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metabolic flux analysis

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https://www.readbyqxmd.com/read/29774488/the-effect-of-oxygen-in-sirt3-mediated-myocardial-protection-a-proof-of-concept-study-in-cultured-cardiomyoblasts
#1
Philipp Diehl, Daniel S Gaul, Jonas Sogl, Ulrike Flierl, Darren Henstridge, Juergen Pahla, Heiko Bugger, Maximilian Y Emmert, Frank Ruschitzka, Christoph Bode, Thomas F Lüscher, Martin Moser, Christian M Matter, Karlheinz Peter, Stephan Winnik
Sirtuin 3 is a nicotinamide adenine dinucleotide dependent mitochondrial deacetylase that governs mitochondrial metabolism and oxidative defense. The demise in myocardial function following myocardial ischemia has been associated with mitochondrial dysfunction. Sirt3 maintains myocardial contractile function and protects from cardiac hypertrophy. The role of Sirt3 in ischemia is controversial. Our objective was to understand, under what circumstances Sirt3 is protective in different facets of ischemia, using an in vitro proof-of-concept approach based on simulated ischemia in cultured cardiomyoblasts...
May 17, 2018: Journal of Thrombosis and Thrombolysis
https://www.readbyqxmd.com/read/29774023/ferritin-h-deficiency-in-myeloid-compartments-dysregulates-host-energy-metabolism-and-increases-susceptibility-to-mycobacterium-tuberculosis-infection
#2
Vineel P Reddy, Krishna C Chinta, Vikram Saini, Joel N Glasgow, Travis D Hull, Amie Traylor, Fernanda Rey-Stolle, Miguel P Soares, Rajhmun Madansein, Md Aejazur Rahman, Coral Barbas, Kievershen Nargan, Threnesan Naidoo, Pratistadevi K Ramdial, James F George, Anupam Agarwal, Adrie J C Steyn
Iron is an essential factor for the growth and virulence of Mycobacterium tuberculosis ( Mtb) . However, little is known about the mechanisms by which the host controls iron availability during infection. Since ferritin heavy chain (FtH) is a major intracellular source of reserve iron in the host, we hypothesized that the lack of FtH would cause dysregulated iron homeostasis to exacerbate TB disease. Therefore, we used knockout mice lacking FtH in myeloid-derived cell populations to study Mtb disease progression...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29764852/combined-hdac-and-bromodomain-protein-inhibition-reprograms-tumor-cell-metabolism-and-elicits-synthetic-lethality-in-glioblastoma
#3
Yiru Zhang, Chiaki Tsuge Ishida, Wataru Ishida, Sheng-Fu L Lo, Junfei Zhao, Chang Shu, Elena Bianchetti, Giulio Kleiner, Maria Sanchez-Quintero, Catarina M Quinzii, Mike-Andrew Westhoff, Georg Karpel-Massler, Peter Canoll, Markus D Siegelin
PURPOSE: Glioblastoma remain a challenge in oncology in part due to tumor heterogeneity. EXPERIMENTAL DESIGN: Patient-derived xenograft and stem-like glioblastoma cells were used as the primary model systems. RESULTS: Based on a transcriptome and subsequent gene set enrichment analysis (GSEA), we show by using clinically validated compounds that combined histone deacetylase (HDAC) inhibition and Bromodomain protein (BRD) inhibition results in pronounced synergistic reduction in cellular viability in patient-derived xenograft and stem-like glioblastoma cells...
May 15, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29763898/fgfr4-links-glucose-metabolism-and-chemotherapy-resistance-in-breast-cancer
#4
Min Xu, Shuzheng Chen, Weibin Yang, Xue Cheng, Yani Ye, Jianting Mao, Xulu Wu, Li Huang, Jiansong Ji
BACKGROUND/AIMS: Poor response to chemotherapy leads to the relapse and metastatic progression of tumors. Reprogrammed glucose metabolism is one of the important hallmarks of cancer that facilitates cancer cell survival, proliferation and chemoresistance. However, the precise fate of glucose metabolism and its role in therapy responsiveness in cancers remains largely unexplored. METHODS: The glycolytic phenotype of doxorubicin (ADR)-resistant breast cancer cells and their parental cells was assessed by measuring glucose uptake, lactate release, and extracellular acidification rate (ECAR)...
