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metabolic flux analysis

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https://www.readbyqxmd.com/read/29142823/investigation-of-useful-carbon-tracers-for-13-c-metabolic-flux-analysis-of-escherichia-coli-by-considering-five-experimentally-determined-flux-distributions
#1
Kousuke Maeda, Nobuyuki Okahashi, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu
The (13)C-MFA experiments require an optimal design since the precision or confidence intervals of the estimated flux levels depends on factors such as the composition of (13)C-labeled carbon sources, as well as the metabolic flux distribution of interest. In this study, useful compositions of (13)C-labeled glucose for (13)C-metabolic flux analysis ((13)C-MFA) of Escherichia coli are investigated using a computer simulation of the stable isotope labeling experiment. Following the generation of artificial mass spectra datasets of amino acid fragments using five literature-reported flux distributions of E...
December 2016: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29142819/liposomes-modified-with-cardiolipin-can-act-as-a-platform-to-regulate-the-potential-flux-of-nadp-dependent-isocitrate-dehydrogenase
#2
Keishi Suga, Akari Hamasaki, Junpei Chinzaka, Hiroshi Umakoshi
Cardiolipin (CL) is a phospholipid found in the outer mitochondrial membrane (OMM) and inner mitochondrial membrane (IMM) in animal cells. Isocitrate dehydrogenase (ICDH) is an important catalytic enzyme that is localized at the cytosol and mitochondria; the metabolic pathway catalyzed by ICDH differs between the OMM and IMM. To estimate the possible role of lipid membrane in the enzymatic activity of NADP(+)-dependent ICDH, CL-modified liposomes were prepared using CL/1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC)/cholesterol (Ch), and their characteristics were analyzed based on the fluorescent probe method...
December 2016: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29137184/cell-type-specific-metabolic-flux-analysis-a-challenge-for-metabolic-phenotyping-and-a-potential-solution-in-plants
#3
Merja T Rossi, Monika Kalde, Chaiyakorn Srisakvarakul, Nicholas J Kruger, R George Ratcliffe
Stable isotope labelling experiments are used routinely in metabolic flux analysis (MFA) to determine the metabolic phenotype of cells and tissues. A complication arises in multicellular systems because single cell measurements of transcriptomes, proteomes and metabolomes in multicellular organisms suggest that the metabolic phenotype will differ between cell types. In silico analysis of simulated metabolite isotopomer datasets shows that cellular heterogeneity confounds conventional MFA because labelling data averaged over multiple cell types does not necessarily yield averaged flux values...
November 13, 2017: Metabolites
https://www.readbyqxmd.com/read/29136931/understanding-regulation-in-substrate-dependent-modulation-of-growth-and-production-of-alcohols-in-clostridium-sporogenes-ncim-2918-through-metabolic-network-reconstruction-and-flux-balance-analysis
#4
Mehak Kaushal, K Venkata Narayana Chary, Saumya Ahlawat, Basavaraj Palabhanvi, Gargi Goswami, Debasish Das
Flux Balance Analysis was performed for Clostridium sporogenes NCIM 2918 grown on sole glucose and glycerol or glucose-glycerol combinations at varied concentrations. During acidogenesis, glucose and glucose-glycerol combinations favored improved growth and butyric acid production. Glycerol fermentation was however marked by reduced growth and predominant ethanol synthesis. Further, with increase of glycerol fraction in glucose-glycerol blend, flux towards ethanol synthesis linearly increased with simultaneous decrease in butanol flux...
November 1, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29134458/animal-cell-expression-systems
#5
M Butler, Ing U Reichl
The glycan profile of therapeutic recombinant proteins such as monoclonal antibodies is a critical quality attribute, which affects the efficacy of the final product. The cellular glycosylation process during protein expression is dependent upon a number of factors such as the availability of substrates in the media, the intracellular content of nucleotide sugars, and the enzyme repertoire of the host cells. In order to control the variability of glycosylation it is important to understand the critical process parameters and their acceptable range of values to enable reproducible production of proteins with a predetermined glycan profile providing the desired biological function or therapeutic effect...
