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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
#1
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/28805660/prolyl-hydroxylase-2-inactivation-enhances-glycogen-storage-and-promotes-excessive-neutrophilic-responses
#2
Pranvera Sadiku, Joseph A Willson, Rebecca S Dickinson, Fiona Murphy, Alison J Harris, Amy Lewis, David Sammut, Ananda S Mirchandani, Eilise Ryan, Emily R Watts, A A Roger Thompson, Helen M Marriott, David H Dockrell, Cormac T Taylor, Martin Schneider, Patrick H Maxwell, Edwin R Chilvers, Massimilliano Mazzone, Veronica Moral, Chris W Pugh, Peter J Ratcliffe, Christopher J Schofield, Bart Ghesquiere, Peter Carmeliet, Moira Kb Whyte, Sarah R Walmsley
Fully activated innate immune cells are required for effective responses to infection, but their prompt deactivation and removal are essential for limiting tissue damage. Here, we have identified a critical role for the prolyl hydroxylase enzyme Phd2 in maintaining the balance between appropriate, predominantly neutrophil-mediated pathogen clearance and resolution of the innate immune response. We demonstrate that myeloid-specific loss of Phd2 resulted in an exaggerated inflammatory response to Streptococcus pneumonia, with increases in neutrophil motility, functional capacity, and survival...
August 14, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28805306/bioprocess-scale-up-down-as-integrative-enabling-technology-from-fluid-mechanics-to-systems-biology-and-beyond
#3
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/28803913/synthetic-rescue-couples-nadph-generation-to-metabolite-overproduction-in-saccharomyces-cerevisiae
#4
Siavash Partow, Patrick B Hyland, Radhakrishnan Mahadevan
Engineering the redox cofactor metabolism is known to be a key challenge in developing a platform strain for biosynthesis of valuable products. Hence, general strategies for manipulation of co-factor metabolism in industrially relevant hosts are of significance. Here, we demonstrate an improvement in α-ketoglutarate (AKG) production in S. cerevisiae using a novel approach based on synthetic rescue. Here, we first perturb the cytosolic NADPH metabolism via deletion of glucose-6-phosphate dehydrogenase (ZWF1)...
August 10, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28801717/vitamin-b6-is-essential-for-serine-de-novo-biosynthesis
#5
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/28801625/the-tomato-histone-deacetylase-slhda1-contributes-to-the-repression-of-fruit-ripening-and-carotenoid-accumulation
#6
Jun-E Guo, Zongli Hu, Mingku Zhu, Fenfen Li, Zhiguo Zhu, Yu Lu, Guoping Chen
Histone deacetylation is one of the well characterized post-translational modifications related to transcriptional repression in eukaryotes. The process of histone deacetylation is achieved by histone deacetylases (HDACs). Over the last decade, substantial advances in our understanding of the mechanism of fruit ripening have been achieved, but the role of HDACs in this process has not been elucidated. In our study, an RNA interference (RNAi) expression vector targeting SlHDA1 was constructed and transformed into tomato plants...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28801560/imaging-active-infection-in-vivo-using-d-amino-acid-derived-pet-radiotracers
#7
Kiel D Neumann, Javier E Villanueva-Meyer, Christopher A Mutch, Robert R Flavell, Joseph E Blecha, Tiffany Kwak, Renuka Sriram, Henry F VanBrocklin, Oren S Rosenberg, Michael A Ohliger, David M Wilson
Occult bacterial infections represent a worldwide health problem. Differentiating active bacterial infection from sterile inflammation can be difficult using current imaging tools. Present clinically viable methodologies either detect morphologic changes (CT/ MR), recruitment of immune cells ((111)In-WBC SPECT), or enhanced glycolytic flux seen in inflammatory cells ((18)F-FDG PET). However, these strategies are often inadequate to detect bacterial infection and are not specific for living bacteria. Recent approaches have taken advantage of key metabolic differences between prokaryotic and eukaryotic organisms, allowing easier distinction between bacteria and their host...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28798305/revealing-extracellular-electron-transfer-mediated-parasitism-energetic-considerations
#8
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/28797596/an-update-on-aureochromes-phylogeny-mechanism-function
#9
REVIEW
Peter G Kroth, Christian Wilhelm, Tilman Kottke
Light is important for algae, as it warrants metabolic independence via photosynthesis. In addition to the absorption of light by the photosystems, algae possess a variety of specific photoreceptors that allow the quantification of the light fluxes as well as the assessment of light qualities. About a decade ago, aureochromes have been described in the xanthophyte alga Vaucheria frigida. These proteins represent a new type of blue light photoreceptor as they possess both a light-oxygen-voltage (LOV) domain for light reception as well as a basic region leucine zipper (bZIP) domain for DNA binding, indicating that they represent light-driven transcription factors...
July 11, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28796780/transcriptome-and-proteome-analysis-of-salmonella-enterica-serovar-typhimurium-systemic-infection-of-wild-type-and-immune-deficient-mice
#10
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/28795720/restoring-calcium-homeostasis-in-diabetic-cardiomyocytes-an-investigation-through-mathematical-modelling
#11
Phonindra Nath Das, Ajay Kumar, Nandadulal Bairagi, Samrat Chatterjee
Calcium homeostasis is a key factor in the regulation of cardiac excitation-contraction coupling. Calcium dynamics in cardiomyocytes is governed by ATP which depends on insulin dependent glucose concentration, via the glucose transporter type 4 (GLUT4) transporter. It would therefore be interesting to see how calcium dynamics changes in a cardiomyocyte under diabetic conditions. We proposed and analysed a four dimensional ordinary differential equation (ODE) model to capture the interdependency of calcium dynamics on glucose uptake and ATP generation...
August 10, 2017: Molecular BioSystems
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/28793929/shifts-in-coastal-sediment-oxygenation-cause-pronounced-changes-in-microbial-community-composition-and-associated-metabolism
#13
Elias Broman, Johanna Sjöstedt, Jarone Pinhassi, Mark Dopson
BACKGROUND: A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability...
August 9, 2017: Microbiome
https://www.readbyqxmd.com/read/28792512/distinct-age-and-differentiation-state-dependent-metabolic-profiles-of-oligodendrocytes-under-optimal-and-stress-conditions
#14
Vijayaraghava T S Rao, Damla Khan, Qiao-Ling Cui, Shih-Chieh Fuh, Shireen Hossain, Guillermina Almazan, Gerhard Multhaup, Luke M Healy, Timothy E Kennedy, Jack P Antel
Within the microenvironment of multiple sclerosis lesions, oligodendrocytes are subject to metabolic stress reflecting effects of focal ischemia and inflammation. Previous studies have shown that under optimal conditions in vitro, the respiratory activity of human adult brain-derived oligodendrocytes is lower and more predominantly glycolytic compared to oligodendrocytes differentiated in vitro from post natal rat brain oligodendrocyte progenitor cells. In response to sub-lethal metabolic stress, adult human oligodendrocytes reduce overall energy production rate impacting the capacity to maintain myelination...
2017: PloS One
https://www.readbyqxmd.com/read/28791723/indigenously-associated-methanogens-intensified-the-metabolism-in-hydrogenosomes-of-anaerobic-fungi-with-xylose-as-substrate
#15
Yuanfei Li, Wei Jin, Chunlong Mu, Yanfen Cheng, Weiyun Zhu
Anaerobic fungi are potent lignocellulose degraders, but have not yet been exploited in this capacity, largely owing to their poor metabolic characterization. In the current study, a time course of fermentation was conducted to study the effect of the co-cultured methanogens on xylose metabolism by anaerobic fungi. The fermentation end-products from anaerobic fungal monoculture were H2 (6.7 ml), CO2 (65.7 ml), formate (17.90 mM), acetate (9.00 mM), lactate (11.89 mM), ethanol, and malate after 96 h fermentation...
August 9, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28791562/production-of-fumaric-acid-by-bioconversion-of-corncob-hydrolytes-using-an-improved-rhizopus-oryzae-strain
#16
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/28790859/dyslipidemia-and-associated-factors-among-diabetic-patients-attending-durame-general-hospital-in-southern-nations-nationalities-and-people-s-region
#17
Shiferaw Bekele, Tagesech Yohannes, Abdurehman Eshete Mohammed
BACKGROUND: Diabetes mellitus is a group of metabolic disorders that are caused by deficiency in insulin secretion or the decreased ability of insulin to act effectively on target tissues, particularly muscle, liver, and fat. As a result of insulin resistance in the target tissues, particularly in the adipocytes, free fatty acid flux is increased, leading to increased lipid synthesis in hepatocytes, which is responsible for diabetic dyslipidemia. OBJECTIVE: The objective of this study was to determine the prevalence and associated factors of dyslipidemia among diabetic patients in Durame General Hospital in Kembata Tembaro zone...
2017: Diabetes, Metabolic Syndrome and Obesity: Targets and Therapy
https://www.readbyqxmd.com/read/28790206/cellobiose-consumption-uncouples-extracellular-glucose-sensing-and-glucose-metabolism-in-saccharomyces-cerevisiae
#18
Kulika Chomvong, Daniel I Benjamin, Daniel K Nomura, Jamie H D Cate
Glycolysis is central to energy metabolism in most organisms and is highly regulated to enable optimal growth. In the yeast Saccharomyces cerevisiae, feedback mechanisms that control flux through glycolysis span transcriptional control to metabolite levels in the cell. Using a cellobiose consumption pathway, we decoupled glucose sensing from carbon utilization, revealing new modular layers of control that induce ATP consumption to drive rapid carbon fermentation. Alterations of the beta subunit of phosphofructokinase-1 (PFK2), H(+)-plasma membrane ATPase (PMA1), and glucose sensors (SNF3 and RGT2) revealed the importance of coupling extracellular glucose sensing to manage ATP levels in the cell...
August 8, 2017: MBio
https://www.readbyqxmd.com/read/28790027/increased-mitochondrial-calcium-uniporter-in-adipocytes-underlies-mitochondrial-alterations-associated-with-insulin-resistance
#19
Lauren E Wright, Denis Vecellio Reane, Gabriella Milan, Anna Terrin, Giorgia di Bello, Anna Belligoli, Marta Sanna, Mirto Foletto, Francesca Favaretto, Anna Raffaello, Cristina Mammucari, Donato Nitti, Roberto Vettor, Rosario Rizzuto
Intracellular calcium influences an array of pathways and affects cellular processes. With the rapidly progressing research investigating the molecular identity and the physiological roles of the Mitochondrial Calcium Uniporter (MCU) complex, we now have the tools to understand the functions of mitochondrial Ca(2+) in the regulation of pathophysiological processes. Herein, we describe the role of key MCU complex components in insulin resistance in mouse and human adipose tissue. Adipose tissue gene expression was analysed from several models of obese and diabetic rodents and in obese patients, as well as in vitro insulin-resistant adipocytes...
August 8, 2017: American Journal of Physiology. Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28780284/pathway-optimization-and-key-enzyme-evolution-of-n-acetylneuraminate-biosynthesis-using-an-in-vivo-aptazyme-based-biosensor
#20
Peng Yang, Jing Wang, Qingxiao Pang, Fengyu Zhang, Junshu Wang, Qian Wang, Qingsheng Qi
N-acetylneuraminate (NeuAc) biosynthesis has drawn much attention owing to its wide applications in many aspects. Previously, we engineered for the first time an artificial NeuAc biosynthetic pathway in Escherichia coli using glucose as sole substrate. However, rigorous requirements for the flux and cofactor balance make subsequent strain improvement rather difficult. In this study, an in vivo NeuAc biosensor was designed and applied for genetic screening the mutant library of NeuAc producer. Its NeuAc responsive manner was demonstrated using sfgfp as a reporter and a Ni(2+)-based selection system was developed to couple the cell growth with in vivo NeuAc concentration...
August 2, 2017: Metabolic Engineering
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