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https://www.readbyqxmd.com/read/28813025/association-between-promoter-methylation-of-gene-ercc3-and-benzene-hematotoxicity
#1
Min Zheng, Feiliang Lin, Fenxia Hou, Guilan Li, Caiying Zhu, Peiyu Xu, Caihong Xing, Qianfei Wang
Benzene is a primary industrial chemical and a ubiquitous environmental pollutant. ERCC3 is a key player in nucleotide excision repair. Recent studies suggested that site-specific methylation is a possible mechanism of the transcriptional dysregulation by blocking transcription factors binding. We previously found that the average promoter methylation level of ERCC3 was increased in benzene-exposed workers. In order to test whether specific CpG sites of ERCC3 play an important role in benzene-induced epigenetic changes and whether the specific methylation patterns are associated with benzene hematotoxicity, we analyzed the promoter methylation levels of individual CpG sites, transcription factor binding motif and the correlation between aberrant CpG methylation and hematotoxicity in 76 benzene-exposed workers and 24 unexposed controls in China...
August 16, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28813015/transcriptional-responses-of-creeping-bentgrass-to-2-3-butanediol-a-bacterial-volatile-compound-bvc-analogue
#2
Yi Shi, Kuiju Niu, Bingru Huang, Wenhui Liu, Huiling Ma
Bacterial volatile compounds (BVCs) have been reported to enhance plant growth and elicit plant defenses against fungal infection and insect damage. The objective of this study was to determine transcriptomic changes in response to synthetic BVC that could be associated with plant resistance to Rhizoctonia solani in creeping bentgrass. The 2,3-butanediol (BD) (250 µM) was sprayed on creeping bentgrass leaves grown in jam jars. The result showed that synthetic BD induced plant defense against R. solani for creeping bentgrass...
August 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28812992/endolysosomal-degradation-of-allergenic-ole-e-1-like-proteins-analysis-of-proteolytic-cleavage-sites-revealing-t-cell-epitope-containing-peptides
#3
Sabrina Wildner, Brigitta Elsässer, Teresa Stemeseder, Peter Briza, Wai Tuck Soh, Mayte Villalba, Jonas Lidholm, Hans Brandstetter, Gabriele Gadermaier
Knowledge of the susceptibility of proteins to endolysosomal proteases provides valuable information on immunogenicity. Though Ole e 1-like proteins are considered relevant allergens, little is known about their immunogenic properties and T cell epitopes. Thus, six representative molecules, i.e., Ole e 1, Fra e 1, Sal k 5, Che a 1, Phl p 11 and Pla l 1, were investigated. Endolysosomal degradation and peptide generation were simulated using microsomal fractions of JAWS II dendritic cells. Kinetics and peptide patterns were evaluated by gel electrophoresis and mass spectrometry...
August 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28812944/binding-forces-between-a-novel-schiff-base-palladium-ii-complex-and-two-carrier-proteins-human-serum-albumi-and%C3%AE-lactoglobulin
#4
Somaye Shahraki, Ali Heydari
Ligand binding studies on carrier proteins are crucial in determining the pharmacological properties of drug candidates. Here, a new palladium(II) complex was synthesized and characterized. The in vitro binding studies of this complexwith two carrier proteins, human serum albumin (HSA) and β-lactoglobulin (βLG) was investigated by employing biophysical techniques as well as computational modeling. The experimental results showed thatthe Pd(II) complex interacted with two carrier proteins with moderate binding affinity (Kb ~̴ 0...
August 16, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28812623/a-thousand-empirical-adaptive-landscapes-and-their-navigability
#5
José Aguilar-Rodríguez, Joshua L Payne, Andreas Wagner
The adaptive landscape is an iconic metaphor that pervades evolutionary biology. It was mostly applied in theoretical models until recent years, when empirical data began to allow partial landscape reconstructions. Here, we exhaustively analyse 1,137 complete landscapes from 129 eukaryotic species, each describing the binding affinity of a transcription factor to all possible short DNA sequences. We find that the navigability of these landscapes through single mutations is intermediate to that of additive and shuffled null models, suggesting that binding affinity-and thereby gene expression-is readily fine-tuned via mutations in transcription factor binding sites...