October 3, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/29133820/early-postnatal-cardiomyocyte-proliferation-requires-high-oxidative-energy-metabolism
#6
Ana Elisa Teófilo Saturi de Carvalho, Vinícius Bassaneze, Maria Fernanda Forni, Aline Alfonso Keusseyan, Alicia Juliana Kowaltowski, José Eduardo Krieger
Cardiac energy metabolism must cope with early postnatal changes in tissue oxygen tensions, hemodynamics, and cell proliferation to sustain development. Here, we tested the hypothesis that proliferating neonatal cardiomyocytes are dependent on high oxidative energy metabolism. We show that energy-related gene expression does not correlate with functional oxidative measurements in the developing heart. Gene expression analysis suggests a gradual overall upregulation of oxidative-related genes and pathways, whereas functional assessment in both cardiac tissue and cultured cardiomyocytes indicated that oxidative metabolism decreases between the first and seventh days after birth...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29131522/when-do-two-stage-processes-outperform-one-stage-processes
#7
Steffen Klamt, Radhakrishnan Mahadevan, Oliver Hädicke
Apart from product yield and titer, volumetric productivity is a key performance indicator for many biotechnological processes. Due to the inherent trade-off between the production of biomass as catalyst and of the actual target product, yield and volumetric productivity cannot be optimized simultaneously. Therefore, in combination with genetic techniques for dynamic regulation of metabolic fluxes, two-stage fermentations (TSFs) with separated growth and production phase have recently gained much interest because of their potential to improve the productivity of bioprocesses while still allowing high product yields...
November 13, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/29120091/running-wheel-activity-delays-mitochondrial-respiratory-flux-decline-in-aging-mouse-muscle-via-a-post-transcriptional-mechanism
#8
Sarah Stolle, Jolita Ciapaite, Aaffien C Reijne, Alzbeta Talarovicova, Justina C Wolters, Raúl Aguirre-Gamboa, Pieter van der Vlies, Kim de Lange, Pieter B Neerincx, Gerben van der Vries, Patrick Deelen, Morris A Swertz, Yang Li, Rainer Bischoff, Hjalmar P Permentier, Peter L Horvatovitch, Albert K Groen, Gertjan van Dijk, Dirk-Jan Reijngoud, Barbara M Bakker
Loss of mitochondrial respiratory flux is a hallmark of skeletal muscle aging, contributing to a progressive decline of muscle strength. Endurance exercise alleviates the decrease in respiratory flux, both in humans and in rodents. Here, we dissect the underlying mechanism of mitochondrial flux decline by integrated analysis of the molecular network. Mice were given a lifelong ad libitum low-fat or high-fat sucrose diet and were further divided into sedentary and running-wheel groups. At 6, 12, 18 and 24 months, muscle weight, triglyceride content and mitochondrial respiratory flux were analysed...
November 9, 2017: Aging Cell
https://www.readbyqxmd.com/read/29117636/chlamydia-trachomatis-regulates-growth-and-development-in-response-to-host-cell-fatty-acid-availability-in-the-absence-of-lipid-droplets
#9
Manu Sharma, Maria A Recuero-Checa, Francis Yue Fan, Deborah Dean
Chlamydia trachomatis (Ct) is a Gram-negative obligate intracellular pathogen of humans that causes significant morbidity from sexually transmitted and ocular diseases globally. Ct acquires host fatty acids (FA) to meet the metabolic and growth requirements of the organism. Lipid droplets (LDs) are storehouses of FAs in host cells and have been proposed to be a source of FAs for the parasitophorous vacuole, termed inclusion, in which Ct replicates. Previously, cells devoid of LDs were shown to produce reduced infectious progeny at 24 hours post-infection (hpi)...
November 8, 2017: Cellular Microbiology
https://www.readbyqxmd.com/read/29113281/direct-effects-of-phenformin-on-metabolism-bioenergetics-and-viability-of-sh-sy5y-neuroblastoma-cells
#10
Fintan Geoghegan, Naomi Chadderton, G Jane Farrar, Daniela M Zisterer, Richard K Porter
Phenformin, a member of the biguanides class of drugs, has been reported to be efficacious in cancer treatment. The focus of the current study was to establish whether there were direct effects of phenformin on the metabolism and bioenergetics of neuroblastoma SH-SY5Y cancer cells. Cell viability was assessed using the alamar blue assay, flow cytometry analysis using propidium iodide and annexin V stain and poly (ADP-ribose) polymerase analysis. Cellular and mitochondrial oxygen consumption was determined using a Seahorse Bioscience Flux analyser and an Oroboros Oxygraph respirometer...
