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Flux balance analysis

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)
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
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
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
Gavin Gillmore, David Wertheim, Simon Crust
Solid State Nuclear Track Detectors (SSNTDs) are used extensively for monitoring alpha particle radiation, neutron flux and cosmic ray radiation. Radon gas inhalation is regarded as being a significant contributory factor to lung cancer deaths in the UK each year. Gas concentrations are often monitored using CR39 based SSNTDs as the natural decay of radon results in alpha particles which form tracks in these detectors. Such tracks are normally etched for about 4h to enable microscopic analysis. This study examined the effect of etching time on the appearance of alpha tracks in SSNTDs by collecting 2D and 3D image datasets using laser confocal microscope imaging techniques...
September 29, 2016: Science of the Total Environment
Sayed-Rzgar Hosseini, Olivier C Martin, Andreas Wagner
Recombination is an important source of metabolic innovation, especially in prokaryotes, which have evolved the ability to survive on many different sources of chemical elements and energy. Metabolic systems have a well-understood genotype-phenotype relationship, which permits a quantitative and biochemically principled understanding of how recombination creates novel phenotypes. Here, we investigate the power of recombination to create genome-scale metabolic reaction networks that enable an organism to survive in new chemical environments...
September 28, 2016: Proceedings. Biological Sciences
Michael J Opperman, Yair Shachar-Hill
Pseudomonas aeruginosa is a metabolically versatile wide-ranging opportunistic pathogen. In humans P. aeruginosa causes infections of the skin, urinary tract, blood, and the lungs of Cystic Fibrosis patients. In addition, P. aeruginosa's broad environmental distribution, relatedness to biotechnologically useful species, and ability to form biofilms have made it the focus of considerable interest. We used (13)C metabolic flux analysis (MFA) and flux balance analysis to understand energy and redox production and consumption and to explore the metabolic phenotypes of one reference strain and five strains isolated from the lungs of cystic fibrosis patients...
September 13, 2016: Metabolic Engineering
Michael F A Bradfield, Willie Nicol
Increased pentose phosphate pathway flux, relative to total substrate uptake flux, is shown to enhance succinic acid (SA) yields under continuous, non-growth conditions of Actinobacillus succinogenes biofilms. Separate fermentations of glucose and xylose were conducted in a custom, continuous biofilm reactor at four different dilution rates. Glucose-6-phosphate dehydrogenase assays were performed on cell extracts derived from in situ removal of biofilm at each steady state. The results of the assays were coupled to a kinetic model that revealed an increase in oxidative pentose phosphate pathway (OPPP) flux relative to total substrate flux with increasing SA titre, for both substrates...
September 9, 2016: Applied Microbiology and Biotechnology
Mauro DiNuzzo, Federico Giove, Bruno Maraviglia, Silvia Mangia
Brain activity involves essential functional and metabolic interactions between neurons and astrocytes. The importance of astrocytic functions to neuronal signaling is supported by many experiments reporting high rates of energy consumption and oxidative metabolism in these glial cells. In the brain, almost all energy is consumed by the Na(+)/K(+) ATPase, which hydrolyzes 1 ATP to move 3 Na(+) outside and 2 K(+) inside the cells. Astrocytes are commonly thought to be primarily involved in transmitter glutamate cycling, a mechanism that however only accounts for few % of brain energy utilization...
September 14, 2016: Neurochemical Research
Ying Liu, Siyao Wang, Carrie A McDonough, Mohammed Khairy, Derek Muir, Rainer Lohmann
Compared with dry and wet deposition fluxes, air-water exchange flux cannot be directly measured experimentally. Its model-based calculation contains considerable uncertainty because of the uncertainties in input parameters. To capture the inherent variability of air-water exchange flux of PCBs across the lower Great Lakes and to calculate their annual gross volatilization loss, 57 pairs of air and water samples from 19 sites across Lakes Erie and Ontario were collected using passive sampling technology during 2011-2012...
October 18, 2016: Environmental Science & Technology
Ziwei Dai, Alexander A Shestov, Luhua Lai, Jason W Locasale
The Warburg effect, or aerobic glycolysis, is marked by the increased metabolism of glucose to lactate in the presence of oxygen. Despite its widespread prevalence in physiology and cancer biology, the causes and consequences remain incompletely understood. Here, we show that a simple balance of interacting fluxes in glycolysis creates constraints that impose the necessary conditions for glycolytic flux to generate lactate as opposed to entering into the mitochondria. These conditions are determined by cellular redox and energy demands...
September 6, 2016: Biophysical Journal
Yixing Zhang, Fan Zeng, Keith Hohn, Praveen V Vadlani
Metabolic flux analyses were performed based on the carbon balance of six different Lactobacillus strains used in this study. Results confirmed that L. delbrueckii, L. plantarum ATCC 21028, L. plantarum NCIMB 8826 ΔldhL1, L. plantarum NCIMB 8826 ΔldhL1-pCU-PxylAB, and L. plantarum NCIMB 8826 ΔldhL1-pLEM415-xylAB metabolized glucose via EMP: whereas, L. brevis metabolized glucose via PK pathway. Xylose was metabolized through the PK pathway in L. brevis, L. plantarum NCIMB 8826 ΔldhL1-pCU-PxylAB and L. plantarum NCIMB 8826 ΔldhL1-pLEM415-xylAB...
