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metabolic flux analysis

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https://www.readbyqxmd.com/read/28918196/expression-and-purification-of-human-and-saccharomyces-cerevisiae-equilibrative-nucleoside-transporters
#1
Rebba C Boswell-Casteel, Jennifer M Johnson, Zygy Roe-Žurž, Kelli D Duggan, Hannah Schmitz, Franklin A Hays
Nucleosides play an essential role in the physiology of eukaryotes by acting as metabolic precursors in de novo nucleic acid synthesis and energy metabolism. Nucleosides also act as ligands for purinergic receptors. Equilibrative nucleoside transporters (ENTs) are polytopic integral membrane proteins that aid in regulating plasmalemmal flux of purine and pyrimidine nucleosides and nucleobases. ENTs exhibit broad substrate selectivity across different isoforms and utilize diverse mechanisms to drive substrate flux across membranes...
September 13, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28916726/the-nqo1-bioactivatable-drug-%C3%AE-lapachone-alters-the-redox-state-of-nqo1-pancreatic-cancer-cells-causing-perturbation-in-central-carbon-metabolism
#2
Molly A Silvers, Stanislaw Deja, Naveen Singh, Robert A Egnatchik, Jessica Sudderth, Xiuquan Luo, Muhammad S Beg, Shawn C Burgess, Ralph J DeBerardinis, David A Boothman, Matthew E Merritt
Many cancer treatments, such as those for managing recalcitrant tumors like pancreatic ductal adenocarcinoma, cause off-target toxicities in normal, healthy tissue, highlighting the need for more tumor-selective chemotherapies. β-Lapachone is bioactivated by NAD(P)H:quinone oxidoreductase 1 (NQO1). This enzyme exhibits elevated expression in most solid cancers and therefore is a potential cancer-specific target. β-Lapachone's therapeutic efficacy partially stems from the drug's induction of a futile NQO1-mediated redox cycle that causes high levels of superoxide, then peroxide formation, which damages DNA and causes hyperactivation of poly (ADP-ribose) polymerase (PARP), resulting in extensive NAD+/ATP depletion...
September 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28913155/hepatic-metabolism-of-11-c-methionine-and-secretion-of-11-c-protein-measured-by-pet-in-pigs
#3
Jacob Horsager, Susanne Bach Lausten, Dirk Bender, Ole Lajord Munk, Susanne Keiding
Hepatic amino acid metabolism and protein secretion are essential liver functions that may be altered during metabolic stress, e.g. after surgery. We wished to develop a dynamic liver PET method using the radiolabeled amino acid (11)C-methionine to examine this question. Eleven 40-kg pigs were allocated to either laparotomy or pneumoperitoneum. 24 hours after surgery a 70-min dynamic PET scanning of the liver with arterial blood sampling was performed immediately after intravenous injection of (11)C-methionine...
2017: American Journal of Nuclear Medicine and Molecular Imaging
https://www.readbyqxmd.com/read/28904365/rnai-mediated-silencing-of-a-pyruvate-dehydrogenase-kinase-enhances-triacylglycerol-biosynthesis-in-the-oleaginous-marine-alga-nannochloropsis-salina
#4
Xiaonian Ma, Lina Yao, Bo Yang, Yuan Kun Lee, Feng Chen, Jin Liu
Oleaginous microalgae have been emerging as the third-generation feedstocks for biofuel production. Genetic manipulation for improving triacylglycerol (TAG) accumulation represents a promising approach towards the economics of microalgal biofuels. Acetyl-CoA, the essential carbon precursor for de novo fatty acid biosynthesis, can be derived from pyruvate catalyzed by pyruvate dehydrogenase, which is negatively regulated by pyruvate dehydrogenase kinase (PDK). In the present study, we characterized a PDK gene (NsPDK) from Nannochloropsis salina...
September 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28903046/genome-scale-architecture-of-small-molecule-regulatory-networks-and-the-fundamental-trade-off-between-regulation-and-enzymatic-activity
#5
Ed Reznik, Dimitris Christodoulou, Joshua E Goldford, Emma Briars, Uwe Sauer, Daniel Segrè, Elad Noor
Metabolic flux is in part regulated by endogenous small molecules that modulate the catalytic activity of an enzyme, e.g., allosteric inhibition. In contrast to transcriptional regulation of enzymes, technical limitations have hindered the production of a genome-scale atlas of small molecule-enzyme regulatory interactions. Here, we develop a framework leveraging the vast, but fragmented, biochemical literature to reconstruct and analyze the small molecule regulatory network (SMRN) of the model organism Escherichia coli, including the primary metabolite regulators and enzyme targets...
