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https://www.readbyqxmd.com/read/29028684/toxic-metals-increase-serum-tumor-necrosis-factor-%C3%AE-levels-modified-by-essential-elements-and-different-types-of-tumor-necrosis-factor-%C3%AE-promoter-single-nucleotide-polymorphisms
#1
Yung-Cheng Huang, Wei-Chiao Chang, Ya-Han Shan, Chao-Yi Lin, Chao-Ling Wang, Chia-Yen Dai, Chi-Kung Ho, Ming-Tsang Wu, Hung-Yi Chuang
BACKGROUND: Lead (Pb), cadmium (Cd), and arsenic (As) could cause health issues through oxidative stress that is indicated in the elevated tumor necrosis factor-alpha (TNF-α). However, some of the essential elements-selenium (Se), zinc (Zn), cobalt (Co), and copper (Cu)-are cofactors or structural components of antioxidant enzymes. It is suggested that single-nucleotide polymorphisms (SNPs) in the TNF-α gene have different TNF-α responses. This study aims to evaluate the effect of serum TNF-α levels through the interactions between toxic metals and essential elements and how the interactions between the toxic metals and TNF-α SNPs (-1031 T > C, -863 C > A, -857 C > T, -308 G > A, -238 G > A) influence serum TNF-α levels...
October 2017: Epidemiology
https://www.readbyqxmd.com/read/29027347/a-two-step-evolutionary-process-establishes-a-non-native-vitamin-b6-pathway-in-bacillus-subtilis
#2
Jonathan Rosenberg, KahYen C Yeak, Fabian M Commichau
Pyridoxal 5'-phosphate (PLP), the most important form of vitamin B6 serves as a cofactor for many proteins. Two alternative pathways for de novo PLP biosynthesis are known: the short deoxy-xylulose-5-phosphate (DXP)-independent pathway, which is present in the Gram-positive model bacterium Bacillus subtilis and the longer DXP-dependent pathway, which has been intensively studied in the Gram-negative model bacterium Escherichia coli. Previous studies revealed that bacteria contain many promiscuous enzymes causing a so-called "underground metabolism", which can be important for the evolution of novel pathways...
October 13, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29027293/determination-of-chemical-identity-and-occupancy-from-experimental-density-maps
#3
Jimin Wang
Three basic electronic properties of molecules, electron density (ED), charge density (CD), and electrostatic potentials (ESP), are dependent on both atomic mobility and occupancy of components in the molecules. Small protein subunits may bind large macromolecular complexes with a reduced occupancy or an increased atomic mobility or both due to affinity-based functional regulation, and so may substrates, products, cofactors, ions or solvent molecule to the active sites of enzymes. A quantitative theory is presented in this study that describes the dependence of atomic functions on atomic B-factor in Fourier transforms of the corresponding maps...
October 13, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29027164/chromatin-immunoprecipitation-from-mouse-embryonic-tissue-or-adherent-cells-in-culture-followed-by-next-generation-sequencing
#4
Mário A F Soares, Diogo S Castro
Chromatin immunoprecipitation (ChIP) is considered the method of choice for characterizing interactions between a protein of interest and specific genomic regions. It is of paramount importance in gene-regulation studies, as it can be used to map the target regions of sequence-specific transcription factors and cofactors, or histone marks that characterize distinct chromatin states. ChIP can be used directly to probe interactions with candidate regions (ChIP-PCR), or coupled to Next-Generation Sequencing (ChIP-seq) to generate genome-wide information...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29026785/evaluation-of-p16-ink4%C3%AE-hypermethylation-from-liquid-based-pap-test-samples-in-vietnamese-population
#5
Phuong Kim Truong, Thuan Duc Lao, Thuy Ai Huyen LE
BACKGROUND: Human papillomavirus (HPV) infection has been considered as main cause of cervical cancer. Recently, aberrant DNA methylation at tumor suppressor genes (TSGs), leading to inactivation, has also been an early epigenetic event and cofactor in cervical carcinogenesis. This study was performed to evaluate an association between the hypermethylation of p16(INK4α) gene's promoter and HPV exposure in non-invasive samples (liquid-based papanicolaous samples) in Vietnamese population...
