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Flux balance analysis

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https://www.readbyqxmd.com/read/29787798/comprehensive-analysis-of-a-metabolic-model-for-lipid-production-in-rhodosporidium-toruloides
#1
María Teresita Castañeda, Sebastián Nuñez, Fabricio Garelli, Claudio Voget, Hernán De Battista
The yeast Rhodosporidium toruloides has been extensively studied for its application in biolipid production. The knowledge of its metabolism capabilities and the application of constraint-based flux analysis methodology provide useful information for process prediction and optimization. The accuracy of the resulting predictions is highly dependent on metabolic models. A metabolic reconstruction for R. toruloides metabolism has been recently published. On the basis of this model, we developed a curated version that unblocks the central nitrogen metabolism and, in addition, completes charge and mass balances in some reactions neglected in the former model...
May 19, 2018: Journal of Biotechnology
https://www.readbyqxmd.com/read/29741374/ligand-effect-on-bonding-in-gold-iii-carbonyl-complexes
#2
Diego Sorbelli, Leonardo Belpassi, Francesco Tarantelli, Paola Belanzoni
We quantitatively assess the Dewar-Chatt-Duncanson (DCD) components of the Au(III)-CO bond and the charge density polarization at the CO, in a series of neutral, cationic, and dicationic bis- and monocyclometalated gold(III) complexes via charge-displacement (CD) analysis. A striking feature concerns the very small net electron charge flux from CO to the metal fragment which is unexpectedly stable toward both the charge of the complex and the oxidation state of gold (I, III). All systems exhibit a similar trend for the σ charge rearrangement in the region of the carbonyl bond, where, by contrast, the π back-donation trend variation is large, which is strictly correlated to the change in CO bond distance and the shift in CO stretching frequencies, in close analogy with the gold(I) carbonyl complexes...
May 9, 2018: Inorganic Chemistry
https://www.readbyqxmd.com/read/29736982/climatic-role-of-terrestrial-ecosystem-under-elevated-co-2-a-bottom-up-greenhouse-gases-budget
#3
REVIEW
Shuwei Liu, Cheng Ji, Cong Wang, Jie Chen, Yaguo Jin, Ziheng Zou, Shuqing Li, Shuli Niu, Jianwen Zou
The net balance of greenhouse gas (GHG) exchanges between terrestrial ecosystems and the atmosphere under elevated atmospheric carbon dioxide (CO2 ) remains poorly understood. Here, we synthesise 1655 measurements from 169 published studies to assess GHGs budget of terrestrial ecosystems under elevated CO2 . We show that elevated CO2 significantly stimulates plant C pool (NPP) by 20%, soil CO2 fluxes by 24%, and methane (CH4 ) fluxes by 34% from rice paddies and by 12% from natural wetlands, while it slightly decreases CH4 uptake of upland soils by 3...
May 7, 2018: Ecology Letters
https://www.readbyqxmd.com/read/29730670/haemodialysis-membranes
#4
REVIEW
Claudio Ronco, William R Clark
Haemodialysis is an extracorporeal process in which the blood is cleansed via removal of uraemic retention products by a semipermeable membrane. Traditionally, dialysis membranes have been broadly classified on the basis of their composition (cellulosic or noncellulosic) and water permeability (low flux or high flux). However, advances in materials technology and polymer chemistry have led to the development of membranes with specific characteristics and refined properties that mandate a reconsideration of traditional membrane classification systems...
May 5, 2018: Nature Reviews. Nephrology
https://www.readbyqxmd.com/read/29710420/partitioning-of-the-net-co-2-exchange-using-an-automated-chamber-system-reveals-plant-phenology-as-key-control-of-production-and-respiration-fluxes-in-a-boreal-peatland
#5
Järvi Järveoja, Mats B Nilsson, Michal Gažovič, Patrick M Crill, Matthias Peichl
The net ecosystem CO2 exchange (NEE) drives the carbon (C) sink-source strength of northern peatlands. Since NEE represents a balance between various production and respiration fluxes, accurate predictions of its response to global changes require an in depth understanding of these underlying processes. Currently, however, detailed information of the temporal dynamics as well as the separate biotic and abiotic controls of the NEE component fluxes is lacking in peatland ecosystems. In this study, we address this knowledge gap by using an automated chamber system established across natural and trenching-/vegetation removal plots to partition NEE into its production (i...