May 10, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29761433/quantification-of-soluble-sugars-and-sugar-alcohols-by-lc-ms-ms
#5
Regina Feil, John Edward Lunn
Sugars are simple carbohydrates composed primarily of carbon, hydrogen, and oxygen. They play a central role in metabolism as sources of energy and as building blocks for synthesis of structural and nonstructural polymers. Many different techniques have been used to measure sugars, including refractometry, colorimetric and enzymatic assays, gas chromatography, high-performance liquid chromatography, and nuclear magnetic resonance spectroscopy. In this chapter we describe a method that combines an initial separation of sugars by high-performance anion-exchange chromatography (HPAEC) with detection and quantification by tandem mass spectrometry (MS/MS)...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29761431/carbon-atomic-survey-for-identification-of-selected-metabolic-fluxes
#6
Leonardo Perez de Souza, Alisdair R Fernie, Takayuki Tohge
Stable-isotope-labeling experiments have become a frequently used tool to investigate different metabolic systems. They have been recently applied to several comprehensive studies in plant metabolomics providing interesting insights into metabolic dynamics and regulation. However, the complexity of mass spectrometry data originating from such experiments is rarely fully explored. Data analysis often considers metabolites in their entirety which obscures important information at the atomic level. Recently, the use of mass spectrometry fragmentation for obtaining positional-labeling information was described for a few specific metabolites...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29761430/gas-chromatography-mass-spectrometry-based-13-c-labeling-studies-in-plant-metabolomics
#7
Valéria F Lima, Leonardo Perez de Souza, Thomas C R Williams, Alisdair R Fernie, Danilo M Daloso
Stable-isotope labeling analysis has been used to discover new metabolic pathways and their key regulatory points in a wide range of organisms. Given the complexity of the plant metabolic network, this analysis provides information complementary to that obtained from metabolite profiling that can be used to understand how plants cope with adverse conditions, and how metabolism varies between different cells, tissues, and organs. Here we describe the experimental procedures from sample harvesting and extraction to mass spectral analysis and interpretation that allow the researcher to perform 13 C-labeling experiments...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29760217/temporal-manipulation-of-mitochondrial-function-by-virulent-francisella-tularensis-to-limit-inflammation-and-control-cell-death
#8
Forrest Jessop, Benjamin Schwarz, Emily Heitmann, Robert Buntyn, Tara Wehrly, Catharine M Bosio
Francisella tularensis ssp tularensis (Ftt) is a highly pathogenic intracellular bacterium that suppresses host inflammation by impairing the metabolic shift from oxidative phosphorylation to glycolysis. Decreased mitochondrial metabolism is central to initiating a metabolic shift to glycolysis and regulating inflammation, but Ftt manipulation of host mitochondrial function has not been explored. We demonstrate using extracellular flux analysis that Ftt infection initially improves host macrophage mitochondrial bioenergetics in a capsule dependent manner...
May 14, 2018: Infection and Immunity
https://www.readbyqxmd.com/read/29746779/energy-metabolism-drugs-block-triple-negative-breast-metastatic-cancer-cell-phenotype
#9
Silvia Cecilia Pacheco-Velazquez, Diana Xochiquetzal Robledo-Cadena, Ileana Hernández-Reséndiz, Juan Carlos Gallardo-Pérez, Rafael Moreno-Sánchez, Sara Rodríguez-Enríquez
To establish alternative targeted therapies against triple negative (TN) breast cancer, (1) the energy metabolism and (2) the sensitivity of cell growth, migration and invasiveness towards metabolic, canonical and NSAID inhibitors was analyzed in MDA-MB-231 and MDA-MB-468, two TN metastatic breast cancer cell lines, under both normoxia (21% O2) and hypoxia (0.1% O2). For comparative purposes, analysis was also carried out in the less-metastatic breast MCF-7 cancer cells. Under normoxia, oxidative phosphorylation (OxPhos) was significantly higher (2-times) in MDA-MB-468 than in MDA-MB-231 and MCF-7 whereas their glycolytic fluxes and OxPhos and glycolytic protein contents were all similar...
