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Metabolic flux

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https://www.readbyqxmd.com/read/28214243/synthetic-metabolic-bypass-for-a-metabolic-toggle-switch-enhances-acetyl-coa-supply-for-isopropanol-production-by-escherichia-coli
#1
Yuki Soma, Taiki Yamaji, Fumio Matsuda, Taizo Hanai
Almost all synthetic pathways for biofuel production are designed to require endogenous metabolites in glycolysis, such as phosphoenolpyruvate, pyruvate, and acetyl-CoA. However, such metabolites are also required for bacterial cell growth. To reduce the metabolic imbalance between cell growth and target chemical production, we previously constructed a metabolic toggle switch (MTS) as a conditional flux redirection tool controlling metabolic flux of TCA cycle toward isopropanol production. This approach succeeded to improve the isopropanol production titer and yield while ensuring sufficient cell growth...
February 14, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28213469/insulin-signaling-via-the-pi3k-akt-pathway-regulates-airway-glucose-uptake-and-barrier-function-in-a-cftr-dependent-manner
#2
Samuel A Molina, Hannah K Moriarty, Danny T Infield, Barry R Imhoff, Rachel J Vance, Agnes H Kim, Jason M Hansen, William R Hunt, Michael Koval, Nael A McCarty
Cystic fibrosis-related diabetes (CFRD) is the most common co-morbidity associated with cystic fibrosis (CF) and correlates with increased rates of lung function decline. Since glucose is a nutrient present in the airways of patients with bacterial airway infections and since insulin controls glucose metabolism, the effect of insulin on CF airway epithelia was investigated to determine the role of insulin receptors and glucose transport in regulating glucose availability in the airway. The response to insulin by human airway epithelial cells was characterized by qPCR, immunoblot, immunofluorescence, and glucose uptake assays...
February 17, 2017: American Journal of Physiology. Lung Cellular and Molecular Physiology
https://www.readbyqxmd.com/read/28213171/13c-labeling-analysis-of-sugars-by-high-resolution-mass-spectrometry-for-metabolic-flux-analysis
#3
Sébastien Acket, Anthony Degournay, Franck Merlier, Brigitte Thomasset
Metabolic flux analysis is particularly complex in plant cells because of highly compartmented metabolism. Analysis of free sugars is interesting because it provides data to define fluxes around hexose, pentose, and triose phosphate pools in different compartment. In this work, we present a method to analyze the isotopomer distribution of free sugars labeled with carbon 13 using a liquid chromatography-high resolution mass spectrometry, without derivatized procedure, adapted for Metabolic flux analysis. Our results showed a good sensitivity, reproducibility and better accuracy to determine isotopic enrichments of free sugars compared to our previous methods [5, 6]...
February 14, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28212815/systematic-testing-of-enzyme-perturbation-sensitivities-via-graded-dcas9-modulation-in-saccharomyces-cerevisiae
#4
Matthew Deaner, Hal S Alper
Dissecting genotype-phenotype relationships in a high-throughput and scalable manner is still an unresolved problem facing metabolic engineers. While the RNA-guided nuclease Cas9 has been repurposed as a programmable transcription regulator, its application has typically been limited to binary on/off regulation and thus misses informative and potentially optimal intermediate levels of gene expression. In this work, we establish a rapid method for fine-tuned, graded expression of pathway enzymes via dCas9 regulation by varying sgRNA target location as the dominant parameter...
February 14, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28212377/optimality-principles-reveal-a-complex-interplay-of-intermediate-toxicity-and-kinetic-efficiency-in-the-regulation-of-prokaryotic-metabolism
#5
Jan Ewald, Martin Bartl, Thomas Dandekar, Christoph Kaleta
A precise and rapid adjustment of fluxes through metabolic pathways is crucial for organisms to prevail in changing environmental conditions. Based on this reasoning, many guiding principles that govern the evolution of metabolic networks and their regulation have been uncovered. To this end, methods from dynamic optimization are ideally suited since they allow to uncover optimality principles behind the regulation of metabolic networks. We used dynamic optimization to investigate the influence of toxic intermediates in connection with the efficiency of enzymes on the regulation of a linear metabolic pathway...