April 30, 2018: Global Change Biology
https://www.readbyqxmd.com/read/29704449/contribution-of-sea-ice-microbial-production-to-antarctic-benthic-communities-is-driven-by-sea-ice-dynamics-and-composition-of-functional-guilds
#6
Stephen R Wing, James J Leichter, Lucy C Wing, Dale Stokes, Sal J Genovese, Rebecca M McMullin, Olya A Shatova
Organic matter produced by the sea ice microbial community (SIMCo) is an important link between sea ice dynamics and secondary production in near-shore food webs of Antarctica. Sea ice conditions in McMurdo Sound were quantified from time series of MODIS satellite images for Sept. 1 through Feb. 28 of 2007-2015. A predictable sea ice persistence gradient along the length of the Sound and evidence for a distinct change in sea ice dynamics in 2011 were observed. We used stable isotope analysis (δ13 C and δ15 N) of SIMCo, suspended particulate organic matter (SPOM) and shallow water (10-20 m) macroinvertebrates to reveal patterns in trophic structure of, and incorporation of organic matter from SIMCo into, benthic communities at eight sites distributed along the sea ice persistence gradient...
April 28, 2018: Global Change Biology
https://www.readbyqxmd.com/read/29677222/understanding-the-impact-of-the-cofactor-swapping-of-isocitrate-dehydrogenase-over-the-growth-phenotype-of-escherichia-coli-on-acetate-by-using-constraint-based-modeling
#7
Erick Armingol, Eduardo Tobar, Ricardo Cabrera
It has been proposed that NADP+-specificity of isocitrate dehydrogenase (ICDH) evolved as an adaptation of microorganisms to grow on acetate as the sole source of carbon and energy. In Escherichia coli, changing the cofactor specificity of ICDH from NADP+ to NAD+ (cofactor swapping) decreases the growth rate on acetate. However, the metabolic basis of this phenotype has not been analyzed. In this work, we used constraint-based modeling to investigate the effect of the cofactor swapping of ICDH in terms of energy production, response of alternative sources of NADPH, and partitioning of fluxes between ICDH and isocitrate lyase (ICL) -a crucial bifurcation when the bacterium grows on acetate-...
2018: PloS One
https://www.readbyqxmd.com/read/29667627/propofol-inhibits-hela-cells-by-impairing-autophagic-flux-via-amp-activated-protein-kinase-ampk-activation-and-endoplasmic-reticulum-stress-regulated-by-calcium
#8
Xi Chen, Kai Li, Guoqing Zhao
BACKGROUND Propofol has antitumor effects against various cancers. However, the mechanism of action of propofol in HeLa human cervical cancer cells has not been elucidated. MATERIAL AND METHODS We treated HeLa human cervical cancer cells with different concentrations of propofol. Cell viability was evaluated with Cell Counting Kit-8 and apoptosis was analyzed by annexin V-fluorescein isothiocyanate and propidium iodide staining and flow cytometry. Autophagosome formation was evaluated based on microtubule-associated protein light chain (LC)3 conversion and light chain 3 puncta formation...
April 18, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29660877/probabilistic-modelling-and-uncertainty-analysis-of-flux-and-water-balance-changes-in-a-regional-aquifer-system-due-to-coal-seam-gas-development
#9
J Sreekanth, Tao Cui, Trevor Pickett, David Rassam, Mat Gilfedder, Damian Barrett
Large scale development of coal seam gas (CSG) is occurring in many sedimentary basins around the world including Australia, where commercial production of CSG has started in the Surat and Bowen basins. CSG development often involves extraction of large volumes of water that results in depressurising aquifers that overlie and/or underlie the coal seams thus perturbing their flow regimes. This can potentially impact regional aquifer systems that are used for many purposes such as irrigation, and stock and domestic water...
April 12, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29578608/optimization-of-bioprocess-productivity-based-on-metabolic-genetic-network-models-with-bilevel-dynamic-programming
#10
Banafsheh Jabarivelisdeh, Steffen Waldherr
One of the main goals of metabolic engineering is to obtain high levels of a microbial product through genetic modifications. To improve the productivity of such a process, the dynamic implementation of metabolic engineering strategies has been proven to be more beneficial compared to static genetic manipulations in which the gene expression is not controlled over time, by resolving the trade-off between growth and production. In this work, a bilevel optimization framework based on constraint-based models is applied to identify an optimal strategy for dynamic genetic and process level manipulations to increase productivity...
March 26, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29575448/comparison-of-closely-related-uncultivated-coxiella-tick-endosymbiont-population-genomes-reveals-clues-about-the-mechanisms-of-symbiosis
#11
Despina Tsementzi, Juan Castro Gordillo, Mustafa Mahagna, Yuval Gottlieb, Konstantinos T Konstantinidis
Understanding the symbiotic interaction between Coxiella-like endosymbionts (CLE) and their tick hosts is challenging due to lack of isolates and difficulties in tick functional assays. Here we sequenced the metagenome of a CLE population from wild Rhipicephalus sanguineus ticks (CRs) and compared it to the previously published genome of its close relative, CLE of R. turanicus (CRt). The tick hosts are closely related sympatric species, and their two endosymbiont genomes are highly similar with only minor differences in gene content...
March 24, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29552648/a-review-of-computational-tools-for-design-and-reconstruction-of-metabolic-pathways
#12
REVIEW
Lin Wang, Satyakam Dash, Chiam Yu Ng, Costas D Maranas
Metabolic pathways reflect an organism's chemical repertoire and hence their elucidation and design have been a primary goal in metabolic engineering. Various computational methods have been developed to design novel metabolic pathways while taking into account several prerequisites such as pathway stoichiometry, thermodynamics, host compatibility, and enzyme availability. The choice of the method is often determined by the nature of the metabolites of interest and preferred host organism, along with computational complexity and availability of software tools...
December 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29550298/understanding-start-up-problems-in-yeast-glycolysis
#13
Gosse B Overal, Bas Teusink, Frank J Bruggeman, Josephus Hulshof, Robert Planqué
Yeast glycolysis has been the focus of research for decades, yet a number of dynamical aspects of yeast glycolysis remain poorly understood at present. If nutrients are scarce, yeast will provide its catabolic and energetic needs with other pathways, but the enzymes catalysing upper glycolytic fluxes are still expressed. We conjecture that this overexpression facilitates the rapid transition to glycolysis in case of a sudden increase in nutrient concentration. However, if starved yeast is presented with abundant glucose, it can enter into an imbalanced state where glycolytic intermediates keep accumulating, leading to arrested growth and cell death...
May 2018: Mathematical Biosciences
https://www.readbyqxmd.com/read/29526552/on-structural-identifiability-analysis-of-the-cascaded-linear-dynamic-systems-in-isotopically-non-stationary-13c-labelling-experiments
#14
Weilu Lin, Zejian Wang, Mingzhi Huang, Yingping Zhuang, Siliang Zhang
The isotopically non-stationary 13C labelling experiments, as an emerging experimental technique, can estimate the intracellular fluxes of the cell culture under an isotopic transient period. However, to the best of our knowledge, the issue of the structural identifiability analysis of non-stationary isotope experiments is not well addressed in the literature. In this work, the local structural identifiability analysis for non-stationary cumomer balance equations is conducted based on the Taylor series approach...
March 8, 2018: Mathematical Biosciences
https://www.readbyqxmd.com/read/29523936/streptomyces-clavuligerus-shows-a-strong-association-between-tca-cycle-intermediate-accumulation-and-clavulanic-acid-biosynthesis
#15
Howard Ramirez-Malule, Stefan Junne, Mariano Nicolás Cruz-Bournazou, Peter Neubauer, Rigoberto Ríos-Estepa
Clavulanic acid (CA) is produced by Streptomyces clavuligerus (S. clavuligerus) as a secondary metabolite. Knowledge about the carbon flux distribution along the various routes that supply CA precursors would certainly provide insights about metabolic performance. In order to evaluate metabolic patterns and the possible accumulation of tricarboxylic acid (TCA) cycle intermediates during CA biosynthesis, batch and subsequent continuous cultures with steadily declining feed rates were performed with glycerol as the main substrate...