May 10, 2018: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/29744293/comparative-metabolomics-and-glycolysis-enzyme-profiling-of-embryogenic-and-nonembryogenic-grape-cells
#10
Jonathan Parrilla, Cécile Gaillard, Jérémy Verbeke, Mickaël Maucourt, Radoslav A Aleksandrov, Florence Thibault, Pierrette Fleurat-Lessard, Yves Gibon, Dominique Rolin, Rossitza Atanassova
A novel biological model was created for the comparison of grapevine embryogenic cells (EC) and nonembryogenic cells (NEC) sharing a common genetic background but distinct phenotypes, when cultured on their respective most appropriate media. Cytological characterization, 1 H-NMR analysis of intracellular metabolites, and glycolytic enzyme activities provided evidence for the marked metabolic differences between EC and NEC. The EC were characterized by a moderate and organized cell proliferation, coupled with a low flux through glycolysis, high capacity of phosphoenolpyruvate carboxylase and glucokinase, and high oxygen consumption...
May 2018: FEBS Open Bio
https://www.readbyqxmd.com/read/29743557/inhibition-of-bcl-2-bcl-xl-and-c-met-causes-synthetic-lethality-in-model-systems-of-glioblastoma
#11
Yiru Zhang, Chiaki Tsuge Ishida, Chang Shu, Giulio Kleiner, Maria J Sanchez-Quintero, Elena Bianchetti, Catarina M Quinzii, Mike-Andrew Westhoff, Georg Karpel-Massler, Markus D Siegelin
Recent data suggest that glioblastomas (GBM) activate the c-MET signaling pathway and display increased levels in anti-apoptotic Bcl-2 family members. Therefore, targeting these two deregulated pathways for therapy might yield synergistic treatment responses. We applied extracellular flux analysis to assess tumor metabolism. We found that combined treatment with ABT263 and Crizotinib synergistically reduces the proliferation of glioblastoma cells, which was dependent on dual inhibition of Bcl-2 and Bcl-xL. The combination treatment led to enhanced apoptosis with loss of mitochondrial membrane potential and activation of caspases...
May 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29743275/thermodynamic-constraints-for-identifying-elementary-flux-modes
#12
REVIEW
Sabine Peres, Stefan Schuster, Philippe Dague
Metabolic pathway analysis is a key method to study metabolism and the elementary flux modes (EFMs) is one major concept allowing one to analyze the network in terms of minimal pathways. Their practical use has been hampered by the combinatorial explosion of their number in large systems. The EFMs give the possible pathways at steady state, but the real pathways are limited by biological constraints. In this review, we display three different methods that integrate thermodynamic constraints in terms of Gibbs free energy in the EFMs computation...
May 9, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29740742/prospects-for-engineering-dynamic-crispr-cas-transcriptional-circuits-to-improve-bioproduction
#13
REVIEW
Jason Fontana, William E Voje, Jesse G Zalatan, James M Carothers
Dynamic control of gene expression is emerging as an important strategy for controlling flux in metabolic pathways and improving bioproduction of valuable compounds. Integrating dynamic genetic control tools with CRISPR-Cas transcriptional regulation could significantly improve our ability to fine-tune the expression of multiple endogenous and heterologous genes according to the state of the cell. In this mini-review, we combine an analysis of recent literature with examples from our own work to discuss the prospects and challenges of developing dynamically regulated CRISPR-Cas transcriptional control systems for applications in synthetic biology and metabolic engineering...
May 8, 2018: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/29739849/a-novel-inhibitor-of-pyruvate-dehydrogenase-kinase-stimulates-myocardial-carbohydrate-oxidation-in-diet-induced-obesity
#14
Cheng-Yang Wu, Santhosh Satapati, Wenjun Gui, Richard M Wynn, Gaurav Sharma, Mingliang Lou, Xiangbing Qi, Shawn C Burgess, Craig Malloy, Chalermchai Khemtong, A Dean Sherry, David Chuang, Matthew E Merritt
The pyruvate dehydrogenase complex (PDC) is a key control point of energy metabolism and is subject to regulation by multiple mechanisms, including post-translational phosphorylation by pyruvate dehydrogenase kinase (PDK). Pharmacological modulation of PDC activity could provide a new treatment for diabetic cardiomyopathy, as dysregulated substrate selection is concomitant with decreased heart function. Dichloroacetate (DCA), a classic PDK inhibitor, has been used to treat diabetic cardiomyopathy, but the lack of specificity and side effects of DCA indicate a more specific inhibitor of PDK is needed...