September 12, 2017: Cell Reports
https://www.readbyqxmd.com/read/28900755/quantitative-physiology-and-elemental-composition-of-kluyveromyces-lactis-cbs-2359-during-growth-on-glucose-at-different-specific-growth-rates
#6
Oscar Dias, Thiago O Basso, Isabel Rocha, Eugénio C Ferreira, Andreas K Gombert
The yeast Kluyveromyces lactis has received attention both from academia and industry due to some important features, such as its capacity to grow in lactose-based media, its safe status, its suitability for large-scale cultivation and for heterologous protein synthesis. It has also been considered as a model organism for genomics and metabolic regulation. Despite this, very few studies were carried out hitherto under strictly controlled conditions, such as those found in a chemostat. Here we report a set of quantitative physiological data generated during chemostat cultivations with the K...
September 12, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28899391/mixomics-analysis-of-bacillus-subtilis-effect-of-oxygen-availability-on-riboflavin-production
#7
Junlang Hu, Pan Lei, Ali Mohsin, Xiaoyun Liu, Mingzhi Huang, Liang Li, Jianhua Hu, Haifeng Hang, Yingping Zhuang, Meijin Guo
BACKGROUND: Riboflavin, an intermediate of primary metabolism, is one kind of important food additive with high economic value. The microbial cell factory Bacillus subtilis has already been proven to possess significant importance for the food industry and have become one of the most widely used riboflavin-producing strains. In the practical fermentation processes, a sharp decrease in riboflavin production is encountered along with a decrease in the dissolved oxygen (DO) tension. Influence of this oxygen availability on riboflavin biosynthesis through carbon central metabolic pathways in B...
September 12, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28892295/transcriptome-and-proteome-dynamics-in-chemostat-culture-reveal-how-campylobacter-jejuni-modulates-metabolism-stress-responses-and-virulence-factors-upon-changes-in-oxygen-availability
#8
Edward J Guccione, John J Kendall, Andrew Hitchcock, Nitanshu Garg, Michael A White, Francis Mulholland, Robert K Poole, David J Kelly
Campylobacter jejuni, the most frequent cause of food-borne bacterial gastroenteritis worldwide, is a microaerophile that has to survive high environmental oxygen tensions, adapt to oxygen limitation in the intestine and resist host oxidative attack. Here, oxygen-dependent changes in C. jejuni physiology were studied at constant growth rate using carbon (serine)-limited continuous chemostat cultures. We show that a perceived aerobiosis scale can be calibrated by the acetate excretion flux, which becomes zero when metabolism is fully aerobic (100% aerobiosis)...
September 11, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28886026/population-fba-predicts-metabolic-phenotypes-in-yeast
#9
Piyush Labhsetwar, Marcelo C R Melo, John A Cole, Zaida Luthey-Schulten
Using protein counts sampled from single cell proteomics distributions to constrain fluxes through a genome-scale model of metabolism, Population flux balance analysis (Population FBA) successfully described metabolic heterogeneity in a population of independent Escherichia coli cells growing in a defined medium. We extend the methodology to account for correlations in protein expression arising from the co-regulation of genes and apply it to study the growth of independent Saccharomyces cerevisiae cells in two different growth media...
September 8, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28881985/popfba-tackling-intratumour-heterogeneity-with-flux-balance-analysis
#10
Chiara Damiani, Marzia Di Filippo, Dario Pescini, Davide Maspero, Riccardo Colombo, Giancarlo Mauri
Motivation: Intratumour heterogeneity poses many challenges to the treatment of cancer. Unfortunately, the transcriptional and metabolic information retrieved by currently available computational and experimental techniques portrays the average behaviour of intermixed and heterogeneous cell subpopulations within a given tumour. Emerging single-cell genomic analyses are nonetheless unable to characterize the interactions among cancer subpopulations. In this study, we propose popFBA , an extension to classic Flux Balance Analysis, to explore how metabolic heterogeneity and cooperation phenomena affect the overall growth of cancer cell populations...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28874733/mitochondrial-permeability-transition-pore-sensitivity-to-opening-and-mechanistic-dependence-on-substrate-availability
#11
Thomas Briston, Malcolm Roberts, Sian Lewis, Ben Powney, James M Staddon, Gyorgy Szabadkai, Michael R Duchen
Mitochondrial Ca(2+) uptake has a key role in cellular Ca(2+) homeostasis. Excessive matrix Ca(2+) concentrations, especially when coincident with oxidative stress, precipitate opening of an inner mitochondrial membrane, high-conductance channel: the mitochondrial permeability transition pore (mPTP). mPTP opening has been implicated as a final cell death pathway in numerous diseases and therefore understanding conditions dictating mPTP opening is crucial for developing targeted therapies. Here, we have investigated the impact of mitochondrial metabolic state on the probability and consequences of mPTP opening...
