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metabolic flux analysis

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https://www.readbyqxmd.com/read/28213171/13c-labeling-analysis-of-sugars-by-high-resolution-mass-spectrometry-for-metabolic-flux-analysis
#1
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/28212377/optimality-principles-reveal-a-complex-interplay-of-intermediate-toxicity-and-kinetic-efficiency-in-the-regulation-of-prokaryotic-metabolism
#2
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/28208288/-15-n-nmr-based-approach-for-amino-acids-based-13-c-metabolic-flux-analysis-of-metabolism
#3
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/28188893/ultra-deep-next-generation-mitochondrial-genome-sequencing-reveals-widespread-heteroplasmy-in-chinese-hamster-ovary-cells
#4
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
#5
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
#6
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
#7
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/28179998/phlpp-regulates-hexokinase-2-dependent-glucose-metabolism-in-colon-cancer-cells
#8
Xiaopeng Xiong, Yang-An Wen, Mihail I Mitov, Mary C Oaks, Shigeki Miyamoto, Tianyan Gao
Increased glucose metabolism is considered as one of the most important metabolic alterations adapted by cancer cells in order to generate energy as well as high levels of glycolytic intermediates to support rapid proliferation. PH domain leucine-rich repeat protein phosphatase (PHLPP) belongs to a novel family of Ser/Thr protein phosphatases that function as tumor suppressors in various types of human cancer. Here we determined the role of PHLPP in regulating glucose metabolism in colon cancer cells. Knockdown of PHLPP increased the rate of glucose consumption and lactate production, whereas overexpression of PHLPP had the opposite effect...
2017: Cell Death Discovery
https://www.readbyqxmd.com/read/28179898/metatranscriptomic-analysis-reveals-unexpectedly-diverse-microbial-metabolism-in-a-biogeochemical-hot-spot-in-an-alluvial-aquifer
#9
Talia N M Jewell, Ulas Karaoz, Markus Bill, Romy Chakraborty, Eoin L Brodie, Kenneth H Williams, Harry R Beller
Organic matter deposits in alluvial aquifers have been shown to result in the formation of naturally reduced zones (NRZs), which can modulate aquifer redox status and influence the speciation and mobility of metals, affecting groundwater geochemistry. In this study, we sought to better understand how natural organic matter fuels microbial communities within anoxic biogeochemical hot spots (NRZs) in a shallow alluvial aquifer at the Rifle (CO) site. We conducted a 20-day microcosm experiment in which NRZ sediments, which were enriched in buried woody plant material, served as the sole source of electron donors and microorganisms...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28179004/understanding-the-interplay-of-carbon-and-nitrogen-supply-for-ectoines-production-and-metabolic-overflow-in-high-density-cultures-of-chromohalobacter-salexigens
#10
María J Salar-García, Vicente Bernal, José M Pastor, Manuel Salvador, Montserrat Argandoña, Joaquín J Nieto, Carmen Vargas, Manuel Cánovas
BACKGROUND: The halophilic bacterium Chromohalobacter salexigens has been proposed as promising cell factory for the production of the compatible solutes ectoine and hydroxyectoine. This bacterium has evolved metabolic adaptations to efficiently grow under high salt concentrations by accumulating ectoines as compatible solutes. However, metabolic overflow, which is a major drawback for the efficient conversion of biological feedstocks, occurs as a result of metabolic unbalances during growth and ectoines production...
February 8, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28173837/insulin-like-growth-factor-1-receptor-activation-promotes-mammary-gland-tumor-development-by-increasing-glycolysis-and-promoting-biomass-production
#11
Bas Ter Braak, Christine L Siezen, Joo S Lee, Pooja Rao, Charlotte Voorhoeve, Eytan Ruppin, Jan Willem van der Laan, Bob van de Water
BACKGROUND: The insulin-like growth factor 1 (IGF1) signaling axis plays a major role in tumorigenesis. In a previous experiment, we chronically treated mice with several agonists of the IGF1 receptor (IGF1R). We found that chronic treatment with insulin analogues with high affinity towards the IGF1R (IGF1 and X10) decreased the mammary gland tumor latency time in a p53(R270H/+)WAPCre mouse model. Frequent injections with insulin analogues that only mildly activated the IGF1R in vivo (glargine and insulin) did not significantly decrease the tumor latency time in this mouse model...
