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https://www.readbyqxmd.com/read/28549169/regulatory-dynamics-of-11p13-suggest-a-role-for-ehf-in-modifying-cf-lung-disease-severity
#1
Lindsay R Stolzenburg, Rui Yang, Jenny L Kerschner, Sara Fossum, Matthew Xu, Andrew Hoffmann, Kay-Marie Lamar, Sujana Ghosh, Sarah Wachtel, Shih-Hsing Leir, Ann Harris
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF), but are not good predictors of lung phenotype. Genome-wide association studies (GWAS) previously identified additional genomic sites associated with CF lung disease severity. One of these, at chromosome 11p13, is an intergenic region between Ets homologous factor (EHF) and Apaf-1 interacting protein (APIP). Our goal was to determine the functional significance of this region, which being intergenic is probably regulatory...
May 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28545143/haemophilus-parasuis-cytolethal-distending-toxin-induces-cell-cycle-arrest-and-p53-dependent-apoptosis
#2
Gang Li, Hui Niu, Yanhe Zhang, Yanling Li, Fang Xie, Paul R Langford, Siguo Liu, Chunlai Wang
Haemophilus parasuis is the causative agent of Glasser's disease in pigs. Cytolethal distending toxin (CDT) is an important virulence factor of H. parasuis. It is composed of three subunits: CdtA, CdtB and CdtC and all were successfully expressed in soluble form in Escherichia coli when the signal peptides were removed. Purified CdtB had DNase activity, i.e. caused DNA double strand damage, in vitro and in vivo prior to cell arrest and apoptosis. Flow cytometry analysis showed CdtB alone could induce cell cycle arrest and apoptosis in PK-15 porcine kidney and pulmonary alveolar macrophage (PAM) cells, which could be enhanced by CdtA or/and CdtC...
2017: PloS One
https://www.readbyqxmd.com/read/28544514/dynamic-enhancer-function-in-the-chromatin-context
#3
REVIEW
Ido Goldstein, Gordon L Hager
Enhancers serve as critical regulatory elements in higher eukaryotic cells. The characterization of enhancer function has evolved primarily from genome-wide methodologies, including chromatin immunoprecipitation (ChIP-seq), DNase-I hypersensitivity (DNase-seq), digital genomic footprinting (DGF), and the chromosome conformation capture techniques (3C, 4C, and Hi-C). These population-based assays average signals across millions of cells and lead to enhancer models characterized by static and sequential binding...
May 22, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28543094/mechanism-of-graphene-induced-cytotoxicity-role-of-endonucleases
#4
Tariq Fahmi, La Donna Branch, Zeid A Nima, Dae Song Jang, Alena V Savenka, Alexandru S Biris, Alexei G Basnakian
Graphene, a crystalline allotrope or carbon, presents numerous useful properties; however, its toxicity is yet to be determined. One of the most dramatic and irreversible toxic abilities of carbon nanomaterials is the induction of DNA fragmentation produced by endogenous cellular endonucleases. This study demonstrated that pristine graphene exposed to cultured kidney tubular epithelial cells is capable of inducing DNA fragmentation measured by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, which is usually associated with cell death...
May 24, 2017: Journal of Applied Toxicology: JAT
https://www.readbyqxmd.com/read/28542600/snp-in-human-arhgef3-promoter-is-associated-with-dnase-hypersensitivity-transcript-level-and-platelet-function-and-arhgef3-ko-mice-have-increased-mean-platelet-volume
#5
Siying Zou, Alexandra M Teixeira, Myrto Kostadima, William J Astle, Aparna Radhakrishnan, Lukas Mikolaj Simon, Lucy Truman, Jennifer S Fang, John Hwa, Ping-Xia Zhang, Pim van der Harst, Paul F Bray, Willem H Ouwehand, Mattia Frontini, Diane S Krause
Genome-wide association studies have identified a genetic variant at 3p14.3 (SNP rs1354034) that strongly associates with platelet number and mean platelet volume in humans. While originally proposed to be intronic, analysis of mRNA expression in primary human hematopoietic subpopulations reveals that this SNP is located directly upstream of the predominantly expressed ARHGEF3 isoform in megakaryocytes (MK). We found that ARHGEF3, which encodes a Rho guanine exchange factor, is dramatically upregulated during both human and murine MK maturation...
