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metabolic flux analysis

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https://www.readbyqxmd.com/read/28820904/parametric-studies-of-metabolic-cooperativity-in-escherichia-coli-colonies-strain-and-geometric-confinement-effects
#1
Joseph R Peterson, John A Cole, Zaida Luthey-Schulten
Characterizing the complex spatial and temporal interactions among cells in a biological system (i.e. bacterial colony, microbiome, tissue, etc.) remains a challenge. Metabolic cooperativity in these systems can arise due to the subtle interplay between microenvironmental conditions and the cells' regulatory machinery, often involving cascades of intra- and extracellular signalling molecules. In the simplest of cases, as demonstrated in a recent study of the model organism Escherichia coli, metabolic cross-feeding can arise in monoclonal colonies of bacteria driven merely by spatial heterogeneity in the availability of growth substrates; namely, acetate, glucose and oxygen...
2017: PloS One
https://www.readbyqxmd.com/read/28817667/glycoprotein-ib-activation-by-thrombin-stimulates-the-energy-metabolism-in-human-platelets
#2
Norma Corona de la Peña, Manuel Gutiérrez-Aguilar, Ileana Hernández-Reséndiz, Álvaro Marín-Hernández, Sara Rodríguez-Enríquez
Thrombin-induced platelet activation requires substantial amounts of ATP. However, the specific contribution of each ATP-generating pathway i.e., oxidative phosphorylation (OxPhos) versus glycolysis and the biochemical mechanisms involved in the thrombin-induced activation of energy metabolism remain unclear. Here we report an integral analysis on the role of both energy pathways in human platelets activated by several agonists, and the signal transducing mechanisms associated with such activation. We found that thrombin, Trap-6, arachidonic acid, collagen, A23187, epinephrine and ADP significantly increased glycolytic flux (3-38 times vs...
2017: PloS One
https://www.readbyqxmd.com/read/28815517/autophagy-in-adipocyte-differentiation
#3
Zhipeng Tao, Longhua Liu, Louise D Zheng, Zhiyong Cheng
Adipose tissue regulates metabolic homeostasis by acting as an endocrine organ and energy reservoir. Adipose tissue development and functional maintenance are dependent on adipocyte differentiation, in which autophagy plays an important role. It has been shown that autophagy deficiency dampens adipocyte differentiation, compromises adipose tissue development, dysregulates adipocytokine secretion, and even causes sudden death in young animals. Therefore, accurate assessment of autophagy in adipocyte is critical for the study of adipose biology or pathology of metabolic diseases...
August 17, 2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28811563/crosstalk-between-diurnal-rhythm-and-water-stress-reveals-an-altered-primary-carbon-flux-into-soluble-sugars-in-drought-treated-rice-leaves
#4
Seo-Woo Kim, Sang-Kyu Lee, Hee-Jeong Jeong, Gynheung An, Jong-Seong Jeon, Ki-Hong Jung
Plants retain rhythmic physiological responses when adapting to environmental challenges. However, possible integrations between drought conditions and those responses have not received much focus, especially regarding crop plants, and the relationship between abiotic stress and the diurnal cycle is generally not considered. Therefore, we conducted a genome-wide analysis to identify genes showing both diurnal regulation and water-deficiency response in rice (Oryza sativa). Among the 712 drought-responsive genes primary identified, 56...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811322/analysis-of-sphingolipids-sterols-and-phospholipids-in-human-pathogenic-cryptococcus-strains
#5
Ashutosh Singh, Andrew MacKenzie, Geoffrey Girnun, Maurizio Del Poeta
Cryptococcus species cause invasive infections in humans. Lipids play an important role in the progression of these infections. Independent studies done by our group and others provide some detail about the functions of these lipids in Cryptococcus infections. However, pathways of biosynthesis and metabolism of these lipids are not completely understood. To thoroughly understand the physiological role of these Cryptococcus lipids, a proper structure and composition analyses of Cryptococcus lipids is demanded...