February 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28211546/differential-effects-of-hormones-on-cellular-metabolism-in-keratoconus-in-vitro
#6
Tina B McKay, Jesper Hjortdal, Henrik Sejersen, Dimitrios Karamichos
Keratoconus (KC) is a corneal thinning disease with an onset commonly immediately post-puberty and stabilization by 40 to 50 years of age. The role of hormones in regulating corneal tissue structure in homeostatic and pathological conditions is unknown. Our group recently linked altered hormone levels to KC. Our current study sought to investigate and delineate the effects of exogenous hormones, such as androgen, luteotropin, and estrogen, on corneal stroma bioenergetics. We utilized our established 3D in vitro model to characterize the effects of DHEA, prolactin, 17β-estradiol on insulin-growth factor-1 and -2 (IGF-1, -2) signaling and metabolic function in primary corneal fibroblasts from healthy controls (HCFs) and KC patients (HKCs)...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28210255/high-prevalence-of-gammaproteobacteria-in-the-sediments-of-admiralty-bay-and-north-bransfield-basin-northwestern-antarctic-peninsula
#7
Diego C Franco, Camila N Signori, Rubens T D Duarte, Cristina R Nakayama, Lúcia S Campos, Vivian H Pellizari
Microorganisms dominate most Antarctic marine ecosystems, in terms of biomass and taxonomic diversity, and play crucial role in ecosystem functioning due to their high metabolic plasticity. Admiralty Bay is the largest bay on King George Island (South Shetland Islands, Antarctic Peninsula) and a combination of hydro-oceanographic characteristics (bathymetry, sea ice and glacier melting, seasonal entrance of water masses, turbidity, vertical fluxes) create conditions favoring organic carbon deposition on the seafloor and microbial activities...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28209199/making-life-difficult-for-clostridium-difficile-augmenting-the-pathogen-s-metabolic-model-with-transcriptomic-and-codon-usage-data-for-better-therapeutic-target-characterization
#8
Sara Saheb Kashaf, Claudio Angione, Pietro Lió
BACKGROUND: Clostridium difficile is a bacterium which can infect various animal species, including humans. Infection with this bacterium is a leading healthcare-associated illness. A better understanding of this organism and the relationship between its genotype and phenotype is essential to the search for an effective treatment. Genome-scale metabolic models contain all known biochemical reactions of a microorganism and can be used to investigate this relationship. RESULTS: We present icdf834, an updated metabolic network of C...
February 16, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28208288/-15-n-nmr-based-approach-for-amino-acids-based-13-c-metabolic-flux-analysis-of-metabolism
#9
Pierre Millard, Edern Cahoreau, Maud Heuillet, Jean-Charles Portais, Guy Lippens
NMR analysis of the isotope incorporation in amino acids can be used to derive information about the topology and operation of cellular metabolism. Although traditionally performed by (1)H and/or (13)C NMR, we present here novel experiments that exploit the (15)N nucleus to derive the same information with increased efficiency. Combined with a novel Hα-(13)CO experiment, we increase the coverage of the isotopic space that can be probed by obtaining the complete distribution of isotopic species for the first two carbons of amino acids in cellular biomass hydrolysates...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28207880/skeletal-muscle-metabolic-adaptations-to-endurance-exercise-training-are-attainable-in-mice-with-simvastatin-treatment
#10
William M Southern, Anna S Nichenko, Daniel D Shill, Corey C Spencer, Nathan T Jenkins, Kevin K McCully, Jarrod A Call
We tested the hypothesis that a 6-week regimen of simvastatin would attenuate skeletal muscle adaptation to low-intensity exercise. Male C57BL/6J wildtype mice were subjected to 6-weeks of voluntary wheel running or normal cage activities with or without simvastatin treatment (20 mg/kg/d, n = 7-8 per group). Adaptations in in vivo fatigue resistance were determined by a treadmill running test, and by ankle plantarflexor contractile assessment. The tibialis anterior, gastrocnemius, and plantaris muscles were evaluated for exercised-induced mitochondrial adaptations (i...
2017: PloS One
https://www.readbyqxmd.com/read/28204883/metabolic-engineering-of-saccharomyces-cerevisiae-for-2-3-butanediol-production
#11
REVIEW
Soo-Jung Kim, Jin-Woo Kim, Ye-Gi Lee, Yong-Cheol Park, Jin-Ho Seo
Saccharomyces cerevisiae is a work horse for production of valuable biofuels and biochemicals including 2,3-butanediol (2,3-BDO), a platform chemical with wide industrial applications for synthetic rubber, biosolvents and food additives. Recently, a cutting-edge technology of metabolic engineering has enabled S. cerevisiae to produce 2,3-BDO with high yield and productivity. These include (i) amplification of the 2,3-BDO biosynthetic pathway, (ii) redirection of carbon flux from ethanol or glycerol toward 2,3-BDO, and (iii) 2,3-BDO production from sugars derived from renewable biomass...