2017: PloS One
https://www.readbyqxmd.com/read/28542501/a-rho-associated-coiled-coil-containing-kinases-rock-inhibitor-y-27632-enhances-adhesion-viability-and-differentiation-of-human-term-placenta-derived-trophoblasts-in-vitro
#6
Kenichiro Motomura, Naoko Okada, Hideaki Morita, Mariko Hara, Masato Tamari, Keisuke Orimo, Go Matsuda, Ken-Ichi Imadome, Akio Matsuda, Takeshi Nagamatsu, Mikiya Fujieda, Haruhiko Sago, Hirohisa Saito, Kenji Matsumoto
Although human term placenta-derived primary cytotrophoblasts (pCTBs) represent a good human syncytiotrophoblast (STB) model, in vitro culture of pCTBs is not always easily accomplished. Y-27632, a specific inhibitor of Rho-associated coiled-coil containing kinases (ROCK), reportedly prevented apoptosis and improved cell-to-substrate adhesion and culture stability of dissociated cultured human embryonic stem cells and human corneal endothelial cells. The Rho kinase pathway regulates various kinds of cell behavior, some of which are involved in pCTB adhesion and differentiation...
2017: PloS One
https://www.readbyqxmd.com/read/28538187/bivariate-genomic-footprinting-detects-changes-in-transcription-factor-activity
#7
Songjoon Baek, Ido Goldstein, Gordon L Hager
In response to activating signals, transcription factors (TFs) bind DNA and regulate gene expression. TF binding can be measured by protection of the bound sequence from DNase digestion (i.e., footprint). Here, we report that 80% of TF binding motifs do not show a measurable footprint, partly because of a variable cleavage pattern within the motif sequence. To more faithfully portray the effect of TFs on chromatin, we developed an algorithm that captures two TF-dependent effects on chromatin accessibility: footprinting and motif-flanking accessibility...
May 23, 2017: Cell Reports
https://www.readbyqxmd.com/read/28530675/reevaluation-of-snp-heritability-in-complex-human-traits
#8
Doug Speed, Na Cai, Michael R Johnson, Sergey Nejentsev, David J Balding
SNP heritability, the proportion of phenotypic variance explained by SNPs, has been reported for many hundreds of traits. Its estimation requires strong prior assumptions about the distribution of heritability across the genome, but current assumptions have not been thoroughly tested. By analyzing imputed data for a large number of human traits, we empirically derive a model that more accurately describes how heritability varies with minor allele frequency (MAF), linkage disequilibrium (LD) and genotype certainty...
May 22, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28526794/raffinose-induces-biofilm-formation-by-streptococcus-mutans-in-low-concentrations-of-sucrose-by-increasing-production-of-extracellular-dna-and-fructan
#9
Ryo Nagasawa, Tsutomu Sato, Hidenobu Senpuku
Streptococcus mutans is the primary etiological agent of dental caries and causes tooth decay by forming a firmly attached biofilm on tooth surfaces. Biofilm formation is induced by the presence of sucrose, which is a substrate for the synthesis of extracellular polysaccharides, but not in the presence of oligosaccharides. Nonetheless, in this study, we found that raffinose, which is an oligosaccharide with an intestinal regulatory function and antiallergic effect, induced biofilm formation by S. mutans in a mixed culture with sucrose which was at concentrations less than those required to induce biofilm formation directly...
