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https://www.readbyqxmd.com/read/28727789/lumpgem-systematic-generation-of-subnetworks-and-elementally-balanced-lumped-reactions-for-the-biosynthesis-of-target-metabolites
#1
Meric Ataman, Vassily Hatzimanikatis
In the post-genomic era, Genome-scale metabolic networks (GEMs) have emerged as invaluable tools to understand metabolic capabilities of organisms. Different parts of these metabolic networks are defined as subsystems/pathways, which are sets of functional roles to implement a specific biological process or structural complex, such as glycolysis and TCA cycle. Subsystem/pathway definition is also employed to delineate the biosynthetic routes that produce biomass building blocks. In databases, such as MetaCyc and SEED, these representations are composed of linear routes from precursors to target biomass building blocks...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28727413/quantifying-the-metabolome-of-pseudomonas-taiwanensis-vlb120-evaluation-of-hot-and-cold-combined-quenching-extraction-approaches
#2
Gossa Garedew Wordofa, Mette Kristensen, Lars Schrübbers, Douglas McCloskey, Jochen Forster, Konstantin Schneider
Absolute quantification of free intracellular metabolites is a valuable tool in both, pathway discovery and metabolic engineering. In this study, we conducted a comprehensive examination of different hot and cold combined quenching/extraction approaches to extract and quantify intracellular metabolites of Pseudomonas taiwanensis VLB120 to provide a useful reference dataset of absolute intracellular metabolite concentrations. The suitability of commonly used metabolomics tools including pressure driven fast filtration system followed by combined quenching/extraction techniques (such as cold methanol/acetonitrile/water, hot water, boiling ethanol/water, as well as cold ethanol/water) were tested and evaluated for P...
July 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28726980/interdependence-between-osteoprotegerin-and-active-von-willebrand-factor-in-long-term-cardiovascular-mortality-prediction-in-patients-undergoing-percutaneous-coronary-intervention
#3
Jolanta Siller-Matula, Irene M Lang, Christian Schoergenhofer, Mark Roest, Bernd Jilma
The interdependence of the predictive accuracy of serum osteoprotegerin (OPG) and von Willebrand factor (vWF) levels for long-term cardiovascular outcomes has not been investigated so far. This was a prospective observational cohort study in 361 patients with coronary artery disease undergoing percutaneous coronary intervention (PCI). Baseline levels of OPG, vWF, active vWF (act vWF) and ristocetin cofactor activity (vWF:RICO) were measured. Cardiovascular mortality was recorded over a median of five years...
July 20, 2017: Thrombosis and Haemostasis
https://www.readbyqxmd.com/read/28726800/role-of-nicotinamide-n-methyltransferase-in-dorsal-striatum-in-cocaine-place-preference
#4
Li Luo, Fei-Fei Shang, Hailei Long, Linhong Jiang, Ruiming Zhu, Qian Zhao, Hui Gu, Jueying Kong, Wei Xu, Yinglan Zhao, Xiaobo Cen
Nicotinamide N-methyltransferase (NNMT) transfers the methyl from S-adenosyl-L-methionine (SAM) to nicotinamide (NA) to produce S-adenosyl-L-homocysteine (SAH) and 1-methylnicotinamide (MeN). NNMT has been implicated in a variety of diseases; however, the role of NNMT in drug addiction is largely unknown. Here, we found that the expression of Nnmt was significantly upregulated in the dorsal striatum (DS) of cocaine-conditioned mice. Cocaine significantly decreased SAM/SAH ratio levels in the DS, which was accompanied with the decreased activities of Rac1 and RhoA...
July 20, 2017: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28726395/synthesis-and-mechanism-of-formation-of-hydride-sulfide-complexes-of-iron
#5
Nicholas A Arnet, Sean F McWilliams, Daniel E DeRosha, Brandon Q Mercado, Patrick L Holland
Iron-sulfide complexes with hydride ligands provide an experimental precedent for spectroscopically detected hydride species on the iron-sulfur MoFe7S9C cofactor of nitrogenase. In this contribution, we expand upon our recent synthesis of the first iron sulfide hydride complex from an iron hydride and a sodium thiolate ( Arnet, N. A.; Dugan, T. R.; Menges, F. S.; Mercado, B. Q.; Brennessel, W. W.; Bill, E.; Johnson, M. A.; Holland, P. L., J. Am. Chem. Soc. 2015 , 137 , 13220 - 13223 ). First, we describe the isolation of an analogous iron sulfide hydride with a smaller diketiminate supporting ligand, which benefits from easier preparation of the hydride precursor and easier isolation of the product...