February 7, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28168426/mitochondrial-metabolism-regulates-microtubule-acetylome-and-autophagy-trough-sirtuin-2-impact-for-parkinson-s-disease
#12
Ana R Esteves, Daniela M Arduíno, Diana F Silva, Sofia D Viana, Frederico C Pereira, Sandra M Cardoso
Alterations in microtubule-dependent transport, mitochondrial dysfunction, and autophagic pathology are involved in neurodegeneration observed in sporadic Parkinson's disease. However, the mechanistic link connecting these events remains elusive. We observed that NAD(+) metabolism is altered in sporadic Parkinson's disease patient-derived cells, which contributes to Sirtuin-2 activation and subsequent decrease in acetylated-α-tubulin levels. Pharmacological inhibition of sirtuin-2 deacetylase activity selectively enhanced α-tubulin acetylation and facilitated the trafficking and clearance of misfolded proteins...
February 6, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28166948/heat-transfer-analysis-of-skin-during-thermal-therapy-using-thermal-wave-equation
#13
Meisam Kashcooli, Mohammad Reza Salimpour, Ebrahim Shirani
Specifying exact geometry of vessel network and its effect on temperature distribution in living tissues is one of the most complicated problems of the bioheat field. In this paper, the effects of blood vessels on temperature distribution in a skin tissue subjected to various thermal therapy conditions are investigated. Present model consists of counter-current multilevel vessel network embedded in a three-dimensional triple-layered skin structure. Branching angles of vessels are calculated using the physiological principle of minimum work...
February 2017: Journal of Thermal Biology
https://www.readbyqxmd.com/read/28165133/iterative-optimization-of-xylose-catabolism-in-saccharomyces-cerevisiae-using-combinatorial-expression-tuning
#14
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/28163917/mitochondrial-mutations-and-metabolic-adaptation-in-pancreatic-cancer
#15
Rae-Anne Hardie, Ellen van Dam, Mark Cowley, Ting-Li Han, Seher Balaban, Marina Pajic, Mark Pinese, Mary Iconomou, Robert F Shearer, Jessie McKenna, David Miller, Nicola Waddell, John V Pearson, Sean M Grimmond, Leonid Sazanov, Andrew V Biankin, Silas Villas-Boas, Andrew J Hoy, Nigel Turner, Darren N Saunders
BACKGROUND: Pancreatic cancer has a five-year survival rate of ~8%, with characteristic molecular heterogeneity and restricted treatment options. Targeting metabolism has emerged as a potentially effective therapeutic strategy for cancers such as pancreatic cancer, which are driven by genetic alterations that are not tractable drug targets. Although somatic mitochondrial genome (mtDNA) mutations have been observed in various tumors types, understanding of metabolic genotype-phenotype relationships is limited...
2017: Cancer & Metabolism
https://www.readbyqxmd.com/read/28163785/efficient-estimation-of-the-maximum-metabolic-productivity-of-batch-systems
#16
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/28159888/principles-for-circadian-orchestration-of-metabolic-pathways
#17
Kevin Thurley, Christopher Herbst, Felix Wesener, Barbara Koller, Thomas Wallach, Bert Maier, Achim Kramer, Pål O Westermark
Circadian rhythms govern multiple aspects of animal metabolism. Transcriptome-, proteome- and metabolome-wide measurements have revealed widespread circadian rhythms in metabolism governed by a cellular genetic oscillator, the circadian core clock. However, it remains unclear if and under which conditions transcriptional rhythms cause rhythms in particular metabolites and metabolic fluxes. Here, we analyzed the circadian orchestration of metabolic pathways by direct measurement of enzyme activities, analysis of transcriptome data, and developing a theoretical method called circadian response analysis...
February 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28157297/identifying-functional-cysteine-residues-in-the-mitochondria
#18
Daniel W Bak, Mattia D Pizzagalli, Eranthie Weerapana
The mitochondria are dynamic organelles that regulate oxidative metabolism and mediate cellular redox homeostasis. Proteins within the mitochondria are exposed to large fluxes in the surrounding redox environment. In particular, cysteine residues within mitochondrial proteins sense and respond to these redox changes through oxidative modifications of the cysteine thiol group. These oxidative modifications result in a loss in cysteine reactivity, which can be monitored using cysteine-reactive chemical probes and quantitative mass spectrometry (MS)...
February 15, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28150713/discovering-missing-reactions-of-metabolic-networks-by-using-gene-co-expression-data
#19
Zhaleh Hosseini, Sayed-Amir Marashi
Flux coupling analysis is a computational method which is able to explain co-expression of metabolic genes by analyzing the topological structure of a metabolic network. It has been suggested that if genes in two seemingly fully-coupled reactions are not highly co-expressed, then these two reactions are not fully coupled in reality, and hence, there is a gap or missing reaction in the network. Here, we present GAUGE as a novel approach for gap filling of metabolic networks, which is a two-step algorithm based on a mixed integer linear programming formulation...
February 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28149324/exploring-eukaryotic-formate-metabolisms-to-enhance-microbial-growth-and-lipid-accumulation
#20
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
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