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Metabolic flux

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https://www.readbyqxmd.com/read/28545095/feeding-on-dispersed-vs-aggregated-particles-the-effect-of-zooplankton-feeding-behavior-on-vertical-flux
#1
Marja Koski, Julia Boutorh, Christina de la Rocha
Zooplankton feeding activity is hypothesized to attenuate the downward flux of elements in the ocean. We investigated whether the zooplankton community composition could influence the flux attenuation, due to the differences of feeding modes (feeding on dispersed vs. aggregated particles) and of metabolic rates. We fed 5 copepod species-three calanoid, one harpacticoid and one poecilamastoid-microplankton food, in either dispersed or aggregated form and measured rates of respiration, fecal pellet production and egg production...
2017: PloS One
https://www.readbyqxmd.com/read/28544208/ultra-high-field-magnetic-resonance-spectroscopy-in-non-alcoholic-fatty-liver-disease-novel-mechanistic-and-diagnostic-insights-of-energy-metabolism-in-non-alcoholic-steatohepatitis-and-advanced-fibrosis
#2
Stefan Traussnigg, Christian Kienbacher, Martin Gajdošík, Ladislav Valkovič, Emina Halilbasic, Judith Stift, Christian Rechling, Harald Hofer, Petra Steindl-Munda, Peter Ferenci, Fritz Wrba, Siegfried Trattnig, Martin Krššák, Michael Trauner
BACKGROUND & AIMS: With the rising prevalence of non-alcoholic fatty liver disease (NAFLD) and steatohepatitis (NASH) non-invasive tools obtaining pathomechanistic insights to improve risk stratification are urgently needed. We therefore explored high- and ultra-high-field magnetic resonance spectroscopy (MRS) to obtain novel mechanistic and diagnostic insights into alterations of hepatic lipid, cell membrane and energy metabolism across the spectrum of NAFLD. METHODS: MRS and liver biopsy were performed in 30 NAFLD patients with NAFL (n=8) or NASH (n=22)...
April 24, 2017: Liver International: Official Journal of the International Association for the Study of the Liver
https://www.readbyqxmd.com/read/28543565/lactate-supplementation-in-severe-traumatic-brain-injured-adults-by-primed-constant-infusion-of-sodium-l-lactate
#3
Stephanie M Wolahan, Howard C Mao, Courtney Real, Paul M Vespa, Thomas C Glenn
Carbohydrate fuel augmentation following traumatic brain injury may be a viable treatment to improve recovery when cerebral oxidative metabolism of glucose is depressed. We performed a primed constant sodium L-lactate infusion in 11 moderate to severely brain injured adults. Blood was collected before and periodically during the infusion study. We quantified global cerebral uptake of glucose and lactate and other systemic metabolites associated with energy metabolism. Our hypothesis was that cerebral lactate uptake, as measured by the arteriovenous difference of lactate (AVDlac), would increase in severely injured TBI patients in the neurocritical care unit...
May 20, 2017: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/28542616/regulation-of-acetyl-coa-synthetase-transcription-by-the-crbs-r-two-component-system-is-conserved-in-genetically-diverse-environmental-pathogens
#4
Kristin Jacob, Anna Rasmussen, Paul Tyler, Mariah M Servos, Mariame Sylla, Cecilia Prado, Elizabeth Daniele, Josh S Sharp, Alexandra E Purdy
The CrbS/R two-component signal transduction system is a conserved regulatory mechanism through which specific Gram-negative bacteria control acetate flux into primary metabolic pathways. CrbS/R governs expression of acetyl-CoA synthase (acsA), an enzyme that converts acetate to acetyl-CoA, a metabolite at the nexus of the cell's most important energy-harvesting and biosynthetic reactions. During infection, bacteria can utilize this system to hijack host acetate metabolism and alter the course of colonization and pathogenesis...
2017: PloS One
https://www.readbyqxmd.com/read/28542430/ros-regulation-of-axonal-mitochondrial-transport-is-mediated-by-ca2-and-jnk-in-drosophila
#5
Pin-Chao Liao, Lauren C Tandarich, Peter J Hollenbeck
Mitochondria perform critical functions including aerobic ATP production and calcium (Ca2+) homeostasis, but are also a major source of reactive oxygen species (ROS) production. To maintain cellular function and survival in neurons, mitochondria are transported along axons, and accumulate in regions with high demand for their functions. Oxidative stress and abnormal mitochondrial axonal transport are associated with neurodegenerative disorders. However, we know little about the connection between these two...
