The Experts below are selected from a list of 300 Experts worldwide ranked by ideXlab platform
Gregory Stephanopoulos - One of the best experts on this subject based on the ideXlab platform.
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metabolomic and 13c metabolic flux analysis of a xylose consuming saccharomyces cerevisiae strain expressing xylose isomerase
Biotechnology and Bioengineering, 2015Co-Authors: Thomas M Wasylenko, Gregory StephanopoulosAbstract:Over the past two decades, significant progress has been made in the engineering of xylose-consuming Saccharomyces cerevisiae strains for production of lignocellulosic biofuels. However, the ethanol productivities achieved on xylose are still significantly lower than those observed on glucose for reasons that are not well understood. We have undertaken an analysis of central carbon Metabolite Pool sizes and metabolic fluxes on glucose and on xylose under aerobic and anaerobic conditions in a strain capable of rapid xylose assimilation via xylose isomerase in order to investigate factors that may limit the rate of xylose fermentation. We find that during xylose utilization the flux through the non-oxidative Pentose Phosphate Pathway (PPP) is high but the flux through the oxidative PPP is low, highlighting an advantage of the strain employed in this study. Furthermore, xylose fails to elicit the full carbon catabolite repression response that is characteristic of glucose fermentation in S. cerevisiae. We present indirect evidence that the incomplete activation of the fermentation program on xylose results in a bottleneck in lower glycolysis, leading to inefficient re-oxidation of NADH produced in glycolysis. Biotechnol. Bioeng. 2015;112: 470–483. © 2014 Wiley Periodicals, Inc.
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Metabolomic and 13C‐metabolic flux analysis of a xylose‐consuming Saccharomyces cerevisiae strain expressing xylose isomerase
Biotechnology and bioengineering, 2014Co-Authors: Thomas M Wasylenko, Gregory StephanopoulosAbstract:Over the past two decades, significant progress has been made in the engineering of xylose-consuming Saccharomyces cerevisiae strains for production of lignocellulosic biofuels. However, the ethanol productivities achieved on xylose are still significantly lower than those observed on glucose for reasons that are not well understood. We have undertaken an analysis of central carbon Metabolite Pool sizes and metabolic fluxes on glucose and on xylose under aerobic and anaerobic conditions in a strain capable of rapid xylose assimilation via xylose isomerase in order to investigate factors that may limit the rate of xylose fermentation. We find that during xylose utilization the flux through the non-oxidative Pentose Phosphate Pathway (PPP) is high but the flux through the oxidative PPP is low, highlighting an advantage of the strain employed in this study. Furthermore, xylose fails to elicit the full carbon catabolite repression response that is characteristic of glucose fermentation in S. cerevisiae. We present indirect evidence that the incomplete activation of the fermentation program on xylose results in a bottleneck in lower glycolysis, leading to inefficient re-oxidation of NADH produced in glycolysis. Biotechnol. Bioeng. 2015;112: 470–483. © 2014 Wiley Periodicals, Inc.
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Nontargeted Elucidation of Metabolic Pathways Using Stable-Isotope Tracers and Mass Spectrometry
Analytical chemistry, 2010Co-Authors: Karsten Hiller, Christian M. Metallo, Joanne K. Kelleher, Gregory StephanopoulosAbstract:Systems level tools for the quantitative analysis of metabolic networks are required to engineer metabolism for biomedical and industrial applications. While current metabolomics techniques enable high-throughput quantification of Metabolites, these methods provide minimal information on the rates and connectivity of metabolic pathways. Here we present a new method, nontargeted tracer fate detection (NTFD), that expands upon the concept of metabolomics to solve the above problems. Through the combined use of stable isotope tracers and chromatography coupled to mass spectrometry, our computational analysis enables the quantitative detection of all measurable Metabolites derived from a specific labeled compound. Without a priori knowledge of a reaction network or compound library, NTFD provides information about relative flux magnitudes into each Metabolite Pool by determining the mass isotopomer distribution for all labeled compounds. This novel method adds a new dimension to the metabolomics tool box and ...
Weiqi Li - One of the best experts on this subject based on the ideXlab platform.