August 15, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/28808255/critical-role-for-arginase-2-in-obesity-associated-pancreatic-cancer
#6
Tamara Zaytouni, Pei-Yun Tsai, Daniel S Hitchcock, Cory D DuBois, Elizaveta Freinkman, Lin Lin, Vicente Morales-Oyarvide, Patrick J Lenehan, Brian M Wolpin, Mari Mino-Kenudson, Eduardo M Torres, Nicholas Stylopoulos, Clary B Clish, Nada Y Kalaany
Obesity is an established risk factor for pancreatic ductal adenocarcinoma (PDA). Despite recent identification of metabolic alterations in this lethal malignancy, the metabolic dependencies of obesity-associated PDA remain unknown. Here we show that obesity-driven PDA exhibits accelerated growth and a striking transcriptional enrichment for pathways regulating nitrogen metabolism. We find that the mitochondrial form of arginase (ARG2), which hydrolyzes arginine into ornithine and urea, is induced upon obesity, and silencing or loss of ARG2 markedly suppresses PDA...
August 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28805729/systems-biology-approach-to-bioremediation-of-nitroaromatics-constraint-based-analysis-of-2-4-6-trinitrotoluene-biotransformation-by-escherichia-coli
#7
Maryam Iman, Tabassom Sobati, Yunes Panahi, Meysam Mobasheri
Microbial remediation of nitroaromatic compounds (NACs) is a promising environmentally friendly and cost-effective approach to the removal of these life-threating agents. Escherichia coli (E. coli) has shown remarkable capability for the biotransformation of 2,4,6-trinitro-toluene (TNT). Efforts to develop E. coli as an efficient TNT degrading biocatalyst will benefit from holistic flux-level description of interactions between multiple TNT transforming pathways operating in the strain. To gain such an insight, we extended the genome-scale constraint-based model of E...
August 14, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28805306/bioprocess-scale-up-down-as-integrative-enabling-technology-from-fluid-mechanics-to-systems-biology-and-beyond
#8
Frank Delvigne, Ralf Takors, Rob Mudde, Walter van Gulik, Henk Noorman
Efficient optimization of microbial processes is a critical issue for achieving a number of sustainable development goals, considering the impact of microbial biotechnology in agrofood, environment, biopharmaceutical and chemical industries. Many of these applications require scale-up after proof of concept. However, the behaviour of microbial systems remains unpredictable (at least partially) when shifting from laboratory-scale to industrial conditions. The need for robust microbial systems is thus highly needed in this context, as well as a better understanding of the interactions between fluid mechanics and cell physiology...
August 14, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28801717/vitamin-b6-is-essential-for-serine-de-novo-biosynthesis
#9
Rúben J Ramos, Mia L Pras-Raves, Johan Gerrits, Maria van der Ham, Marcel Willemsen, Hubertus Prinsen, Boudewijn Burgering, Judith J Jans, Nanda M Verhoeven-Duif
Pyridoxal 5'-phosphate (PLP), the metabolically active form of vitamin B6, plays an essential role in brain metabolism as a cofactor in numerous enzyme reactions. PLP deficiency in brain, either genetic or acquired, results in severe drug-resistant seizures that respond to vitamin B6 supplementation. The pathogenesis of vitamin B6 deficiency is largely unknown. To shed more light on the metabolic consequences of vitamin B6 deficiency in brain, we performed untargeted metabolomics in vitamin B6-deprived Neuro-2a cells...
August 11, 2017: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/28798305/revealing-extracellular-electron-transfer-mediated-parasitism-energetic-considerations
#10
Roman Moscoviz, Clément Flayac, Elie Desmond-Le Quéméner, Eric Trably, Nicolas Bernet
Extracellular electron transfer (EET) is a mechanism that allows energetic coupling between two microorganisms or between a microorganism and an electrode surface. EET is either supported by direct physical contacts or mediated by electron shuttles. So far, studies dealing with interspecies EET (so-called IET) have mainly focused on possible syntrophic interactions between microorganisms favoured by this mechanism. In this article, the case of fermentative bacteria receiving extracellular electrons while fermenting a substrate is considered...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28796780/transcriptome-and-proteome-analysis-of-salmonella-enterica-serovar-typhimurium-systemic-infection-of-wild-type-and-immune-deficient-mice
#11
Olusegun Oshota, Max Conway, Maria Fookes, Fernanda Schreiber, Roy R Chaudhuri, Lu Yu, Fiona J E Morgan, Simon Clare, Jyoti Choudhary, Nicholas R Thomson, Pietro Lio, Duncan J Maskell, Pietro Mastroeni, Andrew J Grant
Salmonella enterica are a threat to public health. Current vaccines are not fully effective. The ability to grow in infected tissues within phagocytes is required for S. enterica virulence in systemic disease. As the infection progresses the bacteria are exposed to a complex host immune response. Consequently, in order to continue growing in the tissues, S. enterica requires the coordinated regulation of fitness genes. Bacterial gene regulation has so far been investigated largely using exposure to artificial environmental conditions or to in vitro cultured cells, and little information is available on how S...
