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https://www.readbyqxmd.com/read/29149845/early-nutritional-programming-affects-liver-transcriptome-in-diploid-and-triploid-atlantic-salmon-salmo-salar
#1
L M Vera, C Metochis, J F Taylor, M Clarkson, K H Skjærven, H Migaud, D R Tocher
BACKGROUND: To ensure sustainability of aquaculture, plant-based ingredients are being used in feeds to replace marine-derived products. However, plants contain secondary metabolites which can affect food intake and nutrient utilisation of fish. The application of nutritional stimuli during early development can induce long-term changes in animal physiology. Recently, we successfully used this approach to improve the utilisation of plant-based diets in diploid and triploid Atlantic salmon...
November 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29146872/holistic-bioengineering-rewiring-central-metabolism-for-enhanced-bioproduction
#2
REVIEW
Selçuk Aslan, Elad Noor, Arren Bar-Even
What does it take to convert a living organism into a truly productive biofactory? Apart from optimizing biosynthesis pathways as standalone units, a successful bioengineering approach must bend the endogenous metabolic network of the host, and especially its central metabolism, to support the bioproduction process. In practice, this usually involves three complementary strategies which include tuning-down or abolishing competing metabolic pathways, increasing the availability of precursors of the desired biosynthesis pathway, and ensuring high availability of energetic resources such as ATP and NADPH...
November 16, 2017: Biochemical Journal
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
#3
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/29140245/bacterial-fumarase-and-l-malic-acid-are-evolutionary-ancient-components-of-the-dna-damage-response
#4
Esti Singer, Yardena Bh Silas, Sigal Ben-Yehuda, Ophry Pines
Fumarase is distributed between two compartments of the eukaryotic cell. The enzyme catalyses the reversible conversion of fumaric to L-malic acid in mitochondria as part of the tricarboxylic acid (TCA) cycle, and in the cytosol/nucleus as part of the DNA damage response (DDR). Here we show that fumarase of the model prokaryote Bacillus subtilis (Fum-bc) is induced upon DNA damage, co-localized with the bacterial DNA and is required for the DDR. Fum-bc can substitute for both eukaryotic functions in yeast. Furthermore, we found that the fumarase dependent intracellular signaling of the B...
November 15, 2017: ELife
https://www.readbyqxmd.com/read/29137620/isocitrate-dehydrogenase-mutation-in-vibrio-anguillarum-results-in-virulence-attenuation-and-immunoprotection-in-rainbow-trout-oncorhynchus-mykiss
#5
Xiangyu Mou, Edward J Spinard, Shelby L Hillman, David R Nelson
BACKGROUND: Vibrio anguillarum is an extracellular bacterial pathogen that is a causative agent of vibriosis in finfish and crustaceans with mortality rates ranging from 30% to 100%. Mutations in central metabolism (glycolysis and the TCA cycle) of intracellular pathogens often result in attenuated virulence due to depletion of required metabolic intermediates; however, it was not known whether mutations in central metabolism would affect virulence in an extracellular pathogen such as V...
November 14, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/29137367/glycolytic-reprogramming-through-pck2-regulates-tumor-initiation-of-prostate-cancer-cells
#6
Jiangsha Zhao, Jieran Li, Teresa W M Fan, Steven X Hou
Tumor-initiating cells (TICs) play important roles in tumor progression and metastasis. Identifying the factors regulating TICs may open new avenues in cancer therapy. Here, we show that TIC-enriched prostate cancer cell clones use more glucose and secrete more lactate than TIC-low clones. We determined that elevated levels of phosphoenolpyruvate carboxykinase isoform 2 (PCK2) are critical for the metabolic switch and the maintenance of TICs in prostate cancer. Information from prostate cancer patient databases revealed that higher PCK2 levels correlated with more aggressive tumors and lower survival rates...
October 13, 2017: Oncotarget
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
#7
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/29128444/metabolomics-and-gene-expression-analysis-reveal-down-regulation-of-the-citric-acid-tca-cycle-in-non-diabetic-ckd-patients
#8
Stein Hallan, Maryam Afkarian, Leila R Zelnick, Bryan Kestenbaum, Shoba Sharma, Rintaro Saito, Manjula Darshi, Gregory Barding, Daniel Raftery, Wenjun Ju, Matthias Kretzler, Kumar Sharma, Ian H de Boer
Chronic kidney disease (CKD) is a public health problem with very high prevalence and mortality. Yet, there is a paucity of effective treatment options, partly due to insufficient knowledge of underlying pathophysiology. We combined metabolomics (GCMS) with kidney gene expression studies to identify metabolic pathways that are altered in adults with non-diabetic stage 3-4 CKD versus healthy adults. Urinary excretion rate of 27 metabolites and plasma concentration of 33 metabolites differed significantly in CKD patients versus controls (estimate range-68% to +113%)...
