, Massimo Raboni, Firoozeh Arjmand, Paolo Viotti
Low-permeability lenses represent potential sources of long-term release when filled from contaminant solute through direct contact with dissolved plumes. The redistribution of contaminant from low to high permeability aquifer zones (Back-Diffusion) was studied. Redistribution causes a long plume tail, commonly regarded as one of the main obstacles to effective groundwater remediation. Laboratory tests were performed to reproduce the redistribution process and to investigate the effect of pumping water on the remediation time of these contaminated low-permeability lenses...
December 3, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29197779/model-predictive-control-coupled-with-economic-and-environmental-constraints-for-optimum-algal-production
#12
Ankita Juneja, Ganti S Murthy
Algae production process is a key cost center in production of biofuels/bioproducts from microalgae. Decline in the growth of algae in outdoor ponds during non-optimal conditions is one of the hurdles for achieving consistently high algal production rates. An optimal controller can be used to overcome this limitation and provide reliable growth in outdoor conditions. A model predictive controller (MPC) was developed to optimize the algal growth, predicted by flux balance analysis, under natural disturbances, embedding within the cost function, the economic and environmental constraints associated with the process...
November 16, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29193738/cooperative-role-of-the-glp-1-receptor-and-%C3%AE-3-adrenergic-mediated-signaling-on-fat-mass-reduction-through-the-down-regulation-of-pka-akt-ampk-signaling-in-the-adipose-tissue-and-muscle-of-rats
#13
Juan Decara, Patricia Rivera, Sergio Arrabal, Antonio Vargas, Antonia Serrano, Francisco Javier Pavón, Carlos Dieguez, Rubén Nogueiras, Fernando Rodríguez de Fonseca, Juan Suárez
AIM: To explore the cooperation of GLP-1 receptor and β3-adrenergic receptor-mediated signaling in the control of fat mass/feeding behavior by studying the effects of a combined therapy composed of the GLP-1R agonist liraglutide and the β3-AR agonist CL316243. METHODS: The study included the analysis of key mechanisms regulating lipid/cholesterol metabolism, and thermogenesis in brown (BAT) and epididymal white (eWAT) adipose tissues, abdominal muscle and liver of male rats...
November 28, 2017: Acta Physiologica
https://www.readbyqxmd.com/read/29178875/metabolic-engineering-of-synechococcus-elongatus-pcc-7942-for-improvement-of-1-3-propanediol-and-glycerol-production-based-on-in-silico-simulation-of-metabolic-flux-distribution
#14
Yasutaka Hirokawa, Shingo Matsuo, Hiroyuki Hamada, Fumio Matsuda, Taizo Hanai
BACKGROUND: Production directly from carbon dioxide by engineered cyanobacteria is one of the promising technologies for sustainable future. Previously, we have successfully achieved 1,3-propanediol (1,3-PDO) production using Synechococcus elongatus PCC 7942 with a synthetic metabolic pathway. The strain into which the synthetic metabolic pathway was introduced produced 3.48 mM (0.265 g/L) 1,3-PDO and 14.3 mM (1.32 g/L) glycerol during 20 days of incubation. In this study, the productivities of 1,3-PDO were improved by gene disruption selected by screening with in silico simulation...