May 19, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28526032/multiplex-dnase-free-one-step-reverse-transcription-pcr-for-plasmodium-18s-rrna-and-spliced-gametocyte-specific-mrnas
#10
Amelia E Hanron, Zachary P Billman, Annette M Seilie, Tayla M Olsen, Matthew Fishbaugher, Ming Chang, Thomas Rueckle, Nicole Andenmatten, Bryan Greenhouse, Emmanuel Arinaitwe, John Rek, Smita Das, Gonzalo J Domingo, Kelly Shipman, Stefan H Kappe, James G Kublin, Sean C Murphy
BACKGROUND: Plasmodium gametocytes are sexual stages transmitted to female Anopheles mosquitoes. While Plasmodium parasites can be differentiated microscopically on Giemsa-stained blood smears, molecular methods are increasingly used because of their increased sensitivity. Molecular detection of gametocytes requires methods that discriminate between asexual and sexual stage parasites. Commonly tested gametocyte-specific mRNAs are pfs25 and pfs230 detected by reverse transcription polymerase chain reaction (RT-PCR)...
May 19, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28525845/novel-amidino-substituted-benzimidazole-and-benzothiazole-benzo-b-thieno-2-carboxamides-exert-strong-antiproliferative-and-dna-binding-properties
#11
Maja Cindrić, Samy Jambon, Anja Harej, Sabine Depauw, Marie-Hélène David-Cordonnier, Sandra Kraljević Pavelić, Grace Karminski-Zamola, Marijana Hranjec
Within this manuscript design, synthesis of novel 2-imidazolinyl substituted benzo[b]thieno-2-carboxamides bearing either benzimidazole or benzothiazole subunit and biological activity are presented and described. The antiproliferative activities were assessed in vitro on a panel of human cancer cell lines. Tested compounds showed moderate activity while cytotoxicity on normal fibroblasts was lower in comparison with 5-fluorouracile. The variations of 2-imidazolinyl substituent at heteroaromatic subunits in different positions led to different cytotoxic properties...
May 4, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28525337/molecular-characterization-and-detection-of-enterotoxins-methicillin-resistance-genes-and-antimicrobial-resistance-of-staphylococcus-aureus-from-fish-and-ground-beef
#12
S Arslan, F Özdemir
A total of 120 samples including 40 freshwaterfish(Oncorhynchus mykiss), 40 seawater fish (Sparus aurata) and 40 ground beef samples were examined for the presence of Staphylococcus aureus. The isolates were identified using biochemical tests and a PCR for the species-specific fragment (Sa442) and thermonuclease gene (nucA). The presence of staphylococcal enterotoxin genes (sea, seb, sec, sed and see), toxin genes (eta, etb, tsst), methicillin resistance gene (mecA) and some phenotypic virulence factors was also tested...
March 28, 2017: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/28522396/ultrafast-spectroscopy-on-dna-cleavage-by-endonuclease-in-molecular-crowding
#13
Priya Singh, Susobhan Choudhury, Shreyasi Dutta, Aniruddha Adhikari, Siddhartha Bhattacharya, Debasish Pal, Samir Kumar Pal
The jam-packed intracellular environments differ the activity of a biological macromolecule from that in laboratory environments (in vitro) through a number of mechanisms called molecular crowding related to structure, function and dynamics of the macromolecule. Here, we have explored the structure, function and dynamics of a model enzyme protein DNase I in molecular crowing of polyethylene glycol (PEG; MW 3350). We have used steady state and picosecond resolved dynamics of a well-known intercalator ethidium bromide (EB) in a 20-mer double-stranded DNA (dsDNA) to monitor the DNA-cleavage by the enzyme in absence and presence PEG...
