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https://www.readbyqxmd.com/read/29335226/genomic-and-metabolic-characterization-of-spoilage-associated-pseudomonas-species
#1
Tamsyn Stanborough, Narelle Fegan, Shane M Powell, Tanoj Singh, Mark Tamplin, P Scott Chandry
Pseudomonas are common spoilage agents of aerobically stored fresh foods. Their ability to cause spoilage is species- and may be strain-specific. To improve our understanding of the meat and milk spoilage agents Pseudomonas fragi and Pseudomonas lundensis, we sequenced the genomes of 12 P. fragi and seven P. lundensis isolates. These genomes provided a dataset for genomic analyses. Key volatile organic compounds (VOCs) produced or metabolised by the isolates were determined during their growth on a beef paste and where possible, metabolic activity was associated with gene repertoire...
January 5, 2018: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29331050/exercise-counteracts-lipotoxicity-by-improving-lipid-turnover-and-lipid-droplet-quality
#2
Evelyn Zacharewicz, Matthijs K C Hesselink, Patrick Schrauwen
The incidence of obesity and metabolic disease, such as type 2 diabetes mellitus (T2D), are rising globally. Dietary lipid over-supply leads to lipid accumulation at ectopic sites, such as skeletal muscle. Ectopic lipid storage is highly correlated with insulin resistance and T2D, likely due to a loss of metabolic flexibility - the capacity to switch between fat and glucose oxidation upon insulin stimulation - and cellular dysfunction because of lipotoxicity. However, muscle lipid levels are also elevated in endurance trained athletes, presenting a paradoxical phenotype of increased intramuscular lipids along with high insulin sensitivity - the "athletes' paradox"...
January 13, 2018: Journal of Internal Medicine
https://www.readbyqxmd.com/read/29329795/omega-3-fatty-acids-and-adipose-tissue-biology
#3
REVIEW
Ondrej Kuda, Martin Rossmeisl, Jan Kopecky
This review provides evidence for the importance of white and brown adipose tissue (i.e. WAT and BAT) function for the maintenance of healthy metabolic phenotype and its preservation in response to omega-3 polyunsaturated fatty acids (omega-3 PUFA), namely in the context of diseased states linked to aberrant accumulation of body fat, systemic low-grade inflammation, dyslipidemia and insulin resistance. More specifically, the review deals with (i) the concept of immunometabolism, i.e. how adipose-resident immune cells and adipocytes affect each other and define the immune-metabolic interface; and (ii) the characteristic features of "healthy adipocytes" in WAT, which are relatively small fat cells endowed with a high capacity for mitochondrial oxidative phosphorylation, triacylglycerol/fatty acid (TAG/FA) cycling and de novo lipogenesis (DNL)...
January 9, 2018: Molecular Aspects of Medicine
https://www.readbyqxmd.com/read/29327410/genomic-insights-into-the-acidobacteria-reveal-strategies-for-their-success-in-terrestrial-environments
#4
Stephanie A Eichorst, Daniela Trojan, Simon Roux, Craig Herbold, Thomas Rattei, Dagmar Woebken
Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed the largest (to date) comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8, and 23 (n=24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. In contrast to earlier studies, our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low- and high-affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients...
January 12, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29323287/disposition-of-a-glucose-load-into-hepatic-glycogen-by-direct-and-indirect-pathways-in-juvenile-seabass-and-seabream
#5
João Rito, Ivan Viegas, Miguel A Pardal, Isidoro Metón, Isabel V Baanante, John G Jones
In carnivorous fish, conversion of a glucose load to hepatic glycogen is widely used to assess their metabolic flexibility towards carbohydrate utilization, but the activities of direct and indirect pathways in this setting are unclear. We assessed the conversion of an intraperitoneal glucose load (2 g.kg-1) enriched with [U-13C6]glucose to hepatic glycogen in juvenile seabass and seabream. 13C-NMR analysis of glycogen was used to determine the contribution of the load to glycogen synthesis via direct and indirect pathways at 48-hr post-injection...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29319806/comparative-genomics-highlights-symbiotic-capacities-and-high-metabolic-flexibility-of-the-marine-genus-pseudovibrio
#6
Dennis Versluis, Bart Nijsse, Mohd Azrul Naim, Jasper J Koehorst, Jutta Wiese, Johannes F Imhoff, Peter J Schaap, Mark W J van Passel, Hauke Smidt, Detmer Sipkema
Pseudovibrio is a marine bacterial genus members of which are predominantly isolated from sessile marine animals, and particularly sponges. It has been hypothesised that Pseudovibrio spp. form mutualistic relationships with their hosts. Here, we studied Pseudovibrio phylogeny and genetic adaptations that may play a role in host colonization by comparative genomics of 31 Pseudovibrio strains, including 25 sponge isolates. All genomes were highly similar in terms of encoded core metabolic pathways, albeit with substantial differences in overall gene content...