September 2017: Iranian Journal of Public Health
https://www.readbyqxmd.com/read/29026137/opiate-use-inhibits-tlr9-signaling-pathway-in-vivo-possible-role-in-pathogenesis-of-hiv-1-infection
#6
Yanyan Liao, Junjun Jiang, Bingyu Liang, Fumei Wei, Jiegang Huang, Peijiang Pan, Jinming Su, Bo Zhou, Ning Zang, Li Ye, Hao Liang
The molecular mechanism of opiate use promoting HIV-1 infection is not fully understood. TLR9 is expressed in many immune cells, including monocytes, macrophages, which can recognize viruses and viral products and consequently induce the production of antiviral factors and initiate immune responses. Previous studies have shown that chronic viral infections can overcome and impair TLR9 pathway. We aimed to explore whether opiate use enhances HIV infection through inhibition of TLR9 pathway via a population-based study...
October 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29025910/protein-arginine-methyltransferase-6-controls-erythroid-gene-expression-and-differentiation-of-human-cd34-progenitor-cells
#7
Stefanie C Herkt, Olga N Kuvardina, Julia Herglotz, Lucas Schneider, Annekarin Meyer, Claudia Pommerenke, Gabriela Salinas-Riester, Erhard Seifried, Halvard Bonig, Jörn Lausen
Hematopoietic differentiation is driven by transcription factors, which orchestrate a fine tuned transcriptional network. At bipotential branching points lineage decisions are made, where key transcription factors initiate cell type specific gene expression programs. These programs are stabilized by the epigenetic activity of recruited chromatin modifying cofactors. An example gives the association of the transcription factor RUNX1 with the protein arginine methyltransferase 6 (PRMT6) at the megakaryocytic/erythroid bifurcation...
October 12, 2017: Haematologica
https://www.readbyqxmd.com/read/29025858/histone-modifications-regulate-the-developmental-expression-of-human-hepatic-ugt1a1
#8
Ya-Li Nie, Xiang-Guang Meng, Jing-Yang Liu, Liang Yan, Pei Wang, Hong-Zheng Bi, Quan-Cheng Kan, Li-Rong Zhang
Human UDP-glucuronosyltransferase 1A1 (UGT1A1) is a unique enzyme involved in bilirubin conjugation. We previously characterized the hepatic expression of transcription factors affecting UGT1A1 expression during development. Accordingly, in this study, we characterized the ontogenetic expression of hepatic UGT1A1 from the perspective of epigenetic regulation. We observed significant histone-3-lysine-4 dimethylation (H3K4me2) enrichment in the adult liver and histone-3-lysine-27 trimethylation (H3K27me3) enrichment in the fetal liver, indicating that dynamic alterations of histone methylation were associated with ontogenetic UGT1A1 expression...
October 12, 2017: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/29024391/orthogonal-expression-of-an-artificial-metalloenzyme-for-abiotic-catalysis
#9
Eric Brustad, Evan W Reynolds, Timothy D Schwochert, Matthew W McHenry, John W Watters
A cytochrome P450 was engineered to selectively incorporate Ir(Me)-deuteroporphyrin IX (Ir(Me)-DPIX), in lieu of heme, in bacterial cells. Cofactor selectivity was altered by introducing mutations within the heme-binding pocket that discriminate the deuteroporphyrin macrocycle, in combination with mutations to the P450 axial cysteine to accommodate a pendant methyl group on the Ir(Me)-center. This artificial metalloenzyme was investigated for activity in non-native metallocarbenoid-mediated olefin cyclopropanation reactions and showed enhanced activity for aliphatic and electron-deficient olefins when compared to the native heme enzyme...
October 11, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29024318/antiphospholipid-antibody-induced-cellular-responses-depend-on-epitope-specificity-implications-for-treatment-of-aps
#10
Nadine Müller-Calleja, Anne Hollerbach, Friederike Häuser, Antje Canisius, Carolin Orning, Karl J Lackner
BACKGROUND: Antiphospholipid antibodies (aPL) contribute to the pathogenesis of the antiphospholipid syndrome (APS) by induction of an inflammatory and procoagulant state in different cell types and several signaling pathways have been described. OBJECTIVES: We hypothesized that signaling depends on epitope specificity of aPL. METHODS: Cellular effects of three human monoclonal aPL with distinctly different epitope specificities were analyzed in vitro...