2017: PloS One
https://www.readbyqxmd.com/read/28795660/systems-and-synthetic-biology-perspective-of-the-versatile-plant-pathogenic-and-polysaccharide-producing-bacterium-xanthomonas-campestris
#12
Sarah Schatschneider, Jessica Schneider, Jochen Blom, Fabien Létisse, Karsten Niehaus, Alexander Goesmann, Frank-Jörg Vorhölter
Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features...
August 10, 2017: Microbiology
https://www.readbyqxmd.com/read/28791562/production-of-fumaric-acid-by-bioconversion-of-corncob-hydrolytes-using-an-improved-rhizopus-oryzae-strain
#13
Xuefeng Wu, Qing Liu, Yongdong Deng, Xiaoju Chen, Zhi Zheng, Shaotong Jiang, Xingjiang Li
The use of microorganism fermentation for production of fumaric acid (FA), which is widely used in food, medicine, and other fields, can provide technical support for the FA industry. In this study, we aimed to increase the titer of FA production by using an improved Rhizopus oryzae WHT5, which was domesticated to obtain a furfural-resistant strain in corncob hydrolytes. The metabolic pathways and metabolic network of this strain were investigated, and the related enzymes and metabolic flux were analyzed. Metabolic pathway analysis showed that the R...
August 8, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28777381/mixotrophy-drives-niche-expansion-of-verrucomicrobial-methanotrophs
#14
Carlo R Carere, Kiel Hards, Karen M Houghton, Jean F Power, Ben McDonald, Christophe Collet, Daniel J Gapes, Richard Sparling, Eric S Boyd, Gregory M Cook, Chris Greening, Matthew B Stott
Aerobic methanotrophic bacteria have evolved a specialist lifestyle dependent on consumption of methane and other short-chain carbon compounds. However, their apparent substrate specialism runs contrary to the high relative abundance of these microorganisms in dynamic environments, where the availability of methane and oxygen fluctuates. In this work, we provide in situ and ex situ evidence that verrucomicrobial methanotrophs are mixotrophs. Verrucomicrobia-dominated soil communities from an acidic geothermal field in Rotokawa, New Zealand rapidly oxidised methane and hydrogen simultaneously...
August 4, 2017: ISME Journal
https://www.readbyqxmd.com/read/28768294/measurement-of-metabolic-fluxes-using-stable-isotope-tracers-in-whole-animals-and-human-patients
#15
Julie A Reisz, Angelo D'Alessandro
PURPOSE OF REVIEW: Metabolic flux analysis using stable isotope labeled substrates allows for the tracing of carbon, nitrogen, and hydrogen atoms through metabolic pathways and is an invaluable tool for investigating dynamic metabolic changes occurring in health and disease. Studies of flux analysis in vivo are more technically challenging than in vitro or ex vivo but provide a highly detailed view of organ and/or systemic metabolism. We review here recent efforts in studies of diet and nutrition, non-small cell lung cancer, ischemia/reperfusion injury, and hemorrhagic shock where in vivo flux analysis was utilized to analyze metabolic modulation...
