keyword
MENU ▼
Read by QxMD icon Read
search

Flux balance analysis

keyword
https://www.readbyqxmd.com/read/28297949/criticality-and-turbulence-in-a-resistive-magnetohydrodynamic-current-sheet
#1
Alexander J Klimas, Vadim M Uritsky
Scaling properties of a two-dimensional (2d) plasma physical current-sheet simulation model involving a full set of magnetohydrodynamic (MHD) equations with current-dependent resistivity are investigated. The current sheet supports a spatial magnetic field reversal that is forced through loading of magnetic flux containing plasma at boundaries of the simulation domain. A balance is reached between loading and annihilation of the magnetic flux through reconnection at the current sheet; the transport of magnetic flux from boundaries to current sheet is realized in the form of spatiotemporal avalanches exhibiting power-law statistics of lifetimes and sizes...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28295777/can-ldl-cholesterol-be-too-low-possible-risks-of-extremely-low-levels
#2
Anders G Olsson, Bo Angelin, Gerd Assmann, Christoph J Binder, Ingemar Björkhem, Angel Cedazo-Minguez, Jonathan Cohen, Arnold von Eckardstein, Eduardo Farinaro, Dirk Müller-Wieland, Klaus G Parhofer, Paolo Parini, Robert S Rosenson, Jakob Starup-Linde, Matti J Tikkanen, Laurent Yvan-Charvet
Following the continuous accumulation of evidence supporting the beneficial role of reducing low-density lipoprotein cholesterol (LDL-C) levels in the treatment and prevention of atherosclerotic cardiovascular disease and its complications, therapeutic possibilities now exist to lower LDL-C to very low levels, similar to or even lower than those seen in newborns and nonhuman species. In addition to the important task of evaluating potential side-effects of such treatments, the question arises whether extremely low LDL-C levels per se may provoke adverse effects in humans...
March 14, 2017: Journal of Internal Medicine
https://www.readbyqxmd.com/read/28294579/experimental-validation-of-in-silico-estimated-biomass-yields-of-pseudomonas-putida-kt2440
#3
Sarah Beate Hintermayer, Dirk Weuster-Botz
Pseudomonas putida is rapidly becoming a microbial cell platform for biotechnological applications. In order to understand genotype-phenotype relationships genome scale models represent helpful tools. However, the validation of in silico predictions of genome scale models is a task that is rarely performed. In this study the theoretical biomass yields of Pseudomonas putida KT2440 were estimated for 57 different carbon sources based on a genome scale stoichiometric model applying flux balance analysis. The batch growth of P...
March 14, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28289085/the-small-protein-sgrt-controls-transport-activity-of-the-glucose-specific-phosphotransferase-system
#4
Chelsea R Lloyd, Seongjin Park, Jingyi Fei, Carin K Vanderpool
The bacterial small RNA (sRNA) SgrS has been a fruitful model for discovery of novel RNA-based regulatory mechanisms and new facets of bacterial physiology and metabolism. SgrS is one of only a few characterized dual-function sRNAs. SgrS can control gene expression post-transcriptionally via sRNA-mRNA base pairing interactions. Its second function is coding for the small protein SgrT. Previous work demonstrated that both functions contribute to relief of growth inhibition caused by glucose-phosphate stress, a condition characterized by disrupted glycolytic flux and accumulation of sugar-phosphates...
March 13, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28264162/model-based-analysis-of-the-long-term-effects-of-fertilization-management-on-cropland-soil-acidification
#5
Mufan Zeng, Wim de Vries, Luc T C Bonten, Qichao Zhu, Tianxiang Hao, Xuejun Liu, Minggang Xu, Xiaojun Shi, Fusuo Zhang, Jianbo Shen
Agricultural soil acidification in China is known to be caused by the over-application of nitrogen (N) fertilizers, but the long-term impacts of different fertilization practices on intensive cropland soil acidification are largely unknown. Here, we further developed the soil acidification model VSD+ for intensive agricultural systems and validated it against observed data from three long-term fertilization experiments in China. The model simulated well the changes in soil pH and base saturation over the last 20 years...