July 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28726126/characterization-of-a-cold-adapted-dna-photolyase-from-c-psychrerythraea-34h
#6
Sudipto Munshi, Ananthi Rajamoorthi, Robert J Stanley
The phrB gene encoding a putative cold-adapted DNA photolyase was cloned from the bacterial genomic DNA of Colwellia psychrerythraea 34H, a psychrophilic bacterium. Recombinant DNA photolyase, rCpPL, was overexpressed and purified from three different vectors. rCpPL binds its DNA substrate by flipping a cyclobutane pyrimidine dimer (CPD) into its active site and repairs CPD-containing DNA in vitro. rCpPL contains one catalytic flavin adenine dinucleotide (FAD) cofactor, but displays promiscuity in cofactor binding, in which either a flavin mononucleotide (FMN) or a methenyltetrahydrofolate (MTHF) molecule is bound as an antenna molecule and found in sub-stoichiometric amounts...
July 19, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28725334/bloch-surface-wave-coupled-emission-at-ultra-violet-wavelengths
#7
Ramachandram Badugu, Jieying Mao, Steve Blair, Douguo Zhang, Emiliano Descrovi, Angelo Angelini, Yiping Huo, Joseph R Lakowicz
The interaction of fluorophores with nearby metallic structures is now an active area of research. Dielectric photonic structures offer some advantages over plasmonic structures, namely small energy losses and less quenching. We describe a dielectric one-dimensional photonic crystal (1DPC), which supports Bloch surface waves (BSWs) from 280 to 440 nm. This BSW structure is a quartz slide coated with alternating layers of SiO2 and Si3N4. We show that this structure displays BSWs and that the near-UV fluorophore, 2-aminopurine (2-AP), on the top surface of the structure couples with the BSWs...
December 22, 2016: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
https://www.readbyqxmd.com/read/28724886/modulation-of-rna-primer-formation-by-mn-ii-substituted-t7-dna-primase
#8
Stefan Ilic, Sabine R Akabayov, Roy Froimovici, Ron Meiry, Dan Vilenchik, Alfredo Hernandez, Haribabu Arthanari, Barak Akabayov
Lagging strand DNA synthesis by DNA polymerase requires RNA primers produced by DNA primase. The N-terminal primase domain of the gene 4 protein of phage T7 comprises a zinc-binding domain that recognizes a specific DNA sequence and an RNA polymerase domain that catalyzes RNA polymerization. Based on its crystal structure, the RNA polymerase domain contains two Mg(II) ions. Mn(II) substitution leads to elevated RNA primer synthesis by T7 DNA primase. NMR analysis revealed that upon binding Mn(II), T7 DNA primase undergoes conformational changes near the metal cofactor binding site that are not observed when the enzyme binds Mg(II)...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724763/species-specificity-of-vaccinia-virus-complement-control-protein-towards-bovine-classical-pathway-is-governed-primarily-by-direct-interaction-of-its-acidic-residues-with-factor-i
#9
Jitendra Kumar, Viveka Nand Yadav, Swastik Phulera, Ashish Kamble, Avneesh Kumar Gautam, Hemendra Singh Panwar, Arvind Sahu
Poxviruses display species tropism - variola virus is a human-specific virus, while vaccinia virus causes repeated outbreaks in dairy cattle. Consistent with this, variola virus complement regulator SPICE exhibit selectivity in inhibiting the human alternative complement pathway and vaccinia virus complement regulator VCP display selectivity in inhibiting the bovine alternative complement pathway. In the present study, we examined the species-specificity of VCP and SPICE towards the classical pathway (CP). We observed that VCP is ∼43-fold superior in inhibiting bovine CP than SPICE...
July 19, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28724401/deciphering-functional-diversification-within-the-lichen-microbiota-by-meta-omics
#10
Tomislav Cernava, Armin Erlacher, Ines Aline Aschenbrenner, Lisa Krug, Christian Lassek, Katharina Riedel, Martin Grube, Gabriele Berg
BACKGROUND: Recent evidence of specific bacterial communities extended the traditional concept of fungal-algal lichen symbioses by a further organismal kingdom. Although functional roles were already assigned to dominant members of the highly diversified microbiota, a substantial fraction of the ubiquitous colonizers remained unexplored. We employed a multi-omics approach to further characterize functional guilds in an unconventional model system. RESULTS: The general community structure of the lichen-associated microbiota was shown to be highly similar irrespective of the employed omics approach...