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turnover of glycerolipid Metabolite Pool and seed viability
International Journal of Molecular Sciences, 2018Co-Authors: Xiaolong Hu, Hongying Chen, Xiaomei Yu, Weiqi LiAbstract:Hydration–dehydration cycles can frequently cause stress to seeds, but can also be used to improve germination. However, the molecular basis of the stress caused is poorly understood. Herein, we examine the effects of hydration–dehydration cycles on seed viability and profile the membrane glycerolipid molecular species. We find that seed viability was not affected during the first two cycles, but significantly decreased as further cycles were applied, until all viability was lost. The abundances of seven glycerolipid classes increased and decreased through hydration and dehydration, respectively, but the phosphatidic acid and diacylglycerol abundances changed in the opposite sense, while total glycerolipid contents remained constant. This suggests that during hydration–dehydration cycles, turnover of glycerolipid Metabolite Pools take place, while no significant lipid synthesis or degradation is involved. As further hydration–dehydration cycles occurred, lipid unsaturation increased, plastidic lipids decreased, and phosphatidylserine acyl chains lengthened. The latter two could be lethal for seeds. Our findings reveal a novel model of membrane lipid changes, and provide new insights into the responses of seeds to hydration–dehydration cycles.
Xiaolong Hu - One of the best experts on this subject based on the ideXlab platform.
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turnover of glycerolipid Metabolite Pool and seed viability
International Journal of Molecular Sciences, 2018Co-Authors: Xiaolong Hu, Hongying Chen, Xiaomei Yu, Weiqi LiAbstract:Hydration–dehydration cycles can frequently cause stress to seeds, but can also be used to improve germination. However, the molecular basis of the stress caused is poorly understood. Herein, we examine the effects of hydration–dehydration cycles on seed viability and profile the membrane glycerolipid molecular species. We find that seed viability was not affected during the first two cycles, but significantly decreased as further cycles were applied, until all viability was lost. The abundances of seven glycerolipid classes increased and decreased through hydration and dehydration, respectively, but the phosphatidic acid and diacylglycerol abundances changed in the opposite sense, while total glycerolipid contents remained constant. This suggests that during hydration–dehydration cycles, turnover of glycerolipid Metabolite Pools take place, while no significant lipid synthesis or degradation is involved. As further hydration–dehydration cycles occurred, lipid unsaturation increased, plastidic lipids decreased, and phosphatidylserine acyl chains lengthened. The latter two could be lethal for seeds. Our findings reveal a novel model of membrane lipid changes, and provide new insights into the responses of seeds to hydration–dehydration cycles.
Vladimir J. Balcar - One of the best experts on this subject based on the ideXlab platform.
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Effects of L-Glutamate Transport Inhibition by a Conformationally Restricted Glutamate Analogue (2S,1'S,2'R)-2-(Carboxycyclopropyl)Glycine (L-CCG III) on Metabolism in Brain Tissue In Vitro Analysed by NMR Spectroscopy
Neurochemical Research, 2002Co-Authors: Charbel El-hajj Moussa, Ann D. Mitrovic, Robert J. Vandenberg, Tanya Provis, Caroline Rae, William A. Bubb, Vladimir J. BalcarAbstract:(2 S ,1' S ,2' R )-2-(Carboxycyclopropyl)glycine (L-CCG III) was a substrate of Na^+-dependent glutamate transporters (GluT) in Xenopus laevis oocytes (IC_50 ∼ 13 and ∼2 μM for, respectively, EAAT 1 and EAAT 2) and caused an apparent inhibition of [^3H]L-glutamate uptake in “mini-slices“ of guinea pig cerebral cortex (IC_50 ∼ 12 μM). In slices (350 μM) of guinea pig cerebral cortex, 5 μM L-CCG III increased both the flux of label through pyruvate carboxylase and the fractional enrichment of glutamate, GABA, glutamine and lactate, but had no effect on total Metabolite Pool sizes. At 50 μM L-CCG III decreased incorporation of ^13C from [3-^13C]-pyruvate into glutamate C4, glutamine C4, lactate C3 and alanine C3. The total Metabolite Pool sizes were also decreased with no change in the fractional enrichment. Furthermore, L-CCG III was accumulated in the tissue, probably via GluT. At lower concentration, L-CCG III would compete with L-glutamate for GluT and the changes probably reflect a compensation for the “missing” L-glutamate. At 50 μM, intracellular L-CCG III could reach > 10 mM and metabolism might be affected directly.
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Effects of L-glutamate transport inhibition by a conformationally restricted glutamate analogue (2S,1'S,2'R)-2-(carboxycyclopropyl)glycine (L-CCG III) on metabolism in brain tissue in vitro analysed by NMR spectroscopy.