January 8, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29318204/heterologous-biosynthesis-of-natural-product-naringenin-by-co-culture-engineering
#7
Vijaydev Ganesan, Zhenghong Li, Xiaonan Wang, Haoran Zhang
Co-culture engineering is an emerging approach for microbial biosynthesis of a variety of biochemicals. In this study, E. coli-E. coli co-cultures were developed for heterologous biosynthesis of the natural product naringenin. The co-cultures were composed of two independent E. coli strains dedicated to functional expression of different portions of the biosynthetic pathway, respectively. The co-culture biosynthesis was optimized by investigating the effect of carbon source, E. coli strain selection, timing of IPTG induction and the inoculation ratio between the co-culture strains...
September 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29317493/characterization-of-the-interactions-of-potent-allosteric-inhibitors-with-glutaminase-c-a-key-enzyme-in-cancer-cell-glutamine-metabolism
#8
Qingqiu Huang, Clint Stalnecker, Chengliang Zhang, Lee A McDermott, Prema Iyer, Jason O'Neill, Shawn Reimer, Richard A Cerione, William P Katt
Altered glycolytic flux in cancer cells (the Warburg effect) causes their proliferation to rely upon elevated glutamine metabolism (glutamine addiction). This requirement is met by the overexpression of glutaminase C (GAC), which catalyzes the first step in glutamine metabolism and therefore represents a potential therapeutic target. The small molecule CB-839 was reported to be more potent than other allosteric GAC inhibitors, including the parent compound BPTES, and is in clinical trials. Recently, we described the synthesis of BPTES analogs having distinct saturated heterocyclic cores as a replacement for the flexible chain moiety, with improved microsomal stability relative to CB-839 and BPTES...
January 9, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29316482/selective-binding-of-pyrene-in-subdomain-ib-of-human-serum-albumin-combining-energy-transfer-spectroscopy-and-molecular-modelling-to-understand-protein-binding-flexibility
#9
Irene Ling, Mohamed Taha, Nada A Al-Sharji, Osama K Abou-Zied
The ability of human serum albumin (HSA) to bind medium-sized hydrophobic molecules is important for the distribution, metabolism, and efficacy of many drugs. Herein, the interaction between pyrene, a hydrophobic fluorescent probe, and HSA was thoroughly investigated using steady-state and time-resolved fluorescence techniques, ligand docking, and molecular dynamics (MD) simulations. A slight quenching of the fluorescence signal from Trp214 (the sole tryptophan residue in the protein) in the presence of pyrene was used to determine the ligand binding site in the protein, using Förster's resonance energy transfer (FRET) theory...
January 4, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29316143/basal-insulin-peglispro-increases-lipid-oxidation-metabolic-flexibility-thermogenesis-and-ketone-bodies-compared-to-insulin-glargine-in-subjects-with-type-1-diabetes-mellitus
#10
Niels K Porksen, Helle Linnebjerg, Eric Chen Quin Lam, Parag Garhyan, Alok Pachori, Richard E Pratley, Steven R Smith
AIMS: When treated with basal insulin peglispro (BIL), patients with type 1 diabetes mellitus (T1DM) exhibit weight loss and lower prandial insulin requirements versus insulin glargine (GL), while total insulin requirements remain similar. One possible explanation is enhanced lipid oxidation and improved ability to switch between glucose and lipid metabolism with BIL. This study compared the effects of BIL and GL on glucose and lipid metabolism in subjects with T1DM. MATERIALS AND METHODS: Fifteen subjects with T1DM were enrolled into this open-label, randomised, crossover study, and received once-daily stable, individualised, subcutaneous doses of BIL and GL for 4 weeks each...