October 11, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/29023471/combinatorial-action-of-grainyhead-extradenticle-and-notch-in-regulating-hox-mediated-apoptosis-in-drosophila-larval-cns
#11
Risha Khandelwal, Rashmi Sipani, Sriivatsan Govinda Rajan, Raviranjan Kumar, Rohit Joshi
Hox mediated neuroblast apoptosis is a prevalent way to pattern larval central nervous system (CNS) by different Hox genes, but the mechanism of this apoptosis is not understood. Our studies with Abdominal-A (Abd-A) mediated larval neuroblast (pNB) apoptosis suggests that AbdA, its cofactor Extradenticle (Exd), a helix-loop-helix transcription factor Grainyhead (Grh), and Notch signaling transcriptionally contribute to expression of RHG family of apoptotic genes. We find that Grh, AbdA, and Exd function together at multiple motifs on the apoptotic enhancer...
October 12, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29023106/noncoding-rna-surveillance-the-ends-justify-the-means
#12
Cedric Belair, Soyeong Sim, Sandra L Wolin
Numerous surveillance pathways sculpt eukaryotic transcriptomes by degrading unneeded, defective, and potentially harmful noncoding RNAs (ncRNAs). Because aberrant and excess ncRNAs are largely degraded by exoribonucleases, a key characteristic of these RNAs is an accessible, protein-free 5' or 3' end. Most exoribonucleases function with cofactors that recognize ncRNAs with accessible 5' or 3' ends and/or increase the availability of these ends. Noncoding RNA surveillance pathways were first described in budding yeast, and there are now high-resolution structures of many components of the yeast pathways and significant mechanistic understanding as to how they function...
October 12, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/29022156/recent-advances-in-imine-reductase-catalyzed-reactions
#13
REVIEW
Maike Lenz, Niels Borlinghaus, Leonie Weinmann, Bettina M Nestl
Imine reductases are nicotinamide-dependent enzymes that catalyze the asymmetric reduction of various imines to the corresponding amine products. Owing to the increasing roles of chiral amines and heterocyclic compounds as intermediates for pharmaceuticals, the demand for novel selective synthesis strategies is vitally important. Recent studies have demonstrated the discovery and structural characterization of a number of stereoselective imine reductase enzymes. Here, we highlight recent progress in applying imine reductases for the formation of chiral amines and heterocycles...
October 11, 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/29021791/cofactor-tail-length-modulates-catalysis-of-bacterial-f420-dependent-oxidoreductases
#14
Blair Ney, Carlo R Carere, Richard Sparling, Thanavit Jirapanjawat, Matthew B Stott, Colin J Jackson, John G Oakeshott, Andrew C Warden, Chris Greening
F420 is a microbial cofactor that mediates a wide range of physiologically important and industrially relevant redox reactions, including in methanogenesis and tetracycline biosynthesis. This deazaflavin comprises a redox-active isoalloxazine headgroup conjugated to a lactyloligoglutamyl tail. Here we studied the catalytic significance of the oligoglutamate chain, which differs in length between bacteria and archaea. We purified short-chain F420 (two glutamates) from a methanogen isolate and long-chain F420 (five to eight glutamates) from a recombinant mycobacterium, confirming their different chain lengths by HPLC and LC/MS analysis...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29019354/iron-sulfur-cluster-biosynthesis-and-trafficking-impact-on-human-disease-conditions
#15
C Wachnowsky, I Fidai, J A Cowan
Iron-sulfur clusters (Fe-S) are one of the most ancient, ubiquitous and versatile classes of metal cofactors found in nature. Proteins that contain Fe-S clusters constitute one of the largest families of proteins, with varied functions that include electron transport, regulation of gene expression, substrate binding and activation, radical generation, and, more recently discovered, DNA repair. Research during the past two decades has shown that mitochondria are central to the biogenesis of Fe-S clusters in eukaryotic cells via a conserved cluster assembly machinery (ISC assembly machinery) that also controls the synthesis of Fe-S clusters of cytosolic and nuclear proteins...