September 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28871529/assessing-metabolic-flux-in-plants-with-radiorespirometry
#12
Nicholas J Kruger, Shyam K Masakapalli, R George Ratcliffe
Carbohydrates are the dominant respiratory substrate in many plant cells. However, the route of carbohydrate oxidation varies depending on the relative cellular demands for energy, reductant, and precursors for biosynthesis. During these processes individual substrate carbon atoms are differentially released as carbon dioxide by specific reactions in the network, and this can be measured by monitoring the release of (14)CO2 from a range of positionally labeled forms of [(14)C]glucose. Although the relative amounts of carbon dioxide produced from different carbon positions do not allow precise determination of fluxes, they are indicative of the route of carbohydrate utilization...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28868622/proliferation-inhibition-of-cisplatin-resistant-ovarian-cancer-cells-using-drugs-screened-by-integrating-a-metabolic-model-and-transcriptomic-data
#13
E Motamedian, E Taheri, F Bagheri
OBJECTIVES: If screening to find effective drugs is possible, the inhibition of proliferation using existing drugs can be a practical strategy to control the drug resistance of cancer. Development of a system-oriented strategy to find effective drugs was the main aim of this research. MATERIALS AND METHODS: An algorithm (transcriptional regulated flux balance analysis [TRFBA]) integrating a generic human metabolic model with transcriptomic data was used to identify genes affecting the growth of drug-resistant cancer cells...
September 3, 2017: Cell Proliferation
https://www.readbyqxmd.com/read/28867169/nitric-oxide-the-forgotten-child-of-tumor-metabolism
#14
REVIEW
Bahar Salimian Rizi, Abhinav Achreja, Deepak Nagrath
Nitric oxide (NO) is a signaling molecule with pleiotropic physiological roles in normal cells and pathophysiological roles in cancer. NO synthetase expression and NO synthesis are linked to altered metabolism, neoplasticity, invasiveness, chemoresistance, immune evasion, and ultimately to poor prognosis of cancer patients. Exogenous NO in the microenvironment facilitates paracrine signaling, mediates immune responses, and triggers angiogenesis. NO regulates posttranslational protein modifications, S-nitrosation, and genome-wide epigenetic modifications that can have both tumor-promoting and tumor-suppressing effects...
September 2017: Trends in Cancer
https://www.readbyqxmd.com/read/28865116/power-input-effects-on-degeneration-in-prolonged-penicillin-chemostat-cultures-a-systems-analysis-at-flux-residual-glucose-metabolite-and-transcript-levels
#15
Guan Wang, Baofeng Wu, Junfei Zhao, Cees Haringa, Jianye Xia, Ju Chu, Yingping Zhuang, Siliang Zhang, Joseph J Heijnen, Walter van Gulik, Amit T Deshmukh, Henk J Noorman
In the present work, by performing chemostat experiments at 400 and 600 RPM, two typical power inputs representative of industrial penicillin fermentation (P/V, 1.00 kW/m(3) in more remote zones and 3.83 kW/m(3) in the vicinity of the impellers, respectively) were scaled-down to bench-scale bioreactors. It was found that at 400 RPM applied in prolonged glucose-limited chemostat cultures, the previously reported degeneration of penicillin production using an industrial Penicillium chrysogenum strain was virtually absent...