January 8, 2018: Diabetes, Obesity & Metabolism
https://www.readbyqxmd.com/read/29305946/a-whole-grain-diet-reduces-peripheral-insulin-resistance-and-improves-glucose-kinetics-in-obese-adults-a-randomized-controlled-trial
#11
Steven K Malin, Emily L Kullman, Amanda R Scelsi, Jacob M Haus, Julianne Filion, Mangesh R Pagadala, Jean-Philippe Godin, Sunil Kochhar, Alastair B Ross, John P Kirwan
BACKGROUND: Whole-grain intake is associated with lower risk of type 2 diabetes but mechanisms are unclear. PURPOSE: We tested the hypothesis that a WG diet reduces insulin resistance and improves glucose use in individuals at risk for type 2 diabetes compared with an isocaloric-matched refined-grain diet. METHODS: A double-blind, randomized, controlled, crossover trial of 14 moderately obese adults (Age, 38±2 yrs.; BMI, 34.0±1.1kg/m2). Insulin resistance and glucose metabolism was assessed using an oral glucose tolerance test combined with isotopic tracers of [6,6-2H2]-glucose and [U-13C]-glucose, and indirect calorimetry...
January 3, 2018: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/29299670/flexibility-is-the-key-metabolic-and-thermoregulatory-behaviour-in-a-small-endotherm
#12
Franz Langer, Nadine Havenstein, Joanna Fietz
Hibernation is the most effective way to reduce thermoregulatory costs during periods of unfavourable environmental conditions. In preparation to hibernation, fat-storing hibernators accumulate large quantities of body fat, which increases their locomotor costs and also the risk of predation. As a consequence, there should be a strong selective pressure to restrict pre-hibernation fattening to a short-time period before the onset of hibernation. The edible dormouse (Glis glis) is characterized by having adapted its whole life history to the irregularly occurring mast-seeding pattern of the European beech (Fagus sylvaticus)...
January 3, 2018: Journal of Comparative Physiology. B, Biochemical, Systemic, and Environmental Physiology
https://www.readbyqxmd.com/read/29298056/full-enyzme-complex-simulation-interactions-in-human-pyruvate-dehydrogenase-complex
#13
Samira Hezaveh, An-Ping Zeng, Uwe Jandt
The pyruvate dehydrogenase complex (PDC) is a large macromolecular machine consisting of dozens of interacting enzymes that are connected and regulated by highly flexible domains, also called swinging arms. The overall structure and function of these domains and how they organize the complex function is rarely elucidated yet. This lack of structural and dynamic understanding is frequently observed in multi domain enzymatic complexes. Here we present the first full and dynamic structural model of full human PDC (hPDC), including the linking arms binding to the surrounding E1 and E3 enzymes via their binding domains with variable stoichiometries...
January 3, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29290521/th17-plasticity-and-its-relevance-to-inflammatory-bowel-disease
#14
REVIEW
Aito Ueno, Louisa Jeffery, Taku Kobayashi, Toshifumi Hibi, Subrata Ghosh, Humberto Jijon
It is now clear that previously polarized T cells possess the ability to change their phenotype and repolarize towards different fates. This intrinsic flexibility is commonly referred to as plasticity and is influenced by the cytokine milieu, microbial products and products of metabolism which, in turn, regulate transcription factors and epigenetic machinery in the intestinal lamina propria. The intestinal immune system faces a particularly difficult challenge. It serves to protect the largest mucosal surface against infection and injury while maintaining a state of tolerance towards dietary antigens and the largest population of commensal organisms in the body...
December 28, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/29289553/advanced-aging-causes-diaphragm-functional-abnormalities-global-proteome-remodeling-and-loss-of-mitochondrial-cysteine-redox-flexibility-in-mice
#15
Rachel C Kelley, Brian McDonagh, Leonardo F Ferreira
AIM: Inspiratory muscle (diaphragm) function declines with age, contributing to exercise intolerance and impaired airway clearance. Studies of diaphragm dysfunction in rodents have focused on moderate aging (~24months); thus, the impact of advanced age on the diaphragm and potential mechanisms of dysfunction are less clear. Therefore, we aimed to define the effects of advanced age on the mechanics, morphology, and global and redox proteome of the diaphragm. METHODS: We studied diaphragm from young (6months) and very old male mice (30months)...