2017: PloS One
https://www.readbyqxmd.com/read/28542252/metabolic-flux-analysis-of-heterotrophic-growth-in-chlamydomonas-reinhardtii
#6
Nanette R Boyle, Neelanjan Sengupta, John A Morgan
Despite the wealth of knowledge available for C. reinhardtii, the central metabolic fluxes of growth on acetate have not yet been determined. In this study, 13C-metabolic flux analysis (13C-MFA) was used to determine and quantify the metabolic pathways of primary metabolism in C. reinhardtii cells grown under heterotrophic conditions with acetate as the sole carbon source. Isotopic labeling patterns of compartment specific biomass derived metabolites were used to calculate the fluxes. It was found that acetate is ligated with coenzyme A in the three subcellular compartments (cytosol, mitochondria and plastid) included in the model...
2017: PloS One
https://www.readbyqxmd.com/read/28542187/elucidation-of-new-condition-dependent-roles-for-fructose-1-6-bisphosphatase-linked-to-cofactor-balances
#7
Du Toit W P Schabort, Stephanus G Kilian, James C du Preez
The cofactor balances in metabolism is of paramount importance in the design of a metabolic engineering strategy and understanding the regulation of metabolism in general. ATP, NAD+ and NADP+ balances are central players linking the various fluxes in central metabolism as well as biomass formation. NADP+ is especially important in the metabolic engineering of yeasts for xylose fermentation, since NADPH is required by most yeasts in the initial step of xylose utilisation, including the fast-growing Kluyveromyces marxianus...
2017: PloS One
https://www.readbyqxmd.com/read/28540666/evaluation-of-mitochondrial-respiratory-function-in-highly-glycolytic-glioma-cells-reveals-low-adp-phosphorylation-in-relation-to-oxidative-capacity
#8
Erika Rodrigues-Silva, Edilene S Siqueira-Santos, Juliana S Ruas, Raffaela S Ignarro, Tiago R Figueira, Fábio Rogério, Roger F Castilho
High-grade gliomas are aggressive and intensely glycolytic tumors. In the present study, we evaluated the mitochondrial respiratory function of glioma cells (T98G and U-87MG) and fresh human glioblastoma (GBM) tissue. To this end, measurements of oxygen consumption rate (OCR) were performed under various experimental conditions. The OCR of T98G and U-87MG cells was well coupled to ADP phosphorylation based on the ratio of ATP produced per oxygen consumed of ~2.5. In agreement, the basal OCR of GBM tissue was also partially associated with ADP phosphorylation...
May 24, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28537196/electrochemically-applied-potentials-induce-growth-and-metabolic-shift-changes-in-the-hyperthermophilic-bacterium-thermotoga-maritima-msb8
#9
Shin-Ichi Hirano, Norio Matsumoto
Bioelectrochemical systems are an attractive technology for regulating microbial activity. The effect of an applied potential on hydrolysis of starch in Thermotoga maritima as a model bacterium was investigated in this study. A cathodic potential (-0.6 and -0.8 V) induced 5-h earlier growth initiation of T. maritima with starch as the polymeric substrate than that without electrochemical regulation. Moreover, metabolic patterns of starch consumption were altered by the cathodic potential. While acetate, H(2), and CO2 were the major products of starch consumption in the control experiment without electrolysis, lactate accumulation was detected rather than decreased acetate and H2 levels in the bioelectrochemical system experiments with the cathodic potential...
