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Flux balance analysis

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https://www.readbyqxmd.com/read/27910397/enhanced-magnetic-field-probe-array-for-improved-excluded-flux-calculations-on-the-c-2u-advanced-beam-driven-field-reversed-configuration-plasma-experiment
#1
T Roche, M C Thompson, R Mendoza, I Allfrey, E Garate, J Romero, J Douglass
External flux conserving coils were installed onto the exterior of the C-2U [M. W. Binderbauer et al., Phys. Plasmas 22, 056110 (2015)] confinement vessel to increase the flux confinement time of the system. The 0.5 in. stainless steel vessel wall has a skin time of ∼5 ms. The addition of the external copper coils effectively increases this time to ∼7 ms. This led to better-confined/longer-lived field-reversed configuration (FRC) plasmas. The fringing fields generated by the external coils have the side effect of rendering external field measurements invalid...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27909940/enhancement-of-rapamycin-production-by-metabolic-engineering-in-streptomyces-hygroscopicus-based-on-genome-scale-metabolic-model
#2
Lanqing Dang, Jiao Liu, Cheng Wang, Huanhuan Liu, Jianping Wen
Rapamycin, as a macrocyclic polyketide with immunosuppressive, antifungal, and anti-tumor activity produced by Streptomyces hygroscopicus, is receiving considerable attention for its significant contribution in medical field. However, the production capacity of the wild strain is very low. Hereby, a computational guided engineering approach was proposed to improve the capability of rapamycin production. First, a genome-scale metabolic model of Streptomyces hygroscopicus ATCC 29253 was constructed based on its annotated genome and biochemical information...
December 1, 2016: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/27907077/transcriptome-and-multivariable-data-analysis-of-corynebacterium-glutamicum-under-different-dissolved-oxygen-conditions-in-bioreactors
#3
Yang Sun, Wenwen Guo, Fen Wang, Feng Peng, Yankun Yang, Xiaofeng Dai, Xiuxia Liu, Zhonghu Bai
Dissolved oxygen (DO) is an important factor in the fermentation process of Corynebacterium glutamicum, which is a widely used aerobic microbe in bio-industry. Herein, we described RNA-seq for C. glutamicum under different DO levels (50%, 30% and 0%) in 5 L bioreactors. Multivariate data analysis (MVDA) models were used to analyze the RNA-seq and metabolism data to investigate the global effect of DO on the transcriptional distinction of the substance and energy metabolism of C. glutamicum. The results showed that there were 39 and 236 differentially expressed genes (DEGs) under the 50% and 0% DO conditions, respectively, compared to the 30% DO condition...
2016: PloS One
https://www.readbyqxmd.com/read/27905442/quantifying-global-soil-carbon-losses-in-response-to-warming
#4
T W Crowther, K E O Todd-Brown, C W Rowe, W R Wieder, J C Carey, M B Machmuller, B L Snoek, S Fang, G Zhou, S D Allison, J M Blair, S D Bridgham, A J Burton, Y Carrillo, P B Reich, J S Clark, A T Classen, F A Dijkstra, B Elberling, B A Emmett, M Estiarte, S D Frey, J Guo, J Harte, L Jiang, B R Johnson, G Kröel-Dulay, K S Larsen, H Laudon, J M Lavallee, Y Luo, M Lupascu, L N Ma, S Marhan, A Michelsen, J Mohan, S Niu, E Pendall, J Peñuelas, L Pfeifer-Meister, C Poll, S Reinsch, L L Reynolds, I K Schmidt, S Sistla, N W Sokol, P H Templer, K K Treseder, J M Welker, M A Bradford
The majority of the Earth's terrestrial carbon is stored in the soil. If anthropogenic warming stimulates the loss of this carbon to the atmosphere, it could drive further planetary warming. Despite evidence that warming enhances carbon fluxes to and from the soil, the net global balance between these responses remains uncertain. Here we present a comprehensive analysis of warming-induced changes in soil carbon stocks by assembling data from 49 field experiments located across North America, Europe and Asia...
November 30, 2016: Nature
https://www.readbyqxmd.com/read/27881075/modelling-microbial-metabolic-rewiring-during-growth-in-a-complex-medium
#5
Marco Fondi, Emanuele Bosi, Luana Presta, Diletta Natoli, Renato Fani
BACKGROUND: In their natural environment, bacteria face a wide range of environmental conditions that change over time and that impose continuous rearrangements at all the cellular levels (e.g. gene expression, metabolism). When facing a nutritionally rich environment, for example, microbes first use the preferred compound(s) and only later start metabolizing the other one(s). A systemic re-organization of the overall microbial metabolic network in response to a variation in the composition/concentration of the surrounding nutrients has been suggested, although the range and the entity of such modifications in organisms other than a few model microbes has been scarcely described up to now...
November 24, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27867783/convective-and-large-scale-mass-flux-profiles-over-tropical-oceans-determined-from-synergistic-analysis-of-a-suite-of-satellite-observations
#6
Hirohiko Masunaga, Zhengzhao Johnny Luo
A new, satellite-based methodology is developed to evaluate convective mass flux and large-scale total mass flux. To derive the convective mass flux, candidate profiles of in-cloud vertical velocity are first constructed with a simple plume model under the constraint of ambient sounding and then narrowed down to the solution that matches satellite-derived cloud top buoyancy. Meanwhile, the large-scale total mass flux is provided separately from satellite soundings by a method developed previously. All satellite snapshots are sorted into a composite time series that delineates the evolution of a vigorous and organized convective system...
July 16, 2016: Journal of Geophysical Research. Atmospheres: JGR
https://www.readbyqxmd.com/read/27866253/characterization-of-clostridium-ljungdahlii-ota1-a-non-autotrophic-hyper-ethanol-producing-strain
#7
Jason M Whitham, Mark J Schulte, Benjamin G Bobay, Jose M Bruno-Barcena, Mari S Chinn, Michael C Flickinger, Joel J Pawlak, Amy M Grunden
A Clostridium ljungdahlii lab-isolated spontaneous-mutant strain, OTA1, has been shown to produce twice as much ethanol as the C. ljungdahlii ATCC 55383 strain when cultured in a mixotrophic medium containing fructose and syngas. Whole-genome sequencing identified four unique single nucleotide polymorphisms (SNPs) in the C. ljungdahlii OTA1 genome. Among these, two SNPs were found in the gene coding for AcsA and HemL, enzymes involved in acetyl-CoA formation from CO/CO2. Homology models of the respective mutated enzymes revealed alterations in the size and hydrogen bonding of the amino acids in their active sites...
November 19, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27854220/-get-the-balance-right-pathological-significance-of-autophagy-perturbation-in-neuromuscular-disorders
#8
Perrine Castets, Stephan Frank, Michael Sinnreich, Markus A Rüegg
Recent research has revealed that autophagy, a major catabolic process in cells, is dysregulated in several neuromuscular diseases and contributes to the muscle wasting caused by non-muscle disorders (e.g. cancer cachexia) or during aging (i.e. sarcopenia). From there, the idea arose to interfere with autophagy or manipulate its regulatory signalling to help restore muscle homeostasis and attenuate disease progression. The major difficulty for the development of therapeutic strategies is to restore a balanced autophagic flux, due to the dynamic nature of autophagy...
May 27, 2016: Journal of Neuromuscular Diseases
https://www.readbyqxmd.com/read/27845184/thermodynamics-based-metabolite-sensitivity-analysis-in-metabolic-networks
#9
A Kiparissides, V Hatzimanikatis
The increasing availability of large metabolomics datasets enhances the need for computational methodologies that can organize the data in a way that can lead to the inference of meaningful relationships. Knowledge of the metabolic state of a cell and how it responds to various stimuli and extracellular conditions can offer significant insight in the regulatory functions and how to manipulate them. Constraint based methods, such as Flux Balance Analysis (FBA) and Thermodynamics-based flux analysis (TFA), are commonly used to estimate the flow of metabolites through genome-wide metabolic networks, making it possible to identify the ranges of flux values that are consistent with the studied physiological and thermodynamic conditions...
November 11, 2016: Metabolic Engineering
https://www.readbyqxmd.com/read/27825806/genome-scale-metabolic-modeling-of-cancer
#10
Avlant Nilsson, Jens Nielsen
Cancer cells reprogram metabolism to support rapid proliferation and survival. Energy metabolism is particularly important for growth and genes encoding enzymes involved in energy metabolism are frequently altered in cancer cells. A genome scale metabolic model (GEM) is a mathematical formalization of metabolism which allows simulation and hypotheses testing of metabolic strategies. It has successfully been applied to many microorganisms and is now used to study cancer metabolism. Generic models of human metabolism have been reconstructed based on the existence of metabolic genes in the human genome...
November 4, 2016: Metabolic Engineering
https://www.readbyqxmd.com/read/27814681/wuflux-an-open-source-platform-for-13-c-metabolic-flux-analysis-of-bacterial-metabolism
#11
Lian He, Stephen G Wu, Muhan Zhang, Yixin Chen, Yinjie J Tang
BACKGROUND: Flux analyses, including flux balance analysis (FBA) and (13)C-metabolic flux analysis ((13)C-MFA), offer direct insights into cell metabolism, and have been widely used to characterize model and non-model microbial species. Nonetheless, constructing the (13)C-MFA model and performing flux calculation are demanding for new learners, because they require knowledge of metabolic networks, carbon transitions, and computer programming. To facilitate and standardize the (13)C-MFA modeling work, we set out to publish a user-friendly and programming-free platform (WUFlux) for flux calculations in MATLAB(®)...
November 4, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27801935/fluorescence-based-microplate-assays-for-in-vitro-assessment-of-mitochondrial-toxicity-metabolic-perturbation-and-cellular-oxygenation
#12
James Hynes, Conn Carey, Yvonne Will
High-throughput in vitro cell metabolism assays are of particular use for identification and delineation of mitochondrial toxicity and related metabolic perturbation. Here, a panel of fluorescence-based metabolism assays are described for measuring oxygen consumption, glycolytic flux, and cellular oxygenation. They can be applied to analysis of both isolated mitochondria and cell models. Sample data are presented illustrating how these protocols can be used to examine drug treatment, the interplay between oxidative and glycolytic ATP generation, and the impact of cell oxygenation on this balance...
November 1, 2016: Current Protocols in Toxicology
https://www.readbyqxmd.com/read/27790866/identification-of-active-constraints-in-dynamic-flux-balance-analysis
#13
Ali Nikdel, Hector Budman
This study deals with the calibration of dynamic metabolic flux models that are formulated as the maximization of an objective subject to constraints. Two approaches was applied for identifying the constraints from data. In the first approach a minimal active number of limiting constraints is found based on data that are assumed to be bounded within sets whereas, in the second approach, the limiting constraints are found based on parametric sensitivity analysis. The ability of these approaches to finding the active limiting constraints was verified through their application to two case studies: an in-silico (simulated) data based study describing the growth of E...
October 28, 2016: Biotechnology Progress
https://www.readbyqxmd.com/read/27783176/mutations-in-mure-the-essential-udp-n-acetylmuramoylalanyl-d-glutamate-2-6-diaminopimelate-ligase-of-corynebacterium-glutamicum-effect-on-l-lysine-formation-and-analysis-of-systemic-consequences
#14
Jennifer Hochheim, Angela Kranz, Karin Krumbach, Sascha Sokolowsky, Lothar Eggeling, Stephan Noack, Marco Bocola, Michael Bott, Jan Marienhagen
OBJECTIVES: To explore systemic effects of mutations in the UDP-N-acetylmuramoylalanyl-D-glutamate 2,6-diaminopimelate ligase (MurE) of Corynebacterium glutamicum, that leads to extracellular L-lysine accumulation by this bacterium. RESULTS: The analysis of a mutant cohort of C. glutamicum strains carrying all possible 20 amino acids at position 81 of MurE revealed unexpected effects on cellular properties. With increasing L-lysine accumulation the growth rate of the producing strain is reduced...
October 25, 2016: Biotechnology Letters
https://www.readbyqxmd.com/read/27769243/the-potential-for-non-adaptive-origins-of-evolutionary-innovations-in-central-carbon-metabolism
#15
Sayed-Rzgar Hosseini, Andreas Wagner
BACKGROUND: Biological systems are rife with examples of pre-adaptations or exaptations. They range from the molecular scale - lens crystallins, which originated from metabolic enzymes - to the macroscopic scale, such as feathers used in flying, which originally served thermal insulation or waterproofing. An important class of exaptations are novel and useful traits with non-adaptive origins. Whether such origins could be frequent cannot be answered with individual examples, because it is a question about a biological system's potential for exaptation...