November 2017: Oncology Letters
https://www.readbyqxmd.com/read/29111682/monitoring-membrane-lipidome-turnover-by-metabolic-15-n-labeling-and-shotgun-ultra-high-resolution-orbitrap-ft-ms
#11
Kai Schuhmann, Kristina Srzentić, Konstantin O Nagornov, Henrik Thomas, Theresia Gutmann, Ünal Coskun, Yury O Tsybin, Andrej Shevchenko
Lipidomes undergo permanent extensive re-modelling, but how the turnover rate differs between lipid classes and molecular species is poorly understood. We employed metabolic (15)N-labeling and shotgun ultra-high resolution mass spectrometry (sUHR) to quantify the absolute (molar) abundance and determine the turnover rate of glycerophospho- and sphingolipids by the direct analysis of total lipid extracts. sUHR performed on a commercial Orbitrap Elite instrument at the mass resolution of 1.35×10(6) (m/z200) baseline resolved peaks of (13)C isotopes of unlabeled and monoisotopic peaks of (15)N-labeled lipids (Δm = 0...
November 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29108233/mitoketoscins-novel-mitochondrial-inhibitors-for-targeting-ketone-metabolism-in-cancer-stem-cells-cscs
#12
Bela Ozsvari, Federica Sotgia, Katie Simmons, Rachel Trowbridge, Richard Foster, Michael P Lisanti
Previous studies have now well-established that epithelial cancer cells can utilize ketone bodies (3-hydroxybutyrate and aceto-acetate) as mitochondrial fuels, to actively promote tumor growth and metastatic dissemination. The two critical metabolic enzymes implicated in this process are OXCT1 and ACAT1, which are both mitochondrial proteins. Importantly, over-expression of OXCT1 or ACAT1 in human breast cancer cells is sufficient to genetically drive tumorigenesis and/or lung metastasis, validating that they indeed behave as metabolic "tumor promoters"...
October 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/29093752/impairment-of-nadh-dehydrogenase-and-regulation-of-anaerobic-metabolism-by-the-small-rna-ryhb-and-nade-for-improved-biohydrogen-production-in-enterobacter-aerogenes
#13
Yan Wu, Yaqiao Hao, Xuan Wei, Qi Shen, Xuanwei Ding, Liyan Wang, Hongxin Zhao, Yuan Lu
Background: Enterobacter aerogenes is a facultative anaerobe and is one of the most widely studied bacterial strains because of its ability to use a variety of substrates, to produce hydrogen at a high rate, and its high growth rate during dark fermentation. However, the rate of hydrogen production has not been optimized. In this present study, three strategies to improve hydrogen production in E. aerogenes, namely the disruption of nuoCDE, overexpression of the small RNA RyhB and of NadE to regulate global anaerobic metabolism, and the redistribution of metabolic flux...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29090212/metabolism-of-citrate-and-other-carboxylic-acids-in-erythrocytes-as-a-function-of-oxygen-saturation-and-refrigerated-storage
#14
Travis Nemkov, Kaiqi Sun, Julie A Reisz, Tatsuro Yoshida, Andrew Dunham, Edward Y Wen, Alexander Q Wen, Rob C Roach, Kirk C Hansen, Yang Xia, Angelo D'Alessandro
State-of-the-art proteomics technologies have recently helped to elucidate the unanticipated complexity of red blood cell metabolism. One recent example is citrate metabolism, which is catalyzed by cytosolic isoforms of Krebs cycle enzymes that are present and active in mature erythrocytes and was determined using quantitative metabolic flux analysis. In previous studies, we reported significant increases in glycolytic fluxes in red blood cells exposed to hypoxia in vitro or in vivo, an observation relevant to transfusion medicine owing to the potential benefits associated with hypoxic storage of packed red blood cells...
2017: Frontiers in Medicine
https://www.readbyqxmd.com/read/29077809/linking-metabolic-network-features-to-phenotypes-using-sparse-group-lasso
#15
Satya Swarup Samal, Ovidiu Radulescu, Andreas Weber, Holger Fröhlich
Motivation: Integration of metabolic networks with '-omics' data has been a subject of recent research in order to better understand the behaviour of such networks with respect to differences between biological and clinical phenotypes. Under the conditions of steady state of the reaction network and the non-negativity of fluxes, metabolic networks can be algebraically decomposed into a set of sub-pathways often referred to as extreme currents (ECs). Our objective is to find the statistical association of such sub-pathways with given clinical outcomes, resulting in a particular instance of a self-contained gene set analysis method...