May 24, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28536194/wild-tobacco-genomes-reveal-the-evolution-of-nicotine-biosynthesis
#10
Shuqing Xu, Thomas Brockmöller, Aura Navarro-Quezada, Heiner Kuhl, Klaus Gase, Zhihao Ling, Wenwu Zhou, Christoph Kreitzer, Mario Stanke, Haibao Tang, Eric Lyons, Priyanka Pandey, Shree P Pandey, Bernd Timmermann, Emmanuel Gaquerel, Ian T Baldwin
Nicotine, the signature alkaloid of Nicotiana species responsible for the addictive properties of human tobacco smoking, functions as a defensive neurotoxin against attacking herbivores. However, the evolution of the genetic features that contributed to the assembly of the nicotine biosynthetic pathway remains unknown. We sequenced and assembled genomes of two wild tobaccos, Nicotiana attenuata (2.5 Gb) and Nicotiana obtusifolia (1.5 Gb), two ecological models for investigating adaptive traits in nature. We show that after the Solanaceae whole-genome triplication event, a repertoire of rapidly expanding transposable elements (TEs) bloated these Nicotiana genomes, promoted expression divergences among duplicated genes, and contributed to the evolution of herbivory-induced signaling and defenses, including nicotine biosynthesis...
May 23, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28536183/the-nlrp3-inflammasome-contributes-to-sarcopenia-and-lower-muscle-glycolytic-potential-in-old-mice
#11
Marin Jane McBride, Kevin P Foley, Donna M D'souza, Yujin E Li, Trevor C Lau, Thomas J Hawke, Jonathan D Schertzer
The mechanisms underpinning decreased skeletal muscle strength and slowing of movement during aging are ill-defined. "Inflammaging" - increased inflammation with advancing age - may contribute to aspects of sarcopenia, but little is known about the participatory immune components. We discovered that aging was associated with increased caspase-1 activity in mouse skeletal muscle. We hypothesized that the caspase-1 containing NLRP3 inflammasome contributes to sarcopenia in mice. Male C57BL/6J wild type (WT) and NLRP3(-/-) mice were aged to 10 months (adult) and 24 months (old)...
May 23, 2017: American Journal of Physiology. Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28535757/intracellular-product-recycling-in-high-succinic-acid-producing-yeast-at-low-ph
#12
S Aljoscha Wahl, Cristina Bernal Martinez, Zheng Zhao, Walter M van Gulik, Mickel L A Jansen
BACKGROUND: The metabolic engineering of Saccharomyces cerevisiae for the production of succinic acid has progressed dramatically, and a series of high-producing hosts are available. At low cultivation pH and high titers, the product transport can become bidirectional, i.e. the acid is reentering the cell and is again exported or even catabolized. Here, a quantitative approach for the identification of product recycling fluxes is developed. RESULTS: The metabolic flux distributions at two time-points of the fermentation process were analyzed...
May 23, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28534819/ginsenoside-rb2-alleviates-hepatic-lipid-accumulation-by-restoring-autophagy-via-induction-of-sirt1-and-activation-of-ampk
#13
Qi Huang, Ting Wang, Liu Yang, He-Yao Wang
Although Panax ginseng is a famous traditional Chinese medicine and has been widely used to treat a variety of metabolic diseases including hyperglycemia, hyperlipidemia, and hepatosteatosis, the effective mediators and molecular mechanisms remain largely unknown. In this study we found that ginsenoside Rb2, one of the major ginsenosides in Panax ginseng, was able to prevent hepatic lipid accumulation through autophagy induction both in vivo and in vitro. Treatment of male db/db mice with Rb2 significantly improved glucose tolerance, decreased hepatic lipid accumulation, and restored hepatic autophagy...
May 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28533780/innate-immune-function-of-mitochondrial-metabolism
#14
REVIEW
David Sancho, Michel Enamorado, Johan Garaude
Sensing of microbe-associated molecular patterns or danger signals by innate immune receptors drives a complex exchange of information. Innate receptor signaling not only triggers transcriptional events but also induces profound changes in metabolic fluxes, redox balance, and metabolite abundance thereby influencing immune cell function. Mitochondria are at the core of metabolic adaptation to the changing environment. The close interaction between mitochondrial metabolism and immune signaling has emerged as a central regulator of innate sensing...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28531184/bacarena-individual-based-metabolic-modeling-of-heterogeneous-microbes-in-complex-communities
#15
Eugen Bauer, Johannes Zimmermann, Federico Baldini, Ines Thiele, Christoph Kaleta
Recent advances focusing on the metabolic interactions within and between cellular populations have emphasized the importance of microbial communities for human health. Constraint-based modeling, with flux balance analysis in particular, has been established as a key approach for studying microbial metabolism, whereas individual-based modeling has been commonly used to study complex dynamics between interacting organisms. In this study, we combine both techniques into the R package BacArena (https://cran.r-project...