May 8, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29736347/fluxpyt-a-python-based-free-and-open-source-software-for-13-c-metabolic-flux-analyses
#15
Trunil S Desai, Shireesh Srivastava
13 C-Metabolic flux analysis (MFA) is a powerful approach to estimate intracellular reaction rates which could be used in strain analysis and design. Processing and analysis of labeling data for calculation of fluxes and associated statistics is an essential part of MFA. However, various software currently available for data analysis employ proprietary platforms and thus limit accessibility. We developed FluxPyt, a Python-based truly open-source software package for conducting stationary 13 C-MFA data analysis...
2018: PeerJ
https://www.readbyqxmd.com/read/29735428/assessing-flux-distribution-associated-with-metabolic-specialization-of-glandular-trichomes
#16
REVIEW
Jordan J Zager, B Markus Lange
Many aromatic plants accumulate mixtures of secondary (or specialized) metabolites in anatomical structures called glandular trichomes (GTs). Different GT types may also synthesize different mixtures of secreted metabolites, and this contributes to the enormous chemical diversity reported to occur across species. Over the past two decades, significant progress has been made in characterizing the genes and enzymes that are responsible for the unique metabolic capabilities of GTs in different lineages of flowering plants...
May 4, 2018: Trends in Plant Science
https://www.readbyqxmd.com/read/29729318/bioethanol-production-by-a-xylan-fermenting-thermophilic-isolate-clostridium-strain-dbt-ioc-dc21
#17
Nisha Singh, Munish Puri, Deepak K Tuli, Ravi P Gupta, Colin J Barrow, Anshu S Mathur
To overcome the challenges associated with combined bioprocessing of lignocellulosic biomass to biofuel, finding good organisms is essential. An ethanol producing bacteria DBT-IOC-DC21 was isolated from a compost site via preliminary enrichment culture on a pure hemicellulosic substrate and identified as a Clostridium strain by 16S rRNA analysis. This strain presented broad substrate spectrum with ethanol, acetate, lactate, and hydrogen as the primary metabolic end products. The optimum conditions for ethanol production were found to be an initial pH of 7...
May 2, 2018: Anaerobe
https://www.readbyqxmd.com/read/29723850/the-favored-mechanism-for-coping-with-acute-cold-stress-upregulation-of-mir-210-in-rats
#18
Wenjin Guo, Shuai Lian, Li Zhen, Shucheng Zang, Yan Chen, Limin Lang, Bin Xu, Jingru Guo, Hong Ji, Jianfa Wang, Shoupeng Fu, Liping Zhang, Huanmin Yang
BACKGROUND/AIMS: The main aim of this study was to determine the mechanisms by which rno-miR-210-3p affects changes in gene expression, metabolism, apoptosis and proliferation of cells under acute cold stress (ACS) conditions. METHODS: The treatment group (n=6, weight 340±20 g) was exposed to ACS (temperature 4±0.5°C, relative humidity 45±0.5%) and the control group (n=6, weight 340±20 g) to normal temperature (NT) (temperature 24±0.5°C, relative humidity 45±0...
April 28, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29722541/overexpression-of-malonyl-coa-acp-transacylase-in-schizochytrium-sp-to-improve-polyunsaturated-fatty-acids-production
#19
Zhipeng Li, Tong Meng, Xue-Ping Ling, Jun Li, Chuqiang Zheng, Yanyan Shi, Zhen Chen, Zhenqi Li, Qingbiao Li, Yinghua Lu, Ning He
Polyunsaturated fatty acids (PUFAs) have been widely applied in food and medical industry. In this study, malonyl-CoA: Acp transacylase was overexpressed through homologous recombination to improve PUFAs production in Schizochytrium. The results showed that the lipids and PUFAs concentration were increased by 10.1 and 24.5% with MAT overexpression, respectively. Metabolomics analysis revealed that the intracellular tricarboxylic acid cycle was weakened and glucose absorption was accelerated in the engineered strain...
May 3, 2018: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29721328/high-throughput-measurement-of-metabolism-in-planarians-reveals-activation-of-glycolysis-during-regeneration
#20
Edie A Osuma, Daniel W Riggs, Andrew A Gibb, Bradford G Hill
Planarians are outstanding models for studying mechanisms of regeneration; however, there are few methods to measure changes in their metabolism. Examining metabolism in planarians is important because the regenerative process is dependent on numerous integrated metabolic pathways, which provide the energy required for tissue repair as well as the ability to synthesize the cellular building blocks needed to form new tissue. Therefore, we standardized an extracellular flux analysis method to measure mitochondrial and glycolytic activity in live planarians during normal growth as well as during regeneration...
March 2018: Regeneration
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