March 16, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28263984/managing-uncertainty-in-metabolic-network-structure-and-improving-predictions-using-ensemblefba
#6
Matthew B Biggs, Jason A Papin
Genome-scale metabolic network reconstructions (GENREs) are repositories of knowledge about the metabolic processes that occur in an organism. GENREs have been used to discover and interpret metabolic functions, and to engineer novel network structures. A major barrier preventing more widespread use of GENREs, particularly to study non-model organisms, is the extensive time required to produce a high-quality GENRE. Many automated approaches have been developed which reduce this time requirement, but automatically-reconstructed draft GENREs still require curation before useful predictions can be made...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28258322/metabolic-engineering-of-synechocystis-sp-pcc-6803-for-enhanced-ethanol-production-based-on-flux-balance-analysis
#7
Katsunori Yoshikawa, Yoshihiro Toya, Hiroshi Shimizu
Synechocystis sp. PCC 6803 is an attractive host for bio-ethanol production due to its ability to directly convert atmospheric carbon dioxide into ethanol using photosystems. To enhance ethanol production in Synechocystis sp. PCC 6803, metabolic engineering was performed based on in silico simulations, using the genome-scale metabolic model. Comprehensive reaction knockout simulations by flux balance analysis predicted that the knockout of NAD(P)H dehydrogenase enhanced ethanol production under photoautotrophic conditions, where ammonium is the nitrogen source...
March 3, 2017: Bioprocess and Biosystems Engineering
https://www.readbyqxmd.com/read/28256222/multiple-ligand-unbinding-pathways-and-ligand-induced-destabilization-revealed-by-wexplore
#8
Alex Dickson, Samuel D Lotz
We report simulations of full ligand exit pathways for the trypsin-benzamidine system, generated using the sampling technique WExplore. WExplore is able to observe millisecond-scale unbinding events using many nanosecond-scale trajectories that are run without introducing biasing forces. The algorithm generates rare events by dividing the coordinate space into regions, on-the-fly, and balancing computational effort between regions through cloning and merging steps, as in the weighted ensemble method. The averaged exit flux yields a ligand exit rate of 180 μs, which is within an order of magnitude of the experimental value...
February 28, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28194224/carbon-uptake-by-mature-amazon-forests-has-mitigated-amazon-nations-carbon-emissions
#9
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/28187415/estimation-of-biomass-composition-from-genomic-and-transcriptomic-information
#10
Sophia Santos, Isabel Rocha
Given the great potential impact of the growing number of complete genome-scale metabolic network reconstructions of microorganisms, bioinformatics tools are needed to simplify and accelerate the course of knowledge in this field. One essential component of a genome-scale metabolic model is its biomass equation, whose maximization is one of the most common objective functions used in Flux Balance Analysis formulations. Some components of biomass, such as amino acids and nucleotides, can be estimated from genome information, providing reliable data without the need of performing lab experiments...
November 27, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187207/a-multi-objective-constraint-based-approach-for-modeling-genome-scale-microbial-ecosystems
#11
Marko Budinich, Jérémie Bourdon, Abdelhalim Larhlimi, Damien Eveillard
Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs) for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients...
2017: PloS One
https://www.readbyqxmd.com/read/28165133/iterative-optimization-of-xylose-catabolism-in-saccharomyces-cerevisiae-using-combinatorial-expression-tuning
#12
Luke N Latimer, John E Dueber
A common challenge in metabolic engineering is rapidly identifying rate-controlling enzymes in heterologous pathways for subsequent production improvement. We demonstrate a workflow to address this challenge and apply it to improving xylose utilization in Saccharomyces cerevisiae. For eight reactions required for conversion of xylose to ethanol, we screened enzymes for functional expression in S. cerevisiae, followed by a combinatorial expression analysis to achieve pathway flux balancing and identification of limiting enzymatic activities...