November 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29075622/autistic-siblings-with-novel-mutations-in-two-different-genes-insight-for-genetic-workups-of-autistic-siblings-and-connection-to-mitochondrial-dysfunction
#16
Barrett J Burger, Shannon Rose, Sirish C Bennuri, Pritmohinder S Gill, Marie L Tippett, Leanna Delhey, Stepan Melnyk, Richard E Frye
The prevalence of autism spectrum disorder (ASD) is high, yet the etiology of this disorder is still uncertain. Advancements in genetic analysis have provided the ability to identify potential genetic changes that may contribute to ASD. Interestingly, several genetic syndromes have been linked to metabolic dysfunction, suggesting an avenue for treatment. In this case study, we report siblings with ASD who had similar initial phenotypic presentations. Whole exome sequencing (WES) revealed a novel c.795delT mutation in the WDR45 gene affecting the girl, which was consistent with her eventual progression to a Rett-like syndrome phenotype including seizures along with a stereotypical cyclic breathing pattern...
2017: Frontiers in Pediatrics
https://www.readbyqxmd.com/read/29075313/rapid-in-situ-13-c-tracing-of-sucrose-utilization-in-arabidopsis-sink-and-source-leaves
#17
Frederik Dethloff, Isabel Orf, Joachim Kopka
BACKGROUND: Conventional metabolomics approaches face the problem of hidden metabolic phenotypes where only fluxes are altered but pool sizes stay constant. Metabolic flux experiments are used to detect such hidden flux phenotypes. These experiments are, however, time consuming, may be cost intensive, and involve specialists for modeling. We fill the gap between conventional metabolomics and flux modeling. We present rapid stable isotope tracing assays and analysis strategies of (13)C labeling data...
2017: Plant Methods
https://www.readbyqxmd.com/read/29075252/carbon-allocation-in-rhodococcus-jostii-rha1-in-response-to-disruption-and-overexpression-of-nlpr-regulatory-gene-based-on-13-c-labeling-analysis
#18
Martín A Hernández, Gerd Gleixner, Dirk Sachse, Héctor M Alvarez
Nitrogen lipid regulator (NlpR) is a pleiotropic regulator that positively controls genes associated with both nitrogen and lipid metabolism in the oleaginous bacterium Rhodococcus jostii RHA1. In this study, we investigated the effect of nlpR disruption and overexpression on the assimilation of (13)C-labeled glucose as carbon source, during cultivation of cells under nitrogen-limiting and nitrogen-rich conditions, respectively. Label incorporation into the total lipid extract (TLE) fraction was about 30% lower in the mutant strain in comparison with the wild type strain under low-nitrogen conditions...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29074620/the-natural-product-mensacarcin-induces-mitochondrial-toxicity-and-apoptosis-in-melanoma-cells
#19
Birte Plitzko, Elizabeth N Kaweesa, Sandra Loesgen
Mensacarcin is a highly oxygenated polyketide that was first isolated from soil-dwelling Streptomyces bacteria. It exhibits potent cytostatic properties (GI50: 0.2 μM) in almost all cell lines of the National Cancer Institute (NCI)-60 cell line screen and relatively selective cytotoxicity against melanoma cells. Moreover, its low COMPARE correlations with known standard antitumor agents indicate a unique mechanism of action. Effective therapies for managing melanoma are limited, so we sought to investigate mensacarcin's unique cytostatic and cytotoxic effects and its mode of action...
October 26, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29069611/metabolic-modeling-helps-interpret-transcriptomic-changes-during-malaria
#20
Yan Tang, Anuj Gupta, Swetha Garimalla, Mary R Galinski, Mark P Styczynski, Luis L Fonseca, Eberhard O Voit
Disease represents a specific case of malfunctioning within a complex system. Whereas it is often feasible to observe and possibly treat the symptoms of a disease, it is much more challenging to identify and characterize its molecular root causes. Even in infectious diseases that are caused by a known parasite, it is often impossible to pinpoint exactly which molecular profiles of components or processes are directly or indirectly altered. However, a deep understanding of such profiles is a prerequisite for rational, efficacious treatments...
October 22, 2017: Biochimica et Biophysica Acta
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