May 15, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28513628/an-integrated-model-for-detecting-significant-chromatin-interactions-from-high-resolution-hi-c-data
#14
Mark Carty, Lee Zamparo, Merve Sahin, Alvaro González, Raphael Pelossof, Olivier Elemento, Christina S Leslie
Here we present HiC-DC, a principled method to estimate the statistical significance (P values) of chromatin interactions from Hi-C experiments. HiC-DC uses hurdle negative binomial regression account for systematic sources of variation in Hi-C read counts-for example, distance-dependent random polymer ligation and GC content and mappability bias-and model zero inflation and overdispersion. Applied to high-resolution Hi-C data in a lymphoblastoid cell line, HiC-DC detects significant interactions at the sub-topologically associating domain level, identifying potential structural and regulatory interactions supported by CTCF binding sites, DNase accessibility, and/or active histone marks...
May 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28505330/acinetobacter-baumannii-transfers-the-blandm-1-gene-via-outer-membrane-vesicles
#15
Somdatta Chatterjee, Ayan Mondal, Shravani Mitra, Sulagna Basu
Objectives: To investigate the transmission of the gene encoding New Delhi metallo-β-lactamase-1 ( bla NDM-1 ) through outer membrane vesicles (OMVs) released from an Acinetobacter baumannii strain (A_115). Methods: Isolation and purification of OMVs by density gradient from a carbapenem-resistant clinical strain of A. baumannii harbouring plasmid-mediated bla NDM-1 and aac(6')-Ib-cr genes was performed. DNA was purified from the OMVs and used for PCR and dot-blot analysis...
May 12, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28505247/single-cell-regulome-data-analysis-by-scrat
#16
Zhicheng Ji, Weiqiang Zhou, Hongkai Ji
Summary: Emerging single-cell technologies (e.g., single-cell ATAC-seq, DNase-seq or ChIP-seq) have made it possible to assay regulome of individual cells. Single-cell regulome data are highly sparse and discrete. Analyzing such data is challenging. User-friendly software tools are still lacking. We present SCRAT, a Single-Cell Regulome Analysis Toolbox with a graphical user interface, for studying cell heterogeneity using single-cell regulome data. SCRAT can be used to conveniently summarize regulatory activities according to different features (e...
May 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28491057/identification-of-genes-controlled-by-the-essential-yycfg-two-component-system-reveals-a-role-for-biofilm-modulation-in-staphylococcus-epidermidis
#17
Tao Xu, Yang Wu, Zhiwei Lin, Ralph Bertram, Friedrich Götz, Ying Zhang, Di Qu
Biofilms play a crucial role in the pathogenicity of Staphylococcus epidermidis, while little is known about whether the essential YycFG two-component signal transduction system (TCS) is involved in biofilm formation. We used antisense RNA (asRNA) to silence the yycFG TCS in order to study its regulatory functions in S. epidermidis. Strain 1457 expressing asRNA yycF exhibited a significant delay (~4-5 h) in entry to log phase, which was partially complemented by overexpressing ssaA. The expression of asRNA yycF and asRNA yycG resulted in a 68 and 50% decrease in biofilm formation at 6 h, respectively, while they had no significant inhibitory effect on 12 h biofilm formation...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28488944/a-scalable-and-accurate-method-for-quantifying-vector-genomes-of-recombinant-adeno-associated-viruses-in-crude-lysate
#18
Jianzhong Ai, Raed Ibraheim, Phillip W L Tai, Guangping Gao
Increasing interest and application of recombinant adeno-associated viruses (rAAVs) in basic and clinical research have urged efforts to improve rAAV production quality and yield. Standard vector production workflows call for genome titration of purified vectors at the endpoint of production to assess yield. Unfortunately, quality control measures for preparations during mid-production steps and economical means to assess the fidelity of multiple batches of rAAV preparations are lacking. Here we describe a scalable and accurate method for the direct quantitative polymerase chain reaction (qPCR) titration of rAAV genomes in crude lysate...
April 13, 2017: Human Gene Therapy Methods
https://www.readbyqxmd.com/read/28487391/functional-characterization-of-the-gucy1a3-coronary-artery-disease-risk-locus
#19
Thorsten Kessler, