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metabolic flexibility

Kai Tang, Yujie Yang, Dan Lin, Shuhui Li, Wenchu Zhou, Yu Han, Keshao Liu, Nianzhi Jiao
Roseobacter clade bacteria are ubiquitous in marine environments and now thought to be significant contributors to carbon and sulfur cycling. However, only a few strains of roseobacters have been isolated from the deep-sea water column and have not been thoroughly investigated. Here, we present the complete genomes of phylogentically closed related Thiobacimonas profunda JLT2016 and Pelagibaca abyssi JLT2014 isolated from deep-sea water of the Southeastern Pacific. The genome sequences showed that the two deep-sea roseobacters carry genes for versatile metabolisms with functional capabilities such as ribulose bisphosphate carboxylase-mediated carbon fixation and inorganic sulfur oxidation...
October 20, 2016: Scientific Reports
Steven Zhao, AnnMarie Torres, Ryan A Henry, Sophie Trefely, Martina Wallace, Joyce V Lee, Alessandro Carrer, Arjun Sengupta, Sydney L Campbell, Yin-Ming Kuo, Alexander J Frey, Noah Meurs, John M Viola, Ian A Blair, Aalim M Weljie, Christian M Metallo, Nathaniel W Snyder, Andrew J Andrews, Kathryn E Wellen
Mechanisms of metabolic flexibility enable cells to survive under stressful conditions and can thwart therapeutic responses. Acetyl-coenzyme A (CoA) plays central roles in energy production, lipid metabolism, and epigenomic modifications. Here, we show that, upon genetic deletion of Acly, the gene coding for ATP-citrate lyase (ACLY), cells remain viable and proliferate, although at an impaired rate. In the absence of ACLY, cells upregulate ACSS2 and utilize exogenous acetate to provide acetyl-CoA for de novo lipogenesis (DNL) and histone acetylation...
October 18, 2016: Cell Reports
Catherine Duport, Michel Jobin, Philippe Schmitt
Bacillus cereus is a food-borne pathogen that causes diarrheal disease in humans. After ingestion, B. cereus experiences in the human gastro-intestinal tract abiotic physical variables encountered in food, such as acidic pH in the stomach and changing oxygen conditions in the human intestine. B. cereus responds to environmental changing conditions (stress) by reversibly adjusting its physiology to maximize resource utilization while maintaining structural and genetic integrity by repairing and minimizing damage to cellular infrastructure...
2016: Frontiers in Microbiology
András Szilágyi, Dániel Györffy, Péter Závodszky
In an earlier study, we showed that two-domain segment-swapped proteins can evolve by domain swapping and fusion, resulting in a protein with two linkers connecting its domains. We proposed that a potential evolutionary advantage of this topology may be the restriction of interdomain motions, which may facilitate domain closure by a hinge-like movement, crucial for the function of many enzymes. Here, we test this hypothesis computationally on uroporphyrinogen III synthase, a two-domain segment-swapped enzyme essential in porphyrin metabolism...
October 18, 2016: Proteins
Simone Vincenzi, Alain J Crivelli, Stephan Munch, Hans J Skaug, Marc Mangel
Better understanding of variation in growth will always be an important problem in ecology. Individual variation in growth can arise from a variety of processes; for example, individuals within a population vary in their intrinsic metabolic rates and behavioral traits, which may influence their foraging dynamics and access to resources. However, when adopting a growth model, we face trade-offs between model complexity, biological interpretability of parameters, and goodness of fit. We explore how different formulations of the von Bertalanffy growth function (vBGF) with individual random effects and environmental predictors affect these trade-offs...
July 2016: Ecological Applications: a Publication of the Ecological Society of America
Mario Juhas, James W Ajioka
BACKGROUND: Escherichia coli K-12 is a frequently used host for a number of synthetic biology and biotechnology applications and chassis for the development of the minimal cell factories. Novel approaches for integrating high molecular weight DNA into the E. coli chromosome would therefore greatly facilitate engineering efforts in this bacterium. RESULTS: We developed a reliable and flexible lambda Red recombinase-based system, which utilizes overlapping DNA fragments for integration of the high molecular weight DNA into the E...
October 5, 2016: Microbial Cell Factories
Oveis Jamialahmadi, Ehsan Motamedian, Sameereh Hashemi-Najafabadi
Development of an interface tool between the Biochemical, Genetic and Genomic (BiGG) and KEGG databases is necessary for simultaneous access to the features of both databases. For this purpose, we present the BiKEGG toolbox, an open source COBRA toolbox extension providing a set of functions to infer the reaction correspondences between the KEGG reaction identifiers and those in the BiGG knowledgebase using a combination of manual verification and computational methods. Inferred reaction correspondences using this approach are supported by evidence from the literature, which provides a higher number of reconciled reactions between these two databases compared to the MetaNetX and MetRxn databases...