February 15, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28201992/high-flavonoid-accompanied-with-high-starch-accumulation-triggered-by-nutrient-starvation-in-bioenergy-crop-duckweed-landoltia-punctata
#12
Xiang Tao, Yang Fang, Meng-Jun Huang, Yao Xiao, Yang Liu, Xin-Rong Ma, Hai Zhao
BACKGROUND: As the fastest growing plant, duckweed can thrive on anthropogenic wastewater. The purple-backed duckweed, Landoltia punctata, is rich in starch and flavonoids. However, the molecular biological basis of high flavonoid and low lignin content remains largely unknown, as does the best method to combine nutrients removed from sewage and the utilization value improvement of duckweed biomass. RESULTS: A combined omics study was performed to investigate the biosynthesis of flavonoid and the metabolic flux changes in L...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28198817/dynamic-properties-of-calcium-activated-chloride-currents-in-xenopus-laevis-oocytes
#13
Ildefonso M De la Fuente, Iker Malaina, Alberto Pérez-Samartín, María Dolores Boyano, Gorka Pérez-Yarza, Carlos Bringas, Álvaro Villarroel, María Fedetz, Rogelio Arellano, Jesus M Cortes, Luis Martínez
Chloride is the most abundant permeable anion in the cell, and numerous studies in the last two decades highlight the great importance and broad physiological role of chloride currents mediated anion transport. They participate in a multiplicity of key processes, as for instance, the regulation of electrical excitability, apoptosis, cell cycle, epithelial secretion and neuronal excitability. In addition, dysfunction of Cl(-) channels is involved in a variety of human diseases such as epilepsy, osteoporosis and different cancer types...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28191902/dynamic-regulation-of-metabolic-flux-in-engineered-bacteria-using-a-pathway-independent-quorum-sensing-circuit
#14
Apoorv Gupta, Irene M Brockman Reizman, Christopher R Reisch, Kristala L J Prather
Metabolic engineering of microorganisms to produce desirable products on an industrial scale can result in unbalanced cellular metabolic networks that reduce productivity and yield. Metabolic fluxes can be rebalanced using dynamic pathway regulation, but few broadly applicable tools are available to achieve this. We present a pathway-independent genetic control module that can be used to dynamically regulate the expression of target genes. We apply our module to identify the optimal point to redirect glycolytic flux into heterologous engineered pathways in Escherichia coli, resulting in titers of myo-inositol increased 5...
February 13, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28191471/lipids-a-suitable-therapeutic-target-in-diabetic-neuropathy
#15
REVIEW
M C Perez-Matos, M C Morales-Alvarez, C O Mendivil
Diabetic polyneuropathy (DPN) encompasses multiple syndromes with a common pathogenesis. Glycemic control shows a limited correlation with DPN, arguing in favor of major involvement of other factors, one of which is alterations of lipid and lipoprotein metabolism. Consistent associations have been found between plasma triglycerides/remnant lipoproteins and the risk of DPN. Studies in cultured nerve tissue or in murine models of diabetes have unveiled mechanisms linking lipid metabolism to DPN. Deficient insulin action increases fatty acids flux to nerve cells, inducing mitochondrial dysfunction, anomalous protein kinase C signaling, and perturbations in the physicochemical properties of the plasma membrane...
2017: Journal of Diabetes Research
https://www.readbyqxmd.com/read/28188893/ultra-deep-next-generation-mitochondrial-genome-sequencing-reveals-widespread-heteroplasmy-in-chinese-hamster-ovary-cells
#16
Paul S Kelly, Colin Clarke, Alan Costello, Craig Monger, Justine Meiller, Heena Dhiman, Nicole Borth, Michael J Betenbaugh, Martin Clynes, Niall Barron
Recent sequencing of the Chinese hamster ovary (CHO) cell and Chinese hamster genomes has dramatically advanced our ability to understand the biology of these mammalian cell factories. In this study, we focus on the powerhouse of the CHO cell, the mitochondrion. Utilizing a high-resolution next generation sequencing approach we sequenced the Chinese hamster mitochondrial genome for the first time and surveyed the mutational landscape of CHO cell mitochondrial DNA (mtDNA). Depths of coverage ranging from ~3,319X to 8,056X enabled accurate identification of low frequency mutations (>1%) revealing that mtDNA heteroplasmy is widespread in CHO cells...
February 7, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28187415/estimation-of-biomass-composition-from-genomic-and-transcriptomic-information
#17
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
#18
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/28186174/acetate-fluxes-in-escherichia-coli-are-determined-by-the-thermodynamic-control-of-the-pta-acka-pathway
#19
Brice Enjalbert, Pierre Millard, Mickael Dinclaux, Jean-Charles Portais, Fabien Létisse
Escherichia coli excretes acetate upon growth on fermentable sugars, but the regulation of this production remains elusive. Acetate excretion on excess glucose is thought to be an irreversible process. However, dynamic (13)C-metabolic flux analysis revealed a strong bidirectional exchange of acetate between E. coli and its environment. The Pta-AckA pathway was found to be central for both flux directions, while alternative routes (Acs or PoxB) play virtually no role in glucose consumption. Kinetic modelling of the Pta-AckA pathway predicted that its flux is thermodynamically controlled by the extracellular acetate concentration in vivo...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28184304/the-%C3%AE-ketoglutarate-dehydrogenase-complex-in-cancer-metabolic-plasticity
#20
REVIEW
Renaud Vatrinet, Giulia Leone, Monica De Luise, Giulia Girolimetti, Michele Vidone, Giuseppe Gasparre, Anna Maria Porcelli
Deregulated metabolism is a well-established hallmark of cancer. At the hub of various metabolic pathways deeply integrated within mitochondrial functions, the α-ketoglutarate dehydrogenase complex represents a major modulator of electron transport chain activity and tricarboxylic acid cycle (TCA) flux, and is a pivotal enzyme in the metabolic reprogramming following a cancer cell's change in bioenergetic requirements. By contributing to the control of α-ketoglutarate levels, dynamics, and oxidation state, the α-ketoglutarate dehydrogenase is also essential in modulating the epigenetic landscape of cancer cells...
2017: Cancer & Metabolism
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