May 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29522419/sbml-level-3-package-flux-balance-constraints-version-2
#16
Brett G Olivier, Frank T Bergmann
Constraint-based modeling is a well established modeling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size and complexity such steady-state flux models are, typically, analyzed using constraint-based optimization techniques, for example, flux balance analysis (FBA). The Flux balance constraints (FBC) Package extends SBML Level 3 and provides a standardized format for the encoding, exchange and annotation of constraint-based models. It includes support for modeling concepts such as objective functions, flux bounds and model component annotation that facilitates reaction balancing...
March 9, 2018: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/29515760/molecular-characterization-of-breast-cancer-cell-response-to-metabolic-drugs
#17
Lucía Trilla-Fuertes, Angelo Gámez-Pozo, Jorge M Arevalillo, Mariana Díaz-Almirón, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Hilario Navarro, Rosa Aras-López, Irene Dapía, Rocío López-Vacas, Paolo Nanni, Sara Llorente-Armijo, Pedro Arias, Alberto M Borobia, Paloma Maín, Jaime Feliú, Enrique Espinosa, Juan Ángel Fresno Vara
Metabolic reprogramming is a hallmark of cancer. It has been described that breast cancer subtypes present metabolism differences and this fact enables the possibility of using metabolic inhibitors as targeted drugs in specific scenarios. In this study, breast cancer cell lines were treated with metformin and rapamycin, showing a heterogeneous response to treatment and leading to cell cycle disruption. The genetic causes and molecular effects of this differential response were characterized by means of SNP genotyping and mass spectrometry-based proteomics...
February 9, 2018: Oncotarget
https://www.readbyqxmd.com/read/29499995/metabolic-flux-of-the-oxidative-pentose-phosphate-pathway-under-low-light-conditions-in-synechocystis-sp-pcc-6803
#18
Kentaro Ueda, Tsubasa Nakajima, Katsunori Yoshikawa, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu
The role of the oxidative pentose phosphate pathway (oxPPP) in Synechocystis sp. PCC 6803 under mixotrophic conditions was investigated by 13 C metabolic flux analysis. Cells were cultured under low (10 μmol m-2  s-1 ) and high light intensities (100 μmol m-2  s-1 ) in the presence of glucose. The flux of CO2 fixation by ribulose bisphosphate carboxylase/oxygenase under the high light condition was approximately 3-fold higher than that under the low light condition. Although no flux of the oxPPP was observed under the high light condition, flux of 0...
February 27, 2018: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/29496019/insights-on-the-thermal-impacts-of-wing-colorization-of-migrating-birds-on-their-skin-friction-drag-and-the-choice-of-their-flight-route
#19
M Hassanalian, S Ben Ayed, M Ali, P Houde, C Hocut, A Abdelkefi
The thermal effects of wing color in flight is investigated in four species of birds with respect to their flight routes, migration time, and geometric and behavioral characteristics. Considering the marine and atmospheric characteristics of these flight routes, a thermal analysis of the birds' wings is performed during their migration. The surrounding fluxes including the ocean flux and the solar irradiance are considered in an energy balance in order to determine the skin temperature of both sides of the wing...
February 2018: Journal of Thermal Biology
https://www.readbyqxmd.com/read/29494607/predicting-the-accumulation-of-storage-compounds-by-rhodococcus-jostii-rha1-in-the-feast-famine-growth-cycles-using-genome-scale-flux-balance-analysis
#20
Mohammad Tajparast, Dominic Frigon
Feast-famine cycles in biological wastewater resource recovery systems select for bacterial species that accumulate intracellular storage compounds such as poly-β-hydroxybutyrate (PHB), glycogen, and triacylglycerols (TAG). These species survive better the famine phase and resume rapid substrate uptake at the beginning of the feast phase faster than microorganisms unable to accumulate storage. However, ecophysiological conditions favouring the accumulation of either storage compounds remain to be clarified, and predictive capabilities need to be developed to eventually rationally design reactors producing these compounds...
2018: PloS One
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