September 23, 2016: Molecular BioSystems
Łukasz P Zieliński, Anthony C Smith, Alexander G Smith, Alan J Robinson
Mitochondrial respiratory chain dysfunction causes a variety of life-threatening diseases affecting about 1 in 4300 adults. These diseases are genetically heterogeneous, but have the same outcome; reduced activity of mitochondrial respiratory chain complexes causing decreased ATP production and potentially toxic accumulation of metabolites. Severity and tissue specificity of these effects varies between patients by unknown mechanisms and treatment options are limited. So far most research has focused on the complexes themselves, and the impact on overall cellular metabolism is largely unclear...
September 30, 2016: Mitochondrion
Lily Khadempour, Kristin E Burnum-Johnson, Erin S Baker, Carrie D Nicora, Bobbie-Jo M Webb-Robertson, Richard A White, Matthew E Monroe, Eric L Huang, Richard D Smith, Cameron R Currie
Herbivores use symbiotic microbes to help derive energy and nutrients from plant material. Leaf-cutter ants are a paradigmatic example, cultivating their mutualistic fungus Leucoagaricus gongylophorus on plant biomass that workers forage from a diverse collection of plant species. Here, we investigate the metabolic flexibility of the ants' fungal cultivar for utilizing different plant biomass. Using feeding experiments and a novel approach in metaproteomics, we examine the enzymatic response of L. gongylophorus to leaves, flowers, oats, or a mixture of all three...
October 1, 2016: Molecular Ecology
Teri M Furlong, Jhodie R Duncan, Laura H Corbit, Caroline D Rae, Benjamin D Rowlands, Anthony D Maher, Fatima A Nasrallah, Carol J Milligan, Steven Petrou, Andrew J Lawrence, Bernard W Balleine
Toluene is a commonly abused inhalant that is easily accessible to adolescents. Despite the increasing incidence of use, our understanding of its long-term impact remains limited. Here we used a range of techniques to examine the acute and chronic effects of toluene exposure on glutameteric and GABAergic function, and on indices of psychological function in adult rats after adolescent exposure. Metabolomics conducted on cortical tissue established that acute exposure to toluene produces alterations in cellular metabolism indicative of a glutamatergic and GABAergic profile...
October 1, 2016: Journal of Neurochemistry
Olivier Van der Poorten, Astrid Knuhtsen, Daniel Sejer Pedersen, Steven Ballet, Dirk Tourwé
Constraining the conformation of flexible peptides is a proven strategy to increase potency, selectivity and metabolic stability. The focus has mostly been on constraining the backbone dihedral angles; however, the correct orientation of the amino acid side chains (Χ-space) which constitute the peptide pharmacophore is equally important. Control of Χ-space utilizes conformationally constrained amino acids which favor, disfavor or exclude the gauche (‒), the gauche (+) or the trans conformation. In this review we focus on cyclic aromatic amino acids in which the side chain is connected to the peptide backbone to provide control of Χ1- and Χ2-space...
October 3, 2016: Journal of Medicinal Chemistry
Luis Peñailillo, Nicolás Guzmán, José Cangas, Alvaro Reyes, Hermann Zbinden-Foncea
: The aim of this study was to examine the metabolic demand and extent of muscle damage of eccentric cycling targeting knee flexor (FLEX) and knee extensor (EXT) muscles. METHODS: Eight sedentary men (23.3 ± 0.7 y) underwent two eccentric cycling sessions (EXT and FLEX) of 30 min each, at 60% of the maximum power output. Oxygen consumption (VO2), heart rate (HR) and rated perceived exertion (RPE) were measured during cycling. Countermovement and squat jumps (CMJ and SJ), muscle flexibility, muscle soreness and pain pressure threshold (PPT) of knee extensor and flexor muscles were measured before, immediately after and 1-4 days after cycling...
August 15, 2016: European Journal of Sport Science
Aleona Swegen, Sarah Renay Lambourne, R John Aitken, Zamira Gibb
Media used for equine sperm storage often contain relatively high concentrations of glucose, even though stallion spermatozoa preferentially utilize oxidative phosphorylation over glycolysis to generate ATP and support motility. Rosiglitazone is an anti-diabetic compound that enhances metabolic flexibility and glucose utilization in various cell types, but its effects on sperm metabolism are unknown. This study investigated the effects of rosiglitazone on stallion sperm function in vitro, along with the possible role of AMP-activated kinase (AMPK) in mediating these effects...