January 23, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812298/a-gata-type-transcription-factor-acareb-for-nitrogen-metabolism-is-involved-in-regulation-of-cephalosporin-biosynthesis-in-acremonium-chrysogenum
#6
Feifei Guan, Yuanyuan Pan, Jinyang Li, Gang Liu
In filamentous fungi, nitrogen metabolism is repressed by GATA-type zinc finger transcription factors. Nitrogen metabolite repression has been found to affect antibiotic production, but the mechanism is still poorly understood. AcareB, encoding a homologue of fungal GATA-type regulatory protein, was cloned from Acremonium chrysogenum. Gene disruption and genetic complementation demonstrated that AcareB plays a key role in utilization of ammonium, glutamine and urea. In addition, significant reduction of cephalosporin production in the AcareB disruption mutant indicated that AcareB is important for cephalosporin production...
August 14, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28812297/neomycin-biosynthesis-is-regulated-positively-by-afsa-g-and-neor-in-streptomyces-fradiae-cgmcc-4-7387
#7
Xiangxi Meng, Wenzhao Wang, Zhoujie Xie, Pengwei Li, Yue Li, Zhengyan Guo, Yingjian Lu, Jie Yang, Kaile Guan, Zhaoxin Lu, Huarong Tan, Yihua Chen
Neomycins are a group of aminoglycoside antibiotics with both clinical and agricultural applications. To elucidate the regulatory mechanism of neomycin biosynthesis, we completed draft genome sequencing of a neomycin producer Streptomyces fradiae CGMCC 4.7387 from marine sediments, and the neomycin biosynthesis gene cluster was identified. Inactivation of the afsA-g gene encoding a γ-butyrolactone (GBL) synthase in S. fradiae CGMCC 4.7387 resulted in a significant decrease of neomycin production. Quantitative RT-PCR analysis revealed that the transcriptional level of neoR and the aphA-neoGH operon were reduced in the afsA-g::aac(3)IV mutant...
August 14, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28812276/arundic-acid-increases-expression-and-function-of-astrocytic-glutamate-transporter-eaat1-via-the-erk-akt-and-nf-%C3%AE%C2%BAb-pathways
#8
Pratap Karki, Peter Hong, James Johnson, Edward Pajarillo, Deok-Soo Son, Michael Aschner, Eunsook Y Lee
Glutamate is the major excitatory neurotransmitter in the brain, but excessive synaptic glutamate must be removed to prevent excitotoxic injury and death. Two astrocytic glutamate transporters, excitatory amino acid transporter (EAAT) 1 and 2, play a major role in eliminating excess glutamate from the synapse. Dysregulation of EAAT1 contributes to the pathogenesis of multiple neurological disorders, such as Alzheimer's disease (AD), ataxia, traumatic brain injuries, and glaucoma. In the present study, we investigated the effect of arundic acid on EAAT1 to determine its efficacy in enhancing the expression and function of EAAT1, and its possible mechanisms of action...
August 15, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28811833/nsitematch-prediction-of-binding-sites-of-nucleotides-by-identifying-the-structure-similarity-of-local-surface-patches
#9
Jie Sun, Ke Chen
Nucleotides play a central role in life-form metabolism, by interacting with proteins and mediating the function of proteins. It is estimated that nucleotides constitute about 15% of the biologically relevant ligands included in PDB. Prediction of binding sites of nucleotides is useful in understanding the function of proteins and can facilitate the in silico design of drugs. In this study, we propose a nucleotide-binding site predictor, namely, NSiteMatch. The NSiteMatch algorithm integrates three different strategies: geometrical analysis, energy calculation, and template comparison...
2017: Computational and Mathematical Methods in Medicine
https://www.readbyqxmd.com/read/28811710/single-amino-acid-mutation-of-sr-bi-decreases-infectivity-of-hepatitis-c-virus-derived-from-cell-culture-in-a-cell-culture-model
#10
Rong Gao, Wei Gao, Gang Xu, Jie Xu, Hao Ren
AIM: To investigate the effect of a single amino acid mutation in human class B scavenger receptor I (SR-BI) on the infectivity of cell culture-derived hepatitis C virus (HCVcc) in SR-BI knock-down Huh7-siSR-BI cells. METHODS: Site-directed mutagenesis was used to construct the SR-BI S112F mutation, and the mutation was confirmed by nucleotide sequencing. SR-BI knock-down Huh7-siSR-BI cells were transfected with SR-BI S112F, SR-BI wild type (WT) and control plasmids, and then infected with HCVpp (HCV pseudoparticles) and hepatitis C virus derived from cell culture (HCVcc)...