May 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28530708/engineering-rgb-color-vision-into-escherichia-coli
#16
Jesus Fernandez-Rodriguez, Felix Moser, Miryoung Song, Christopher A Voigt
Optogenetic tools use colored light to rapidly control gene expression in space and time. We designed a genetically encoded system that gives Escherichia coli the ability to distinguish between red, green, and blue (RGB) light and respond by changing gene expression. We use this system to produce 'color photographs' on bacterial culture plates by controlling pigment production and to redirect metabolic flux by expressing CRISPRi guide RNAs.
May 22, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28530276/focus-a-metaheuristic-algorithm-for-computing-knockouts-from-genome-scale-models-for-strain-optimization
#17
Sarma Mutturi
Although handful tools are available for constraint-based flux analysis to generate knockout strains, most of these are either based on bilevel-MIP or its modifications. However, metaheuristic approaches that are known for their flexibility and scalability have been less studied. Moreover, in the existing tools, sectioning of search space to find optimal knocks has not been considered. Herein, a novel computational procedure, termed as FOCuS (Flower-pOllination coupled Clonal Selection algorithm), was developed to find the optimal reaction knockouts from a metabolic network to maximize the production of specific metabolites...
May 22, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28526246/impaired-mitophagy-facilitates-mitochondrial-damage-in-danon-disease
#18
Sherin I Hashem, Anne N Murphy, Ajit S Divakaruni, Matthew L Klos, Bradley C Nelson, Emily C Gault, Teisha J Rowland, Cynthia N Perry, Yusu Gu, Nancy D Dalton, William H Bradford, Eric J Devaney, Kirk L Peterson, Kenneth L Jones, Matthew R G Taylor, Ju Chen, Neil C Chi, Eric D Adler
RATIONALE: Lysosomal associated membrane protein type-2 (LAMP-2) is a highly conserved, ubiquitous protein that is critical for autophagic flux. Loss of function mutations in the LAMP-2 gene cause Danon disease, a rare X-linked disorder characterized by developmental delay, skeletal muscle weakness, and severe cardiomyopathy. We previously found that human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) from Danon patients exhibited significant mitochondrial oxidative stress and apoptosis...
May 16, 2017: Journal of Molecular and Cellular Cardiology
https://www.readbyqxmd.com/read/28525376/exploiting-ros-and-metabolic-differences-to-kill-cisplatin-resistant-lung-cancer
#19
Medhi Wangpaichitr, Chunjing Wu, Ying Ying Li, Dan J M Nguyen, Hande Kandemir, Sumedh Shah, Shumei Chen, Lynn G Feun, Jeffrey S Prince, Macus T Kuo, Niramol Savaraj
Cisplatin resistance remains a major problem in the treatment of lung cancer. We have discovered that cisplatin resistant (CR) lung cancer cells, regardless of the signaling pathway status, share the common parameter which is an increase in reactive oxygen species (ROS) and undergo metabolic reprogramming. CR cells were no longer addicted to the glycolytic pathway, but rather relied on oxidative metabolism. They took up twice as much glutamine and were highly sensitive to glutamine deprivation. Glutamine is hydrolyzed to glutamate for glutathione synthesis, an essential factor to abrogate high ROS via xCT antiporter...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28523012/growth-and-accumulation-of-secondary-metabolites-in-perilla-as-affected-by-photosynthetic-photon-flux-density-and-electrical-conductivity-of-the-nutrient-solution
#20
Na Lu, Emmanuel L Bernardo, Chayanit Tippayadarapanich, Michiko Takagaki, Natsuko Kagawa, Wataru Yamori
The global demand for medicinal plants is increasing. The quality of plants grown outdoors, however, is difficult to control. Myriad environmental factors influence plant growth and directly impact biosynthetic pathways, thus affecting the secondary metabolism of bioactive compounds. Plant factories use artificial lighting to increase the quality of medicinal plants and stabilize production. Photosynthetic photon flux density (PPFD) and electrical conductivity (EC) of nutrient solutions are two important factors that substantially influence perilla (Perilla frutescens, Labiatae) plant growth and quality...
2017: Frontiers in Plant Science
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