Neurochemical research, 2002Co-Authors: Charbel El-hajj Moussa, Ann D. Mitrovic, Robert J. Vandenberg, Tanya Provis, Caroline Rae, William A. Bubb, Vladimir J. BalcarAbstract:(2S,1'S,2'R)-2-(Carboxycyclopropyl)glycine (L-CCG III) was a substrate of Na(+)-dependent glutamate transporters (GluT) in Xenopus laevis oocytes (IC50 to approximately 13 and to approximately 2 microM for, respec tively, EAAT 1 and EAAT 2) and caused an apparent inhibition of [3H]L-glutamate uptake in "mini-slices" of guinea pig cerebral cortex (IC50 to approximately 12 microM). In slices (350 microM) of guinea pig cerebral cortex, 5 microM L-CCG III increased both the flux of label through pyruvate carboxylase and the fractional enrichment of glutamate, GABA, glutamine and lactate, but had no effect on total Metabolite Pool sizes. At 50 microM L-CCG III decreased incorporation of 13C from [3-13C]-pyruvate into glutamate C4, glutamine C4, lactate C3 and alanine C3. The total Metabolite Pool sizes were also decreased with no change in the fractional enrichment. Furthermore, L-CCG III was accumulated in the tissue, probably via GluT. At lower concentration, L-CCG III would compete with L-glutamate for GluT and the changes probably reflect a compensation for the "missing" L-glutamate. At 50 microM, intracellular L-CCG III could reach > 10 mM and metabolism might be affected directly.
Thomas M Wasylenko - One of the best experts on this subject based on the ideXlab platform.
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metabolomic and 13c metabolic flux analysis of a xylose consuming saccharomyces cerevisiae strain expressing xylose isomerase
Biotechnology and Bioengineering, 2015Co-Authors: Thomas M Wasylenko, Gregory StephanopoulosAbstract:Over the past two decades, significant progress has been made in the engineering of xylose-consuming Saccharomyces cerevisiae strains for production of lignocellulosic biofuels. However, the ethanol productivities achieved on xylose are still significantly lower than those observed on glucose for reasons that are not well understood. We have undertaken an analysis of central carbon Metabolite Pool sizes and metabolic fluxes on glucose and on xylose under aerobic and anaerobic conditions in a strain capable of rapid xylose assimilation via xylose isomerase in order to investigate factors that may limit the rate of xylose fermentation. We find that during xylose utilization the flux through the non-oxidative Pentose Phosphate Pathway (PPP) is high but the flux through the oxidative PPP is low, highlighting an advantage of the strain employed in this study. Furthermore, xylose fails to elicit the full carbon catabolite repression response that is characteristic of glucose fermentation in S. cerevisiae. We present indirect evidence that the incomplete activation of the fermentation program on xylose results in a bottleneck in lower glycolysis, leading to inefficient re-oxidation of NADH produced in glycolysis. Biotechnol. Bioeng. 2015;112: 470–483. © 2014 Wiley Periodicals, Inc.
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Metabolomic and 13C‐metabolic flux analysis of a xylose‐consuming Saccharomyces cerevisiae strain expressing xylose isomerase
Biotechnology and bioengineering, 2014Co-Authors: Thomas M Wasylenko, Gregory StephanopoulosAbstract:Over the past two decades, significant progress has been made in the engineering of xylose-consuming Saccharomyces cerevisiae strains for production of lignocellulosic biofuels. However, the ethanol productivities achieved on xylose are still significantly lower than those observed on glucose for reasons that are not well understood. We have undertaken an analysis of central carbon Metabolite Pool sizes and metabolic fluxes on glucose and on xylose under aerobic and anaerobic conditions in a strain capable of rapid xylose assimilation via xylose isomerase in order to investigate factors that may limit the rate of xylose fermentation. We find that during xylose utilization the flux through the non-oxidative Pentose Phosphate Pathway (PPP) is high but the flux through the oxidative PPP is low, highlighting an advantage of the strain employed in this study. Furthermore, xylose fails to elicit the full carbon catabolite repression response that is characteristic of glucose fermentation in S. cerevisiae. We present indirect evidence that the incomplete activation of the fermentation program on xylose results in a bottleneck in lower glycolysis, leading to inefficient re-oxidation of NADH produced in glycolysis. Biotechnol. Bioeng. 2015;112: 470–483. © 2014 Wiley Periodicals, Inc.