July 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28811641/joint-inflammation-related-citrullination-of-functional-arginines-in-extracellular-proteins
#11
Kalle H Sipilä, Vipin Ranga, Pekka Rappu, Markku Mali, Laura Pirilä, Ilona Heino, Johanna Jokinen, Jarmo Käpylä, Mark S Johnson, Jyrki Heino
We report the extent, specific sites and structural requirements of joint inflammation related citrullination in extracellular proteins. A total of 40 synovial fluid samples derived from chronically inflamed human joints were analysed by heparin-agarose fractionation and LC-MS/MS. Citrullination of 55 arginines in extracellular proteins was detected. Importantly, 20% of the sites have a characterized function related to the hallmarks of destructive joint inflammation. E.g. four arginine residues, shown here to be citrullinated, are also affected by mutations in inherited diseases causing haemolysis or blood clotting dysfunction...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811616/synthesis-free-pet-imaging-of-brown-adipose-tissue-and-tspo-via-combination-of-disulfiram-and-64-cucl2
#12
Jing Yang, Jian Yang, Lu Wang, Anna Moore, Steven H Liang, Chongzhao Ran
PET imaging is a widely applicable but a very expensive technology. On-site synthesis is one important contributor to the high cost. In this report, we demonstrated the feasibility of a synthesis-free method for PET imaging of brown adipose tissue (BAT) and translocator protein 18 kDa (TSPO) via a combination of disulfiram, an FDA approved drug for alcoholism, and (64)CuCl2 (termed (64)Cu-Dis). In this method, a step-wise injection protocol of (64)CuCl2 and disulfiram was used to accomplish the purpose of synthesis-free...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811548/ligand-binding-modes-from-low-resolution-gpcr-models-and-mutagenesis-chicken-bitter-taste-receptor-as-a-test-case
#13
Antonella Di Pizio, Louisa-Marie Kruetzfeldt, Shira Cheled-Shoval, Wolfgang Meyerhof, Maik Behrens, Masha Y Niv
Bitter taste is one of the basic taste modalities, warning against consuming potential poisons. Bitter compounds activate members of the bitter taste receptor (Tas2r) subfamily of G protein-coupled receptors (GPCRs). The number of functional Tas2rs is species-dependent. Chickens represent an intriguing minimalistic model, because they detect the bitter taste of structurally different molecules with merely three bitter taste receptor subtypes. We investigated the binding modes of several known agonists of a representative chicken bitter taste receptor, ggTas2r1...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811374/recruitment-of-crispr-cas-systems-by-tn7-like-transposons
#14
Joseph E Peters, Kira S Makarova, Sergey Shmakov, Eugene V Koonin
A survey of bacterial and archaeal genomes shows that many Tn7-like transposons contain minimal type I-F CRISPR-Cas systems that consist of fused cas8f and cas5f, cas7f, and cas6f genes and a short CRISPR array. Several small groups of Tn7-like transposons encompass similarly truncated type I-B CRISPR-Cas. This minimal gene complement of the transposon-associated CRISPR-Cas systems implies that they are competent for pre-CRISPR RNA (precrRNA) processing yielding mature crRNAs and target binding but not target cleavage that is required for interference...
August 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28811350/defining-the-dna-binding-site-recognized-by-the-fission-yeast-zn2cys6-transcription-factor-pho7-and-its-role-in-phosphate-homeostasis
#15
Beate Schwer, Ana M Sanchez, Angad Garg, Debashree Chatterjee, Stewart Shuman
Fission yeast phosphate homeostasis entails transcriptional induction of genes encoding phosphate-mobilizing proteins under conditions of phosphate starvation. Transcription factor Pho7, a member of the Zn2Cys6 family of fungal transcription regulators, is the central player in the starvation response. The DNA binding sites in the promoters of phosphate-responsive genes have not been defined, nor have any structure-function relationships been established for the Pho7 protein. Here we narrow this knowledge gap by (i) delineating an autonomous DNA-binding domain (DBD) within Pho7 that includes the Zn2Cys6 module, (ii) deploying recombinant Pho7 DBD in DNase I footprinting and electrophoretic mobility shift assays (EMSAs) to map the Pho7 recognition sites in the promoters of the phosphate-regulated pho1 and tgp1 genes to a 12-nucleotide sequence motif [5'-TCG(G/C)(A/T)xxTTxAA], (iii) independently identifying the same motif as a Pho7 recognition element via in silico analysis of available genome-wide ChIP-seq data, (iv) affirming that mutations in the two Pho7 recognition sites in the pho1 promoter efface pho1 expression in vivo, and (v) establishing that the zinc-binding cysteines and a pair of conserved arginines in the DBD are essential for Pho7 activity in vivoIMPORTANCE Fungi respond to phosphate starvation by inducing the transcription of a set of phosphate acquisition genes that comprise a phosphate regulon...