February 6, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28163785/efficient-estimation-of-the-maximum-metabolic-productivity-of-batch-systems
#13
Peter C St John, Michael F Crowley, Yannick J Bomble
BACKGROUND: Production of chemicals from engineered organisms in a batch culture involves an inherent trade-off between productivity, yield, and titer. Existing strategies for strain design typically focus on designing mutations that achieve the highest yield possible while maintaining growth viability. While these methods are computationally tractable, an optimum productivity could be achieved by a dynamic strategy in which the intracellular division of resources is permitted to change with time...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28149324/exploring-eukaryotic-formate-metabolisms-to-enhance-microbial-growth-and-lipid-accumulation
#14
Zhiguo Liu, Tolutola Oyetunde, Whitney D Hollinshead, Anna Hermanns, Yinjie J Tang, Wei Liao, Yan Liu
BACKGROUND: C1 substrates (such as formate and methanol) are promising feedstock for biochemical/biofuel production. Numerous studies have been focusing on engineering heterologous pathways to incorporate C1 substrates into biomass, while the engineered microbial hosts often demonstrate inferior fermentation performance due to substrate toxicity, metabolic burdens from engineered pathways, and poor enzyme activities. Alternatively, exploring native C1 pathways in non-model microbes could be a better solution to address these challenges...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28129406/diurnal-and-seasonal-variations-in-the-net-ecosystem-co2-exchange-of-a-pasture-in-the-three-river-source-region-of-the-qinghai-tibetan-plateau
#15
Bin Wang, Haiyan Jin, Qi Li, Dongdong Chen, Liang Zhao, Yanhong Tang, Tomomichi Kato, Song Gu
Carbon dioxide (CO2) exchange between the atmosphere and grassland ecosystems is very important for the global carbon balance. To assess the CO2 flux and its relationship to environmental factors, the eddy covariance method was used to evaluate the diurnal cycle and seasonal pattern of the net ecosystem CO2 exchange (NEE) of a cultivated pasture in the Three-River Source Region (TRSR) on the Qinghai-Tibetan Plateau from January 1 to December 31, 2008. The diurnal variations in the NEE and ecosystem respiration (Re) during the growing season exhibited single-peak patterns, the maximum and minimum CO2 uptake observed during the noon hours and night; and the maximum and minimum Re took place in the afternoon and early morning, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28125882/the-dynamic-steady-state-of-an-electrochemically-generated-nanobubble
#16
Yuwen Liu, Martin A Edwards, Sean R German, Qianjin Chen, Henry S White
This article describes the dynamic steady state of individual H2 nanobubbles generated by H(+) reduction at inlaid and recessed Pt nanodisk electrodes. Electrochemical measurements coupled with finite element simulations allow analysis of the nanobubble geometry at dynamic equilibrium. We demonstrate that a bubble is sustainable at Pt nanodisks due to the balance of nanobubble shrinkage due to H2 dissolution and growth due to H2 electrogeneration. Specifically, simulations are used to predict stable geometries of the H2/Pt/solution three-phase interface and the width of exposed Pt at the disk circumference required to sustain the nanobubble via steady-state H2 electrogeneration...
February 13, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28113867/metabolic-flux-analysis-in-isotope-labeling-experiments-using-the-adjoint-approach
#17
Stephane Mottelet, Gil Gaullier, Georges Sadaka
Comprehension of metabolic pathways is considerably enhanced by metabolic flux analysis (MFA-ILE) in isotope labeling experiments. The balance equations are given by hundreds of algebraic (stationary MFA) or ordinary differential equations (nonstationary MFA), and reducing the number of operations is therefore a crucial part of reducing the computation cost. The main bottleneck for deterministic algorithms is the computation of derivatives, particularly for nonstationary MFA. In this article we explain how the overall identification process may be speeded up by using the adjoint approach to compute the gradient of the residual sum of squares...
March 21, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28107392/upon-accounting-for-the-impact-of-isoenzyme-loss-gene-deletion-costs-anticorrelate-with-their-evolutionary-rates
#18
Christopher Jacobs, Luke Lambourne, Yu Xia, Daniel Segrè
System-level metabolic network models enable the computation of growth and metabolic phenotypes from an organism's genome. In particular, flux balance approaches have been used to estimate the contribution of individual metabolic genes to organismal fitness, offering the opportunity to test whether such contributions carry information about the evolutionary pressure on the corresponding genes. Previous failure to identify the expected negative correlation between such computed gene-loss cost and sequence-derived evolutionary rates in Saccharomyces cerevisiae has been ascribed to a real biological gap between a gene's fitness contribution to an organism "here and now" and the same gene's historical importance as evidenced by its accumulated mutations over millions of years of evolution...
2017: PloS One
https://www.readbyqxmd.com/read/28103880/the-use-of-genome-scale-metabolic-network-reconstruction-to-predict-fluxes-and-equilibrium-composition-of-n-fixing-versus-c-fixing-cells-in-a-diazotrophic-cyanobacterium-trichodesmium-erythraeum
#19
Joseph J Gardner, Nanette R Boyle
BACKGROUND: Computational, genome based predictions of organism phenotypes has enhanced the ability to investigate the biological phenomena that help organisms survive and respond to their environments. In this study, we have created the first genome-scale metabolic network reconstruction of the nitrogen fixing cyanobacterium T. erythraeum and used genome-scale modeling approaches to investigate carbon and nitrogen fluxes as well as growth and equilibrium population composition. RESULTS: We created a genome-scale reconstruction of T...
January 19, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28093405/distributedfba-jl-high-level-high-performance-flux-balance-analysis-in-julia
#20
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...
January 16, 2017: Bioinformatics
keyword
keyword
5238
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"