December 28, 2017: Experimental Gerontology
https://www.readbyqxmd.com/read/29278688/stage-specific-metabolic-features-of-differentiating-neurons-implications-for-toxicant-sensitivity
#16
Johannes Delp, Simon Gutbier, Martin Cerff, Christin Zasada, Sebastian Niedenführ, Liang Zhao, Lena Smirnova, Thomas Hartung, Hanna Borlinghaus, Falk Schreiber, Jörg Bergemann, Jochem Gätgens, Martin Beyss, Salah Azzouzi, Tanja Waldmann, Stefan Kempa, Katharina Nöh, Marcel Leist
Developmental neurotoxicity (DNT) may be induced when chemicals disturb a key neurodevelopmental process, and many tests focus on this type of toxicity. Alternatively, DNT may occur when chemicals are cytotoxic only during a specific neurodevelopmental stage. The toxicant sensitivity is affected by the expression of toxicant targets and by resilience factors. Although cellular metabolism plays an important role, little is known how it changes during human neurogenesis, and how potential alterations affect toxicant sensitivity of mature vs...
December 24, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29277874/comparative-rna-genomics
#17
Rolf Backofen, Jan Gorodkin, Ivo L Hofacker, Peter F Stadler
Over the last two decades it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly small RNAs is their reliance of conserved secondary structures. Large scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible noncoding RNAs that exert a vastly diverse array of molecule functions...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29275188/the-effects-of-temperature-and-food-availability-on-growth-flexibility-in-metabolic-rates-and-their-relationships-in-juvenile-common-carp
#18
Ling-Qing Zeng, Cheng Fu, Shi-Jian Fu
Flexibility in phenotypic traits can allow organisms to handle environmental changes. However, the ecological consequences of flexibility in metabolic rates are poorly understood. Here, we investigated whether the links between growth and flexibility in metabolic rates vary between two temperatures. Common carp Cyprinus carpio were raised in three temperature treatments [the 18°C, 28°C and 28°C-food control (28°C-FC)] and fed to satiation of receiving food either once or twice daily for 4weeks. The morphology and metabolic rates (standard metabolic rate, SMR; maximum metabolic rate, MMR) were measured at the beginning and end of the experiment...
December 21, 2017: Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology
https://www.readbyqxmd.com/read/29250098/reconstruction-of-oryza-sativa-indica-genome-scale-metabolic-model-and-its-responses-to-varying-rubisco-activity-light-intensity-and-enzymatic-cost-conditions
#19
Ankita Chatterjee, Benazir Huma, Rahul Shaw, Sudip Kundu
To combat decrease in rice productivity under different stresses, an understanding of rice metabolism is needed. Though there are different genome scale metabolic models (GSMs) of Oryza sativa japonica, no GSM with gene-protein-reaction association exist for Oryza sativa indica. Here, we report a GSM, OSI1136 of O.s. indica, which includes 3602 genes and 1136 metabolic reactions and transporters distributed across the cytosol, mitochondrion, peroxisome, and chloroplast compartments. Flux balance analysis of the model showed that for varying RuBisCO activity (Vc/Vo) (i) the activity of the chloroplastic malate valve increases to transport reducing equivalents out of the chloroplast under increased photorespiratory conditions and (ii) glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase can act as source of cytosolic ATP under decreased photorespiration...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29249140/impact-of-two-hydrogymnastics-class-methodologies-on-the-functional-capacity-and-flexibility-of-elderly-women
#20
Osvaldo Costa Moreira, Grazielle S Lopes, Dihogo G de Matos, Mauro L Mazini-Filho, Felipe J Aidar, Sandro Fernandes da Silva, Claudia E Patrocinio de Oliveira
BACKGROUND: Activities in the aquatic environment can be an interesting alternative of physical exercise for the elderly, due to several properties of water, which can favor the physiological, metabolic, perceptive, and musculoskeletal effects. OBJECTIVE: To compare the effects of performing two hydrogymnastic class methodologies on the functional capacity and flexibility in elderly women. METHODS: 90 women, aged 55-70 years, were divided into three groups, the Control Group (CG; n= 30) who did not exercise during the 12 weeks, Experimental Group 1 (EG1; n= 30), who performed water gymnastics classes with emphasis on lower limb exercises for 12 weeks, and Experimental Group 2 (EG2; n= 30), who performed conventional hydrogymnastics classes for 12 weeks...
December 15, 2017: Journal of Sports Medicine and Physical Fitness
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