October 31, 2017: EBioMedicine
https://www.readbyqxmd.com/read/29125492/towards-an-understanding-of-energy-impairment-in-huntington-s-disease-brain
#9
Janet M Dubinsky
This review systematically examines the evidence for shifts in flux through energy generating biochemical pathways in Huntington's disease (HD) brains from humans and model systems. Compromise of the electron transport chain (ETC) appears not to be the primary or earliest metabolic change in HD pathogenesis. Rather, compromise of glucose uptake facilitates glucose flux through glycolysis and may possibly decrease flux through the pentose phosphate pathway (PPP), limiting subsequent NADPH and GSH production needed for antioxidant protection...
November 9, 2017: Journal of Huntington's Disease
https://www.readbyqxmd.com/read/29120073/astrocytic-and-neuronal-oxidative-metabolism-are-coupled-to-the-rate-of-glutamate-glutamine-cycle-in-the-tree-shrew-visual-cortex
#10
Sarah Sonnay, Jordan Poirot, Nathalie Just, Anne-Catherine Clerc, Rolf Gruetter, Gregor Rainer, João M N Duarte
Astrocytes play an important role in glutamatergic neurotransmission, namely by clearing synaptic glutamate and converting it into glutamine that is transferred back to neurons. The rate of this glutamate-glutamine cycle (VNT ) has been proposed to couple to that of glucose utilization and of neuronal tricarboxylic acid (TCA) cycle. In this study, we tested the hypothesis that glutamatergic neurotransmission is also coupled to the TCA cycle rate in astrocytes. For that we investigated energy metabolism by means of magnetic resonance spectroscopy (MRS) in the primary visual cortex of tree shrews (Tupaia belangeri) under light isoflurane anesthesia at rest and during continuous visual stimulation...
November 9, 2017: Glia
https://www.readbyqxmd.com/read/29116185/targeted-metabolomics-reveals-abnormal-hepatic-energy-metabolism-by-depletion-of-%C3%AE-carotene-oxygenase-2-in-mice
#11
Lei Wu, Xin Guo, Yi Lyu, Stephen L Clarke, Edralin A Lucas, Brenda J Smith, Deana Hildebrand, Weiqun Wang, Denis M Medeiros, Xinchun Shen, Dingbo Lin
β-carotene oxygenase 2 (BCO2) is a carotenoid cleavage enzyme located in the inner mitochondrial membrane. Ablation of BCO2 impairs mitochondrial function leading to oxidative stress. Herein, we performed a targeted metabolomics study using ultrahigh performance liquid chromatography-tandem mass spectroscopy and gas chromatography-mass spectroscopy to discriminate global metabolites profiles in liver samples from six-week-old male BCO2 systemic knockout (KO), heterozygous (Het), and wild type (WT) mice fed a chow diet...
November 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29114203/collagen-vi-null-mice-as-a-model-for-early-onset-muscle-decline-in-aging
#12
Daniele Capitanio, Manuela Moriggi, Sara De Palma, Dario Bizzotto, Sibilla Molon, Enrica Torretta, Chiara Fania, Paolo Bonaldo, Cecilia Gelfi, Paola Braghetta
Collagen VI is an extracellular matrix (ECM) protein playing a key role in skeletal muscles and whose deficiency leads to connective tissue diseases in humans and in animal models. However, most studies have been focused on skeletal muscle features. We performed an extensive proteomic profiling in two skeletal muscles (diaphragm and gastrocnemius) of wild-type and collagen VI null (Col6a1(-/-)) mice at different ages, from 6- (adult) to 12- (aged) month-old to 24 (old) month-old. While in wild-type animals the number of proteins and the level of modification occurring during aging were comparable in the two analyzed muscles, Col6a1(-/-) mice displayed a number of muscle-type specific variations...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29109428/serial-omics-of-p53-brca1-mouse-breast-tumor-and-normal-mammary-gland
#13
Susanne B Breitkopf, Mateus De Oliveira Taveira, Min Yuan, Gerburg M Wulf, John M Asara
This study demonstrates a liquid-liquid extraction for the sequential tandem mass spectrometry (LC-MS/MS) analysis of non-polar lipids, polar metabolites, proteins and phosphorylation sites from a single piece of tissue. Extraction of 10 mg BRCA-/-, p53-/- breast tumor tissue or normal mammary gland tissue with methyl-tert-butyl ether (MTBE) results in three phases: an upper non-polar phase containing 1,382 lipids, a lower polar phase with 805 metabolites and a precipitated protein pellet with 4,792 proteins with 1,072 phosphorylation sites...
November 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29109158/metabolic-mitigation-of-staphylococcus-aureus-vancomycin-intermediate-level-susceptibility
#14
Stewart G Gardner, Darrell D Marshall, Robert S Daum, Robert Powers, Greg A Somerville
Staphylococcus aureus is a major human pathogen whose infections are increasingly difficult to treat due to increased antibiotic resistance, including resistance to vancomycin. Vancomycin intermediate-level susceptibility S. aureus (VISA) strains develop resistance to vancomycin through adaptive changes that are incompletely understood. Central to this adaptation are metabolic changes that permit growth in the presence of vancomycin. To define the metabolic changes associated with adaptive resistance to vancomycin in S...