August 15, 2017: MBio
https://www.readbyqxmd.com/read/28811203/bpn-a-marine-derived-ptp1b-inhibitor-activates-insulin-signaling-and-improves-insulin-resistance-in-c2c12-myotubes
#16
Qi Xu, Jiao Luo, Ning Wu, Renshuai Zhang, Dayong Shi
Insulin resistance is a key feature of type 2 diabetes mellitus (T2DM) and is characterized by defects in insulin signaling. Protein tyrosine phosphatase 1B (PTP1B) is a major negative regulator of insulin signaling cascade and has attracted intensive investigation in recent T2DM therapy study. BPN, a marine-derived bromophenol compound, was isolated from the red alga Rhodomela confervoides. This study investigated the effects of BPN on the insulin signaling pathway in insulin-resistant C2C12 myotubes by inhibiting PTP1B...
August 12, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28811072/evolution-of-hemoglobin-loci-and-their-regulatory-elements
#17
REVIEW
Sjaak Philipsen, Ross C Hardison
Across the expanse of vertebrate evolution, each species produces multiple forms of hemoglobin in erythroid cells at appropriate times and in the proper amounts. The multiple hemoglobins are encoded in two globin gene clusters in almost all species. One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates. This preservation of synteny may reflect the presence of a powerful enhancer of globin gene expression in the NPRL3 gene...
August 9, 2017: Blood Cells, Molecules & Diseases
https://www.readbyqxmd.com/read/28810738/nature-of-the-active-sites-for-co-reduction-on-copper-nanoparticles-suggestions-for-optimizing-performance
#18
Tao Cheng, Hai Xiao, William A Goddard
Recent experiments show that the grain boundaries (GBs) of copper nanoparticles (NP) lead to outstanding performance in reducing CO2 and CO to alcohol products. We report here multiscale simulations that mimic experimental synthesis conditions to predict the structure of a 10nm Cu NP (158,555 atoms). To identify active sites, we first predict the CO binding at a large number of sites and select 4 exhibiting CO binding stronger than the (211) step surface. Then, we predict the formation energy of *OCCOH intermediate as a descriptor for C-C coupling, identifying two active sites, both of which have an undercoordinated surface square site adjacent to a subsurface stacking fault...
August 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28810637/binding-of-line-1-rna-to-psf-transcriptionally-promotes-gage6-and-regulates-cell-proliferation-and-tumor-formation-in-vitro
#19
Jiao Lv, Ziyi Zhao
Hepatocellular carcinoma (HCC) has one of the highest mortality rates among numerous types of cancer. It has been demonstrated that in hepatitis B (HBV)-associated HCC, the expression of chimeric fusion transcript HBx-long interspersed nuclear element-1 (LINE-1) initiated by HBV integration is correlated with hepatocarcinogenesis and poor patient survival rates. Furthermore, increased rates of LINE-1 hypomethylation have been detected in HCC tissues compared with adjacent tissues. This suggests that individual LINE-1 RNA (L1 RNA) serves an important role in the processes of hepatocarcinogenesis...
August 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28810188/novel-tacrine-derivatives-exhibiting-improved-acetylcholinesterase-inhibition-design-synthesis-and-biological-evaluation
#20
Eeda Koti Reddy, Chandran Remya, Kumar Mantosh, Ayyiliath M Sajith, R V Omkumar, C Sadasivan, Shaik Anwar
A novel series of twenty four tacrine derivatives were designed and synthesised. Among these, thirteen were taken for the acetylcholinesterase (AChE) inhibition studies. Three compounds such as 4c, 6c and 6f were found to possess significant AChE inhibitory properties with IC50 values 12.97 ± 0.47 nM, 5.17 ± 0.24 nM and 7.14 ± 0.78 nM respectively. In silico docking studies revealed that these compounds can bind strongly in the active site of the enzyme and prevent enzyme-substrate interactions...
August 5, 2017: European Journal of Medicinal Chemistry
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