November 25, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29170969/two-scale-13-c-metabolic-flux-analysis-for-metabolic-engineering
#15
David Ando, Hector Garcia Martin
Accelerating the Design-Build-Test-Learn (DBTL) cycle in synthetic biology is critical to achieving rapid and facile bioengineering of organisms for the production of, e.g., biofuels and other chemicals. The Learn phase involves using data obtained from the Test phase to inform the next Design phase. As part of the Learn phase, mathematical models of metabolic fluxes give a mechanistic level of comprehension to cellular metabolism, isolating the principle drivers of metabolic behavior from the peripheral ones, and directing future experimental designs and engineering methodologies...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29157227/metabolic-adaptation-of-two-in-silico-mutants-of-mycobacterium-tuberculosis-during-infection
#16
Víctor A López-Agudelo, Andres Baena, Howard Ramirez-Malule, Silvia Ochoa, Luis F Barrera, Rigoberto Ríos-Estepa
BACKGROUND: Up to date, Mycobacterium tuberculosis (Mtb) remains as the worst intracellular killer pathogen. To establish infection, inside the granuloma, Mtb reprograms its metabolism to support both growth and survival, keeping a balance between catabolism, anabolism and energy supply. Mtb knockouts with the faculty of being essential on a wide range of nutritional conditions are deemed as target candidates for tuberculosis (TB) treatment. Constraint-based genome-scale modeling is considered as a promising tool for evaluating genetic and nutritional perturbations on Mtb metabolic reprogramming...
November 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29151887/an-accurate-description-of-aspergillus-niger-organic-acid-batch-fermentation-through-dynamic-metabolic-modelling
#17
Daniel J Upton, Simon J McQueen-Mason, A Jamie Wood
Background: Aspergillus niger fermentation has provided the chief source of industrial citric acid for over 50 years. Traditional strain development of this organism was achieved through random mutagenesis, but advances in genomics have enabled the development of genome-scale metabolic modelling that can be used to make predictive improvements in fermentation performance. The parent citric acid-producing strain of A. niger, ATCC 1015, has been described previously by a genome-scale metabolic model that encapsulates its response to ambient pH...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29136931/understanding-regulation-in-substrate-dependent-modulation-of-growth-and-production-of-alcohols-in-clostridium-sporogenes-ncim-2918-through-metabolic-network-reconstruction-and-flux-balance-analysis
#18
Mehak Kaushal, K Venkata Narayana Chary, Saumya Ahlawat, Basavaraj Palabhanvi, Gargi Goswami, Debasish Das
Flux Balance Analysis was performed for Clostridium sporogenes NCIM 2918 grown on sole glucose and glycerol or glucose-glycerol combinations at varied concentrations. During acidogenesis, glucose and glucose-glycerol combinations favored improved growth and butyric acid production. Glycerol fermentation was however marked by reduced growth and predominant ethanol synthesis. Further, with increase of glycerol fraction in glucose-glycerol blend, flux towards ethanol synthesis linearly increased with simultaneous decrease in butanol flux...
November 1, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29081549/tundra-water-budget-and-implications-of-precipitation-underestimation
#19
Anna K Liljedahl, Larry D Hinzman, Douglas L Kane, Walter C Oechel, Craig E Tweedie, Donatella Zona
Difficulties in obtaining accurate precipitation measurements have limited meaningful hydrologic assessment for over a century due to performance challenges of conventional snowfall and rainfall gauges in windy environments. Here, we compare snowfall observations and bias adjusted snowfall to end-of-winter snow accumulation measurements on the ground for 16 years (1999-2014) and assess the implication of precipitation underestimation on the water balance for a low-gradient tundra wetland near Utqiagvik (formerly Barrow), Alaska (2007-2009)...
August 2017: Water Resources Research
https://www.readbyqxmd.com/read/29055584/nitrosomonas-europaea-adaptation-to-anoxic-oxic-cycling-insights-from-transcription-analysis-proteomics-and-metabolic-network-modeling
#20
Ran Yu, Octavio Perez-Garcia, Huijie Lu, Kartik Chandran
In suboxic or anoxic environments, nitrous oxide (N2O) can be produced by ammonia oxidizing bacteria (AOB) as a potent greenhouse gas. Although N2O producing inventory and pathways have been well-characterized using archetypal AOB, there is little known about their adaptive responses to oxic-anoxic cycling, which is a prevalent condition in soil, sediment, and wastewater treatment bioreactors. In this study, cellular responses of Nitrosomonas europaea 19718 to sustained anoxic-oxic cycling in a chemostat bioreactor were evaluated at transcriptomic, proteomic, and fluxomic levels...
February 15, 2018: Science of the Total Environment
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