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Flux balance analysis

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
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...
March 9, 2018: Applied Microbiology and Biotechnology
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
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
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 by13 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
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
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
Sanu Shameer, Kambiz Baghalian, C Y Maurice Cheung, R George Ratcliffe, Lee J Sweetlove
There is considerable interest in transferring crassulacean acid metabolism (CAM) to C3 crops to improve their water-use efficiency. However, because the CAM biochemical cycle is energetically costly, it is unclear what impact this would have on yield. Using diel flux balance analysis of the CAM and C3 leaf metabolic networks, we show that energy consumption is three-fold higher in CAM at night. However, this additional cost of CAM can be entirely offset by the carbon-concentrating effect of malate decarboxylation behind closed stomata during the day...
February 26, 2018: Nature Plants
Kento Tokuyama, Yoshihiro Toya, Takaaki Horinouchi, Chikara Furusawa, Fumio Matsuda, Hiroshi Shimizu
Gene deletion strategies using flux balance analysis (FBA) have improved the growth-coupled production of various compounds. However, the productivities were often below the expectation because the cells failed to adapt to these genetic perturbations. Here, we demonstrate the productivity of the succinate of the designed gene deletion strain was improved by adaptive laboratory evolution (ALE). Although FBA predicted deletions of adhE-pykAF-gldA-pflB lead to produce succinate from glycerol with a yield of 0...
February 19, 2018: Biotechnology and Bioengineering
Steffen Klamt, Stefan Müller, Georg Regensburger, Jürgen Zanghellini
BACKGROUND: The optimization of metabolic rates (as linear objective functions) represents the methodical core of flux-balance analysis techniques which have become a standard tool for the study of genome-scale metabolic models. Besides (growth and synthesis) rates, metabolic yields are key parameters for the characterization of biochemical transformation processes, especially in the context of biotechnological applications. However, yields are ratios of rates, and hence the optimization of yields (as nonlinear objective functions) under arbitrary linear constraints is not possible with current flux-balance analysis techniques...
February 7, 2018: Metabolic Engineering
Sahely Bhadra, Peter Blomberg, Sandra Castillo, Juho Rousu, Jonathan Wren
Motivation: In the analysis of metabolism, two distinct and complementary approaches are frequently used: Principal component analysis (PCA) and stoichiometric flux analysis. PCA is able to capture the main modes of variability in a set of experiments and does not make many prior assumptions about the data, but does not inherently take into account the flux mode structure of metabolism. Stoichiometric flux analysis methods, such as Flux Balance Analysis (FBA) and Elementary Mode Analysis, on the other hand, are able to capture the metabolic flux modes, however, they are primarily designed for the analysis of single samples at a time, and not best suited for exploratory analysis on a large sets of samples...
February 6, 2018: Bioinformatics
León Toro, Laura Pinilla, Claudio Avignone-Rossa, Rigoberto Ríos-Estepa
In this work, we expanded and updated a genome-scale metabolic model of Streptomyces clavuligerus. The model includes 1021 genes and 1494 biochemical reactions; genome-reaction information was curated and new features related to clavam metabolism and to the biomass synthesis equation were incorporated. The model was validated using experimental data from the literature and simulations were performed to predict cellular growth and clavulanic acid biosynthesis. Flux balance analysis (FBA) showed that limiting concentrations of phosphate and an excess of ammonia accumulation are unfavorable for growth and clavulanic acid biosynthesis...
February 5, 2018: Bioprocess and Biosystems Engineering
Ali Nikdel, Richard D Braatz, Hector M Budman
Dynamic flux balance analysis (DFBA) has become an instrumental modeling tool for describing the dynamic behavior of bioprocesses. DFBA involves the maximization of a biologically meaningful objective subject to kinetic constraints on the rate of consumption/production of metabolites. In this paper, we propose a systematic data-based approach for finding both the biological objective function and a minimum set of active constraints necessary for matching the model predictions to the experimental data. The proposed algorithm accounts for the errors in the experiments and eliminates the need for ad hoc choices of objective function and constraints as done in previous studies...
February 1, 2018: Bioprocess and Biosystems Engineering
Ambarish Nag, Peter C St John, Michael F Crowley, Yannick J Bomble
Succinate is a precursor of multiple commodity chemicals and bio-based succinate production is an active area of industrial bioengineering research. One of the most important microbial strains for bio-based production of succinate is the capnophilic gram-negative bacterium Actinobacillus succinogenes, which naturally produces succinate by a mixed-acid fermentative pathway. To engineer A. succinogenes to improve succinate yields during mixed acid fermentation, it is important to have a detailed understanding of the metabolic flux distribution in A...
2018: PloS One
Jason J Flowers, Matthew A Richards, Nitin Baliga, Birte Meyer, David A Stahl
A refined Desulfovibrio vulgaris Hildenborough flux balance analysis (FBA) model (iJF744) was developed, incorporating 1016 reactions that include 744 genes and 951 metabolites. A draft model was first developed through automatic model reconstruction using the ModelSeed Server and then curated based on existing literature. The curated model was further refined by incorporating three recently proposed redox reactions involving the Hdr-Flx and Qmo complexes and a lactate dehydrogenase (LdhAB, DVU 3027-3028) indicated by mutation and transcript analyses to serve electron transfer reactions central to syntrophic and respiratory growth...
January 26, 2018: Environmental Microbiology Reports
Jacob C Kimmel, Amy Y Chang, Andrew S Brack, Wallace F Marshall
Cell populations display heterogeneous and dynamic phenotypic states at multiple scales. Similar to molecular features commonly used to explore cell heterogeneity, cell behavior is a rich phenotypic space that may allow for identification of relevant cell states. Inference of cell state from cell behavior across a time course may enable the investigation of dynamics of transitions between heterogeneous cell states, a task difficult to perform with destructive molecular observations. Cell motility is one such easily observed cell behavior with known biomedical relevance...
January 16, 2018: PLoS Computational Biology
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
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
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
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
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