July 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28724288/proton-based-structural-analysis-of-a-heptahelical-transmembrane-protein-in-lipid-bilayers
#11
Daniela Lalli, Matthew N Idso, Loren B Andreas, Sunyia Hussain, Naomi Baxter, Songi Han, Bradley F Chmelka, Guido Pintacuda
The structures and properties of membrane proteins in lipid bilayers are expected to closely resemble those in native cell-membrane environments, though have been difficult to elucidate. By performing solid-state NMR measurements at very fast (100 kHz) magic-angle spinning rates and at high (23.5 T) magnetic field, severe sensitivity and resolution challenges are overcome, enabling the atomic-level characterization of membrane proteins in lipid environments. This is demonstrated by extensive (1)H-based resonance assignments of the fully protonated heptahelical membrane protein proteorhodopsin, and the efficient identification of numerous (1)H-(1)H dipolar interactions, which provide distance constraints, inter-residue proximities, relative orientations of secondary structural elements, and protein-cofactor interactions in the hydrophobic transmembrane regions...
July 20, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28723619/a-novel-sharpin-prmt5-h3r2me1-axis-is-essential-for-lung-cancer-cell-invasion
#12
Tingxiong Fu, Xiuwei Lv, Qingzhi Kong, Changjing Yuan
SHARPIN (Shank-associated RH domain interacting protein) is the main component of the linear ubiquitin chain activation complex (LUBAC). SHARPIN is involved in regulating inflammation and cancer progression. However, whether SHARPIN plays an important role in lung cancer metastasis and the potential underlying mechanism are still unknown. Here, for the first time, we reported that SHARPIN expression is closely related to lung cancer progression. Moreover, SHARPIN plays a central role in controlling lung cancer cell metastasis...
July 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28723208/the-triple-roles-of-glutathione-for-a-dna-cleaving-dnazyme-and-development-of-a-fluorescent-glutathione-cu-2-dependent-dnazyme-sensor-for-detection-of-cu-2-in-drinking-water
#13
Shijin Wang, Chengcheng Liu, Guiying Li, Yongjie Sheng, Yanhong Sun, Hongyue Rui, Jin Zhang, Jiacui Xu, Dazhi Jiang
Pistol-like DNAzyme (PLDz) is an oxidative DNA-cleaving catalytic DNA with ascorbic acid as cofactor. Herein, glutathione was induced into the reaction system to maintain reduced ascorbic acid levels for higher efficient cleavage. However, data indicated that glutathione played triple roles in PLDz-catalyzed reactions. Glutathione alone had no effect on PLDz, and showed inhibitory effect on ascorbic acid-induced PLDz catalysis, but exhibited stimulating effect on Cu(2+)-promoted self-cleavage of PLDz. Further analysis of the effect of glutathione/Cu(2+) on PLDz indicated that H2O2 played a key role in PLDz catalysis...
March 24, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28723167/sensitive-detection-of-mmp9-enzymatic-activities-in-single-cell-encapsulated-microdroplets-as-an-assay-of-cancer-cell-invasiveness
#14
Zhao Yu, Lu Zhou, Ting Zhang, Rui Shen, Chenxi Li, Xu Fang, Gareth Griffiths, Jian Liu
Matrix metalloproteinases (MMPs) are typically up-regulated in cancer cells, and play a critical role in assisting metastasis by the breakdown of the extracellular matrix. Here we report an effective strategy for cell invasiveness assay by integrating MMP9 functional activity analysis with single cell-encapsulated microdroplets. A flow focusing capillary microfluidic device has been assembled using "off-the-shelf" fluidic components for high-throughput generation of microdroplets. Tumor cells, MMP9 specific peptides, and other cofactors can be loaded into the device and encapsulated into individual droplets as dynamic microreactors for proteolytic cleavage of the substrate...
May 26, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28722796/extended-catalytic-scope-of-a-well-known-enzyme-asymmetric-reduction-of-iminium-substrates-by-glucose-dehydrogenase
#15
Sebastian Roth, Andreas Präg, Cindy Wechsler, Marija Marolt, Sascha Ferlaino, Steffen Lüdeke, Nicolas Sandon, Dennis Wetzl, Hans Iding, Beat Wirz, Michael Müller
NADP(H)-dependent imine reductases (IREDs) are of interest in biocatalytic research due to their ability to generate chiral amines from imine/iminium substrates. In reaction protocols involving IREDs, glucose dehydrogenase (GDH) is generally used to regenerate the expensive cofactor NADPH by oxidation of d-glucose to gluconolactone. We have characterized different IREDs with regard to reduction of a set of bicyclic iminium compounds and have utilized (1) H NMR and GC analyses to determine degree of substrate conversion and product enantiomeric excess (ee)...