September 2017: Current Opinion in Clinical Nutrition and Metabolic Care
https://www.readbyqxmd.com/read/28767679/compartmentalized-metabolic-network-reconstruction-of-microbial-communities-to-determine-the-effect-of-agricultural-intervention-on-soils
#16
María Camila Alvarez-Silva, Astrid Catalina Álvarez-Yela, Fabio Gómez-Cano, María Mercedes Zambrano, Johana Husserl, Giovanna Danies, Silvia Restrepo, Andrés Fernando González-Barrios
Soil microbial communities are responsible for a wide range of ecological processes and have an important economic impact in agriculture. Determining the metabolic processes performed by microbial communities is crucial for understanding and managing ecosystem properties. Metagenomic approaches allow the elucidation of the main metabolic processes that determine the performance of microbial communities under different environmental conditions and perturbations. Here we present the first compartmentalized metabolic reconstruction at a metagenomics scale of a microbial ecosystem...
2017: PloS One
https://www.readbyqxmd.com/read/28762754/flow-responsive-vegfr-pkc%C3%A9-signaling-mediates-glycolytic-metabolites-for-vascular-repair
#17
Kyung In Baek, Rongsong Li, Nelson Jen, Howard Choi, Amir Kaboodrangi, Peipei Ping, David Liem, Tyler Beebe, Tzung K Hsiai
Aims - Hemodynamic shear stress participates in maintaining vascular redox status. Elucidating flow-mediated endothelial metabolites enables us to discover metabolic biomarkers and therapeutic targets. We posited that flow-responsive VEGF receptor-PKCɛ-PFKFB3 signaling modulates glycolytic metabolites for vascular repair. Results - Bidirectional oscillatory flow (OSS: 0.1 ± 3 dyne·cm<sup>-2</sup> at 1 Hz) up-regulated VEGFR-dependent PKCɛ expression to a greater degree than did unidirectional pulsatile flow (PSS: 23 ± 8 dyne·cm<sup>-2</sup> at 1 Hz) in human aortic endothelial cells (HAEC) (<i>p < 0...
August 1, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28760827/copper-homeostasis-networks-in-the-bacterium-pseudomonas-aeruginosa
#18
Julia Quintana, Lorena Novoa-Aponte, José M Argüello
Bacterial copper (Cu(+)) homeostasis enables both precise metallation of diverse cuproproteins and control of variable metal levels. To this end, protein networks mobilize Cu(+) to cellular targets with remarkable specificity. However, the understanding of these processes is rather fragmented. Here, we use genome-wide transcriptomic analysis by RNA-Seq to characterize the response of Pseudomonas aeruginosa to external 0.5 mM CuSO4, a condition that did not generate pleiotropic effects. Pre-steady (5 min) and steady state (2 h) Cu(+) fluxes, resulted in distinct transcriptome landscapes...
July 31, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28755490/metabolic-engineering-of-isopropyl-alcohol-producing-escherichia-coli-strains-with-13-c-metabolic-flux-analysis
#19
Nobuyuki Okahashi, Fumio Matsuda, Katsunori Yoshikawa, Tomokazu Shirai, Yoshiko Matsumoto, Mitsufumi Wada, Hiroshi Shimizu
Metabolic engineering of isopropyl alcohol (IPA)-producing E. coli strains was conducted along with (13) C-metabolic flux analysis (MFA). A metabolically engineered E. coli strain expressing the adc gene derived from Clostridium acetobutylicum and the IPADH gene from C. beijerinckii did not produce IPA during its exponential growth phase in the aerobic batch culture. (13) C-MFA was carried out, and revealed a deficiency in NADPH regeneration for IPA production in growth phase. Based on these findings, we used nitrogen-starved culture conditions to reduce NADPH consumption for biomass synthesis...
July 29, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28748469/protocols-and-applications-of-cellular-metabolomics-in-safety-studies-using-precision-cut-tissue-slices-and-carbon-13-nmr
#20
Gabriel Baverel, Maha El Hage, Guy Martin
Numerous xenobiotics are toxic to human and animal cells by interacting with their metabolism, but the precise metabolic step affected and the biochemical mechanism behind such a toxicity remain often unknown. In an attempt to reduce the ignorance in this field, we have developed a new approach called cellular metabolomics. This approach, developed in vitro, provides a panoramic view not only of the pathways involved in the metabolism of physiological substrates of any normal or pathological human or animal cell but also of the beneficial and adverse effects of xenobiotics on these metabolic pathways...
2017: Methods in Molecular Biology
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