September 7, 2016: Biotechnology Progress
Regiane Kawasaki, Rafael A Baraúna, Artur Silva, Marta S P Carepo, Rui Oliveira, Rodolfo Marques, Rommel T J Ramos, Maria P C Schneider
Exiguobacterium antarcticum B7 is extremophile Gram-positive bacteria able to survive in cold environments. A key factor to understanding cold adaptation processes is related to the modification of fatty acids composing the cell membranes of psychrotrophic bacteria. In our study we show the in silico reconstruction of the fatty acid biosynthesis pathway of E. antarcticum B7. To build the stoichiometric model, a semiautomatic procedure was applied, which integrates genome information using KEGG and RAST/SEED...
2016: BioMed Research International
Shin-Nosuke Hashida, Taketo Itami, Kentaro Takahara, Takayuki Hirabayashi, Hirofumi Uchimiya, Maki Kawai-Yamada
NAD is a well-known co-enzyme that mediates hundreds of redox reactions and is the basis of various processes regulating cell responses to different environmental and developmental cues. The regulatory mechanism that determines the amount of cellular NAD and the rate of NAD metabolism remains unclear. We created Arabidopsis thaliana plants overexpressing the NAD synthase (NADS) gene that participates in the final step of NAD biosynthesis. NADS overexpression enhanced the activity of NAD biosynthesis but not the amounts of NAD(+), NADH, NADP(+), or NADPH...
September 1, 2016: Plant & Cell Physiology
Keisuke Wada, Yoshihiro Toya, Satomi Banno, Katsunori Yoshikawa, Fumio Matsuda, Hiroshi Shimizu
Mevalonate (MVA) is used to produce various useful products such as drugs, cosmetics and food additives. An MVA-producing strain of Escherichia coli (engineered) was constructed by introducing mvaES genes from Enterococcus faecalis. The engineered strain produced 1.84 mmol/gDCW/h yielding 22% (C-mol/C-mol) of MVA from glucose in the aerobic exponential growth phase. The mass balance analysis revealed that the MVA yield of the engineered strain was close to the upper limit at the biomass yield. Since MVA is synthesized from acetyl-CoA using NADPH as a cofactor, the production of MVA affects central metabolism in terms of carbon utilization and NADPH requirements...
August 25, 2016: Journal of Bioscience and Bioengineering
Pedro A Saa, Lars K Nielsen
MOTIVATION: Computation of steady-state flux solutions in large metabolic models is routinely performed using Flux Balance Analysis based on a simple LP formulation. A minimal requirement for thermodynamic feasibility of the flux solution is the absence of internal loops, which are enforced using 'loopless constraints'. The resulting loopless flux problem is a substantially harder MILP problem, which is computationally expensive for large metabolic models. RESULTS: We developed a pre-processing algorithm that significantly reduces the size of the original loopless problem into an easier and equivalent MILP problem...
August 24, 2016: Bioinformatics
Savina Apolloni, Paola Fabbrizio, Susanna Amadio, Cinzia Volonté
BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a disease with a strong neuroinflammatory component sustained by activated microglia contributing to motoneuron death. However, how to successfully balance neuroprotective versus neurotoxic actions by the use of antinflammatory agents is still under scrutiny. We have recently shown that the antihistamine clemastine, an FDA-approved drug, can influence the M1/M2 switch occurring in SOD1-G93A ALS microglia. METHODS: Here, we have chronically treated female SOD1-G93A mice with clemastine, evaluated disease progression and performed mice lumbar spinal cord analysis at symptomatic and end stage of the disease...
2016: Journal of Neuroinflammation
Tobias Großkopf, Jessika Consuegra, Joël Gaffé, John C Willison, Richard E Lenski, Orkun S Soyer, Dominique Schneider
BACKGROUND: Predicting adaptive trajectories is a major goal of evolutionary biology and useful for practical applications. Systems biology has enabled the development of genome-scale metabolic models. However, analysing these models via flux balance analysis (FBA) cannot predict many evolutionary outcomes including adaptive diversification, whereby an ancestral lineage diverges to fill multiple niches. Here we combine in silico evolution with FBA and apply this modelling framework, evoFBA, to a long-term evolution experiment with Escherichia coli...
2016: BMC Evolutionary Biology
Mark A Keibler, Thomas M Wasylenko, Joanne K Kelleher, Othon Iliopoulos, Matthew G Vander Heiden, Gregory Stephanopoulos
BACKGROUND: The study of cancer metabolism has been largely dedicated to exploring the hypothesis that oncogenic transformation rewires cellular metabolism to sustain elevated rates of growth and division. Intense examination of tumors and cancer cell lines has confirmed that many cancer-associated metabolic phenotypes allow robust growth and survival; however, little attention has been given to explicitly identifying the biochemical requirements for cell proliferation in a rigorous manner in the context of cancer metabolism...
2016: Cancer & Metabolism
Mingjun Li, Dongxia Li, Fengjuan Feng, Sheng Zhang, Fengwang Ma, Lailiang Cheng
Understanding the fruit developmental process is critical for fruit quality improvement. Here, we report a comprehensive proteomic analysis of apple fruit development over five growth stages, from young fruit to maturity, coupled with metabolomic profiling. A tandem mass tag (TMT)-based comparative proteomics approach led to the identification and quantification of 7098 and 6247 proteins, respectively. This large-scale proteomic dataset presents a global view of the critical pathways involved in fruit development and metabolism...
September 2016: Journal of Experimental Botany
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