July 19, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28722470/novel-potent-inhibitors-of-the-histone-demethylase-kdm1a-lsd1-orally-active-in-a-murine-promyelocitic-leukemia-model
#16
Paolo Trifirò, Anna Cappa, Silvia Brambillasca, Oronza A Botrugno, Maria Rosaria Cera, Roberto Dal Zuffo, Paola Dessanti, Giuseppe Meroni, Florian Thaler, Manuela Villa, Saverio Minucci, Ciro Mercurio, Mario Varasi, Paola Vianello
BACKGROUND: Histone lysine demethylases (KDMs) are well-recognized targets in oncology drug discovery. They function at the post-translation level controlling chromatin conformation and gene transcription. KDM1A is a flavin adenine dinucleotide-dependent amine oxidase, overexpressed in several tumor types, including acute myeloid leukemia, neuroblastoma and non-small-cell lung cancer. Among the many known monoamine oxidase inhibitors screened for KDM1A inhibition, tranylcypromine emerged as a moderately active hit, which irreversibly binds to the flavin adenine dinucleotide cofactor...
July 2017: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/28722361/-food-dependent-exercise-induced-anaphylaxis-a-stepwise-diagnosis
#17
Julien Gaillard, Amélie Borgeat-Kaeser, Guillaume Buss, François Spertini
Food-dependent exercise-induced anaphylaxis (FDEIA) is a potentially severe food allergy. Physical exercise, NSAID, alcohol, infectious diseases and estrogens are recognized cofactors, able to reduce the amount of allergen needed to achieve a threshold for the induction of anaphylaxis. Various kinds of causative food but only a few responsible proteins have been identified. The best known is wheat ω5-gliadine. An oral food challenge remains the gold standard to prove the diagnosis. Its clinical application remains difficult and includes an allergen challenge, a cofactor challenge and a third step which integrates both of them in a single test...
April 5, 2017: Revue Médicale Suisse
https://www.readbyqxmd.com/read/28722011/accumulating-the-hydride-state-in-the-catalytic-cycle-of-fefe-hydrogenases
#18
Martin Winkler, Moritz Senger, Jifu Duan, Julian Esselborn, Florian Wittkamp, Eckhard Hofmann, Ulf-Peter Apfel, Sven Timo Stripp, Thomas Happe
H2 turnover at the [FeFe]-hydrogenase cofactor (H-cluster) is assumed to follow a reversible heterolytic mechanism, first yielding a proton and a hydrido-species which again is double-oxidized to release another proton. Three of the four presumed catalytic intermediates (Hox, Hred/Hred and Hsred) were characterized, using various spectroscopic techniques. However, in catalytically active enzyme, the state containing the hydrido-species, which is eponymous for the proposed heterolytic mechanism, has yet only been speculated about...
July 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28721810/centralized-and-local-color-doppler-ultrasound-reading-agreement-for-diagnosis-of-the-chronic-cerebrospinal-venous-insufficiency-in-patients-with-multiple-sclerosis
#19
Maria Grazia Caprio, Karen Marr, Sirin Gandhi, Dejan Jakimovski, Jesper Hagemeier, Bianca Weinstock-Guttman, Robert Zivadinov, Marcello Mancini
BACKGROUND: An impaired cerebrospinal venous drainage was postulated to be a cofactor in the multifactorial pathogenesis of multiple sclerosis (MS). Chronic cerebrospinal venous insufficiency (CCSVI) is characterized by abnormalities of the main extracranial cerebrospinal venous outflow routes, which can be detected by color Doppler Ultrasound (CDUS) using 5 venous hemodynamic (VH) criteria. Discrepant results between different investigators were reported in the past, therefore the usefulness and applicability of the CCSVI CDUS-based diagnosis in clinical research and practice has been questioned...
July 17, 2017: Current Neurovascular Research
https://www.readbyqxmd.com/read/28720589/dynamic-role-of-the-tether-helix-in-pip2-dependent-gating-of-a-g-protein-gated-potassium-channel
#20
Emre Lacin, Prafulla Aryal, Ian W Glaaser, Karthik Bodhinathan, Eric Tsai, Nidaa Marsh, Stephen J Tucker, Mark S P Sansom, Paul A Slesinger
G protein-gated inwardly rectifying potassium (GIRK) channels control neuronal excitability in the brain and are implicated in several different neurological diseases. The anionic phospholipid phosphatidylinositol 4,5 bisphosphate (PIP2) is an essential cofactor for GIRK channel gating, but the precise mechanism by which PIP2 opens GIRK channels remains poorly understood. Previous structural studies have revealed several highly conserved, positively charged residues in the "tether helix" (C-linker) that interact with the negatively charged PIP2 However, these crystal structures of neuronal GIRK channels in complex with PIP2 provide only snapshots of PIP2's interaction with the channel and thus lack details about the gating transitions triggered by PIP2 binding...
July 18, 2017: Journal of General Physiology
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