October 11, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/29019159/alpha-lipoamide-ameliorates-motor-deficits-and-mitochondrial-dynamics-in-the-parkinson-s-disease-model-induced-by-6-hydroxydopamine
#16
Bo Zhou, Min Wen, Xin Lin, Yun-Hua Chen, Yun Gou, Yong Li, Yi Zhang, Hong-Wei Li, Lei Tang
The precise mechanisms underlying neuronal injury in Parkinson's disease (PD) are not yet fully elucidated; however, evidence from the in vitro and in vivo PD models suggest that mitochondrial dysfunction may play a major role in PD pathogenesis. Alpha lipoamide, a neutral amide derivative of the lipoic acid, is a better cofactor for mitochondrial dehydrogenase with a stronger protective effect on mitochondria than lipoic acid. Identification of these protective effects of alpha lipoamide on mitochondria, together with the evidence that mitochondrial dysfunction plays a critical role in PD, we speculate that alpha lipoamide may exert a protective effect in PD by regulating the mitochondrial function...
October 10, 2017: Neurotoxicity Research
https://www.readbyqxmd.com/read/29018978/identification-of-zfpm2-mutations-in-sporadic-conotruncal-heart-defect-patients
#17
Tian Pu, Yang Liu, Rang Xu, Fen Li, Sun Chen, Kun Sun
Conotruncal heart defects (CTDs) are a group of cardiac malformations that involve outflow tract anomalies and the arterial pole of the heart. Recent reports have identified mutations in a number of genes associated with CTDs in human and animal models. ZFPM2 plays a role in cardiac development by acting as a transcriptional cofactor that interacts with GATA4. Because ZFPM2 was found to be important for cardiac development in a knockout mouse model, we screened for ZFPM2 mutations in 528 CTD patients. We identified six rare and nonsynonymous ZFPM2 variants, and this was the first time that five of these variants (R698Q, R736L, E1005K, T32A, and I488V) were reported in East Asians...
October 10, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29018449/mechanisms-cofactors-and-augmenting-factors-involved-in-anaphylaxis
#18
REVIEW
Rosa Muñoz-Cano, Mariona Pascal, Giovanna Araujo, M J Goikoetxea, Antonio L Valero, Cesar Picado, Joan Bartra
Anaphylaxis is an acute and life-threatening systemic reaction. Many triggers have been described, including food, drug, and hymenoptera allergens, which are the most frequently involved. The mechanisms described in anaphylactic reactions are complex and implicate a diversity of pathways. Some of these mechanisms may be key to the development of the anaphylactic reaction, while others may only modify its severity. Although specific IgE, mast cells, and basophils are considered the principal players in anaphylaxis, alternative mechanisms have been proposed in non-IgE anaphylactic reactions...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29018423/the-microbiome-of-seriola-lalandi-of-wild-and-aquaculture-origin-reveals-differences-in-composition-and-potential-function
#19
Carolina Ramírez, Jaime Romero
Seriola lalandi is an economically important species that is globally distributed in temperate and subtropical marine waters. Aquaculture production of this species has had problems associated with intensive fish farming, such as disease outbreaks or nutritional deficiencies causing high mortalities. Intestinal microbiota has been involved in many processes that benefit the host, such as disease control, stimulation of the immune response, and the promotion of nutrient metabolism, among others. However, little is known about the potential functionality of the microbiota and the differences in the composition between wild and aquacultured fish...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29018119/globally-important-haptophyte-algae-use-exogenous-pyrimidine-compounds-more-efficiently-than-thiamin
#20
Magdalena A Gutowska, Brateen Shome, Sebastian Sudek, Darcy L McRose, Maria Hamilton, Stephen J Giovannoni, Tadhg P Begley, Alexandra Z Worden
Vitamin B1 (thiamin) is a cofactor for critical enzymatic processes and is scarce in surface oceans. Several eukaryotic marine algal species thought to rely on exogenous thiamin are now known to grow equally well on the precursor 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), including the haptophyte Emiliania huxleyi Because the thiamin biosynthetic capacities of the diverse and ecologically important haptophyte lineage are otherwise unknown, we investigated the pathway in transcriptomes and two genomes from 30 species representing six taxonomic orders...
October 10, 2017: MBio
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