October 21, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/27761435/-13-c-metabolic-flux-analysis-for-systematic-metabolic-engineering-of-s-cerevisiae-for-overproduction-of-fatty-acids
#16
Amit Ghosh, David Ando, Jennifer Gin, Weerawat Runguphan, Charles Denby, George Wang, Edward E K Baidoo, Chris Shymansky, Jay D Keasling, Héctor García Martín
Efficient redirection of microbial metabolism into the abundant production of desired bioproducts remains non-trivial. Here, we used flux-based modeling approaches to improve yields of fatty acids in Saccharomyces cerevisiae. We combined (13)C labeling data with comprehensive genome-scale models to shed light onto microbial metabolism and improve metabolic engineering efforts. We concentrated on studying the balance of acetyl-CoA, a precursor metabolite for the biosynthesis of fatty acids. A genome-wide acetyl-CoA balance study showed ATP citrate lyase from Yarrowia lipolytica as a robust source of cytoplasmic acetyl-CoA and malate synthase as a desirable target for downregulation in terms of acetyl-CoA consumption...
2016: Frontiers in Bioengineering and Biotechnology
https://www.readbyqxmd.com/read/27735856/understanding-plant-nitrogen-metabolism-through-metabolomics-and-computational-approaches
#17
Perrin H Beatty, Matthias S Klein, Jeffrey J Fischer, Ian A Lewis, Douglas G Muench, Allen G Good
A comprehensive understanding of plant metabolism could provide a direct mechanism for improving nitrogen use efficiency (NUE) in crops. One of the major barriers to achieving this outcome is our poor understanding of the complex metabolic networks, physiological factors, and signaling mechanisms that affect NUE in agricultural settings. However, an exciting collection of computational and experimental approaches has begun to elucidate whole-plant nitrogen usage and provides an avenue for connecting nitrogen-related phenotypes to genes...
October 10, 2016: Plants (Basel, Switzerland)
https://www.readbyqxmd.com/read/27725824/recent-developments-in-systems-biology-and-metabolic-engineering-of-plant-microbe-interactions
#18
Vishal Kumar, Mehak Baweja, Puneet K Singh, Pratyoosh Shukla
Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant-microbe interaction plays an important role to balance the ecosystem. The present review explores plant-microbe interactions using gene editing and system biology tools toward the comprehension in improvement of plant traits...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27720802/in-silico-metabolic-engineering-of-clostridium-ljungdahlii-for-synthesis-gas-fermentation
#19
Jin Chen, Michael A Henson
Synthesis gas fermentation is one of the most promising routes to convert synthesis gas (syngas; mainly comprised of H2 and CO) to renewable liquid fuels and chemicals by specialized bacteria. The most commonly studied syngas fermenting bacterium is Clostridium ljungdahlii, which produces acetate and ethanol as its primary metabolic byproducts. Engineering of C. ljungdahlii metabolism to overproduce ethanol, enhance the synthesize of the native byproducts lactate and 2,3-butanediol, and introduce the synthesis of non-native products such as butanol and butyrate has substantial commercial value...
October 5, 2016: Metabolic Engineering
https://www.readbyqxmd.com/read/27706078/strategies-for-extending-metabolomics-studies-with-stable-isotope-labelling-and-fluxomics
#20
Anubhav Srivastava, Greg M Kowalski, Damien L Callahan, Peter J Meikle, Darren J Creek
This is a perspective from the peer session on stable isotope labelling and fluxomics at the Australian & New Zealand Metabolomics Conference (ANZMET) held from 30 March to 1 April 2016 at La Trobe University, Melbourne, Australia. This report summarizes the key points raised in the peer session which focused on the advantages of using stable isotopes in modern metabolomics and the challenges in conducting flux analyses. The session highlighted the utility of stable isotope labelling in generating reference standards for metabolite identification, absolute quantification, and in the measurement of the dynamic activity of metabolic pathways...
October 1, 2016: Metabolites
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