November 6, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29109155/temporal-fluxomics-reveals-oscillations-in-tca-cycle-flux-throughout-the-mammalian-cell-cycle
#15
Eunyong Ahn, Praveen Kumar, Dzmitry Mukha, Amit Tzur, Tomer Shlomi
Cellular metabolic demands change throughout the cell cycle. Nevertheless, a characterization of how metabolic fluxes adapt to the changing demands throughout the cell cycle is lacking. Here, we developed a temporal-fluxomics approach to derive a comprehensive and quantitative view of alterations in metabolic fluxes throughout the mammalian cell cycle. This is achieved by combining pulse-chase LC-MS-based isotope tracing in synchronized cell populations with computational deconvolution and metabolic flux modeling...
November 6, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/29107293/the-mitochondrial-pyruvate-carrier-mediates-high-fat-diet-induced-increases-in-hepatic-tca-cycle-capacity
#16
Adam J Rauckhorst, Lawrence R Gray, Ryan D Sheldon, Xiaorong Fu, Alvin D Pewa, Charlotte R Feddersen, Adam J Dupuy, Katherine N Gibson-Corley, James E Cox, Shawn C Burgess, Eric B Taylor
OBJECTIVE: Excessive hepatic gluconeogenesis is a defining feature of type 2 diabetes (T2D). Most gluconeogenic flux is routed through mitochondria. The mitochondrial pyruvate carrier (MPC) transports pyruvate from the cytosol into the mitochondrial matrix, thereby gating pyruvate-driven gluconeogenesis. Disruption of the hepatocyte MPC attenuates hyperglycemia in mice during high fat diet (HFD)-induced obesity but exerts minimal effects on glycemia in normal chow diet (NCD)-fed conditions...
November 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/29106770/probing-the-cardiac-malate-aspartate-shuttle-non-invasively-using-hyperpolarized-1-2-13-c2-pyruvate
#17
Albert P Chen, Angus Z Lau, Yi-Ping Gu, Marie A Schroeder, Jennifer Barry, Charles H Cunningham
Previous studies have demonstrated that using hyperpolarized [2-(13) C]pyruvate as a contrast agent can reveal (13) C signals from metabolites associated with the tricarboxylic acid (TCA) cycle. However, the metabolites detectable from TCA cycle-mediated oxidation of [2-(13) C]pyruvate are the result of several metabolic steps. In the instance of the [5-(13) C]glutamate signal, the amplitude can be modulated by changes to the rates of pyruvate dehydrogenase (PDH) flux, TCA cycle flux and metabolite pool size...
November 6, 2017: NMR in Biomedicine
https://www.readbyqxmd.com/read/29104506/skeletal-muscle-specific-overexpression-of-pgc-1%C3%AE-induces-fiber-type-conversion-through-enhanced-mitochondrial-respiration-and-fatty-acid-oxidation-in-mice-and-pigs
#18
Lin Zhang, Ying Zhou, Wangjun Wu, Liming Hou, Hongxing Chen, Bo Zuo, Yuanzhu Xiong, Jinzeng Yang
Individual skeletal muscles in the animal body are heterogeneous, as each is comprised of different fiber types. Type I muscle fibers are rich with mitochondria, and have high oxidative metabolisms while type IIB fibers have few mitochondria and high glycolytic metabolic capacity. Peroxisome proliferator-activated receptor gamma coactivator 1α (PGC-1α), a transcriptional co-activator that regulates mitochondrial biogenesis and respiratory function, is implicated in muscle fiber-type switching. Over-expression of PGC-1α in transgenic mice increased the proportion of red/oxidative type I fiber...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29102602/the-calcium-transient-characteristics-induced-by-fluid-shear-stress-affect-the-osteoblast-proliferation
#19
Liyin Yu, Xiangmiao Wang, Xiaohang Gao, Jie Tong, Jianbao Zhang
Ca(2+) signaling is essential for bone metabolism. Fluid shear stress (FSS), which can induce a rapid release of calcium from endoplasmic reticulum (ER) to produce calcium transients, plays a significant role in osteoblast proliferation and differentiation. However, it is still unclear of how calcium transients induced by FSS activating a number of downstream signals which subsequently regulate cell functions. In this study, we performed a group of Ca(2+) transients models, which were induced by FSS to investigate the effects of different magnitudes of Ca(2+) transients in osteoblast proliferation...
November 1, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/29101155/glucose-indirectly-fuels-the-tca-cycle-in-tumors-via-lactate
#20
(no author information available yet)
Circulating lactate derived from glucose is preferentially used as fuel for the TCA cycle over glucose.
November 3, 2017: Cancer Discovery
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