September 28, 2016: Biology of Reproduction
Marie Portail, Karine Olu, Stanislas F Dubois, Elva Escobar-Briones, Yves Gelinas, Lénaick Menot, Jozée Sarrazin
In the Guaymas Basin, the presence of cold seeps and hydrothermal vents in close proximity, similar sedimentary settings and comparable depths offers a unique opportunity to assess and compare the functioning of these deep-sea chemosynthetic ecosystems. The food webs of five seep and four vent assemblages were studied using stable carbon and nitrogen isotope analyses. Although the two ecosystems shared similar potential basal sources, their food webs differed: seeps relied predominantly on methanotrophy and thiotrophy via the Calvin-Benson-Bassham (CBB) cycle and vents on petroleum-derived organic matter and thiotrophy via the CBB and reductive tricarboxylic acid (rTCA) cycles...
2016: PloS One
Wahyu Sri Kunto Nugroho, Dong-Woo Kim, Jong-Cheol Han, Young Baek Hur, Soo-Wan Nam, Hak Jun Kim
Most cold-adapted enzymes possess higher Km and kcat values than those of their mesophilic counterparts to maximize the reaction rate. This characteristic is often ascribed to a high structural flexibility and improved dynamics in the active site. However, this may be less convincing to cold-adapted metabolic enzymes, which work at substrate concentrations near Km. In this respect, cold adaptation of a shikimate kinase (SK) in the shikimate pathway from psychrophilic Colwellia psychrerythraea (CpSK) was characterized by comparing it with a mesophilic Escherichia coli homolog (EcSK)...
September 23, 2016: Journal of Microbiology and Biotechnology
Paulo Farinatti, Walace D Monteiro, Ricardo B Oliveira
INTRODUCTION: Home-based exercise programs may increase adherence to physical activity among groups with poor access to exercise facilities. However, their effectiveness to lower blood pressure of hypertensive patients remains undefined. AIMS: This controlled clinical trial investigated the influence of a home-based exercise program upon blood pressure, blood metabolic profile, and physical fitness in a Brazilian cohort of low income patients diagnosed with hypertension...
September 22, 2016: High Blood Pressure & Cardiovascular Prevention: the Official Journal of the Italian Society of Hypertension
Anna Dart
No abstract text is available yet for this article.
September 23, 2016: Nature Reviews. Cancer
Theodora Stasinou, Andreas Bourdoumis, Junaid Masood
OBJECTIVES: To investigate a possible causal relationship for stone formation in pelviureteric junction obstruction and to outline management options. MATERIALS AND METHODS: A literature search and evidence synthesis was conducted via electronic databases in the English language using the key words pelviureteric junction obstruction; urolithiasis; hyperoxaluria; laparoscopic pyeloplasty; flexible nephroscopy; percutaneous nephrolithotomy, alone or in combination...
September 20, 2016: International Braz J Urol: Official Journal of the Brazilian Society of Urology
J Kelly Smith, Rhesa Dykes, David S Chi
Although it is recognized that the mechanical stresses associated with physical activity augment bone mineral density and improve bone quality, our understanding of how exercise modulates bone homeostasis at the molecular level is lacking. In a before and after trial involving 43 healthy adults, we measured the effect of six months of supervised exercise training on the spontaneous and phytohemagglutinin-induced production of osteoclastogenic cytokines (interleukin-1α, tumor necrosis factor-α), antiosteoclastogenic cytokines (transforming growth factor-β1 and interleukins 4 and 10), pleiotropic cytokines with variable effects on osteoclastogenesis (interferon-γ, interleukin-6), and T cell growth and differentiation factors (interleukins 2 and 12) by peripheral blood mononuclear cells...
2016: Journal of Osteoporosis
Michael H Limberg, Julia Schulte, Tita Aryani, Regina Mahr, Meike Baumgart, Michael Bott, Wolfgang Wiechert, Marco Oldiges
Performance losses during scale-up are described since decades, but are still one of the major obstacles for industrial bioprocess development. Consequently, robustness to inhomogeneous cultivation environments is an important quality of industrial production organisms. Especially, Corynebacterium glutamicum was proven to have an outstanding resistance against rapid changes of oxygen and substrate availability as occurring in industrial scale bioreactors. This study focuses on the identification of metabolic key mechanisms for this robustness to get a deeper insight and provide future targets for process orientated strain development...
September 19, 2016: Biotechnology and Bioengineering
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