September 2, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28863345/the-stromal-microenvironment-modulates-mitochondrial-oxidative-phosphorylation-in-chronic-lymphocytic-leukemia-cells
#16
Hima V Vangapandu, Mary L Ayres, Christopher A Bristow, William G Wierda, Michael J Keating, Kumudha Balakrishnan, Christine M Stellrecht, Varsha Gandhi
Peripheral blood chronic lymphocytic leukemia (CLL) cells are replicationally quiescent mature B-cells. In short-term cultures, supporting stromal cells provide a survival advantage to CLL cells by inducing transcription and translation without promoting proliferation. We hypothesized that the stromal microenvironment augments malignant B cells' metabolism to enable the cells to cope with their energy demands for transcription and translation. We used extracellular flux analysis to assess the two major energy-generating pathways, mitochondrial oxidative phosphorylation (OxPhos) and glycolysis, in primary CLL cells in the presence of three different stromal cell lines...
August 29, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28862604/-high-resolution-respirometry-in-diagnostic-of-mitochondrial-disorders-caused-by-mitochondrial-complex-i-deficiency
#17
T D Krylova, P G Tsygankova, Yu S Itkis, N L Sheremet, T A Nevinitsyna, S V Mikhaylova, E Yu Zakharova
Complex I (CI) deficiency is one of the most common defects in the OXPHOS system; it represents more than 30% cases of mitochondrial diseases. The group is characterized by clinical and genetic heterogeneity and comprise several nosological forms. The most prevalent phenotypes for CI are LHON and Leigh syndrome. In this study we have analyzed skin fibroblasts from 11 patients with mutations in mtDNA, which cause LHON or Leigh-like phenotypes: m.11778 G>A (n=3), m.3460 A>G (n=2), m.3635 G>A (n=1), m...
July 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/28859811/engineering-escherichia-coli-for-poly-3-hydroxybutyrate-production-guided-by-genome-scale-metabolic-network-analysis
#18
Yangyang Zheng, Qianqian Yuan, Xiaoyan Yang, Hongwu Ma
Poly-(3-hydroxybutyrate) (P3HB) is a promising biodegradable plastic synthesized from acetyl-CoA. One important factor affecting the P3HB production cost is the P3HB yield. Through flux balance analysis of an extended genome-scale metabolic network of E. coli, we found that the introduction of non-oxidative glycolysis pathway (NOG), a previously reported pathway enabling complete carbon conservation, can increase the theoretical carbon yield from 67% to 89%, equivalent to the theoretical mass yield from 0.48g P3HB/g glucose to 0...
November 2017: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/28853155/a-dynamic-metabolic-flux-analysis-of-abe-acetone-butanol-ethanol-fermentation-by-clostridium-acetobutylicum-atcc-824-with-riboflavin-as-a-by-product
#19
Xinhe Zhao, Mayssa Kasbi, Jingkui Chen, Sabine Peres, Mario Jolicoeur
The present study reveals that supplementing sodium acetate (NaAc) strongly stimulates riboflavin production in acetone-butanol-ethanol (ABE) fermentation by Clostridium acetobutylicum ATCC 824 with xylose as carbon source. Riboflavin production increased from undetectable concentrations to ∼0.2 g L(-1) (0.53 mM) when supplementing 60 mM NaAc. Of interest, solvents production and biomass yield were also promoted with fivefold acetone, 2.6-fold butanol, and 2.4-fold biomass adding NaAc. A kinetic metabolic model, developed to simulate ABE biosystem, with riboflavin production, revealed from a dynamic metabolic flux analysis (dMFA) simultaneous increase of riboflavin (ribA) and GTP (precursor of riboflavin) (PurM) synthesis flux rates under NaAc supplementation...
August 29, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28852500/metabolic-profiling-of-triple-negative-breast-cancer-cells-reveals-metabolic-vulnerabilities
#20
Nathan J Lanning, Joshua P Castle, Simar J Singh, Andre N Leon, Elizabeth A Tovar, Amandeep Sanghera, Jeffrey P MacKeigan, Fabian V Filipp, Carrie R Graveel
BACKGROUND: Among breast cancers, the triple-negative breast cancer (TNBC) subtype has the worst prognosis with no approved targeted therapies and only standard chemotherapy as the backbone of systemic therapy. Unique metabolic changes in cancer progression provide innovative therapeutic opportunities. The receptor tyrosine kinases (RTKs) epidermal growth factor receptor (EGFR), and MET receptor are highly expressed in TNBC, making both promising therapeutic targets. RTK signaling profoundly alters cellular metabolism by increasing glucose consumption and subsequently diverting glucose carbon sources into metabolic pathways necessary to support the tumorigenesis...
2017: Cancer & Metabolism
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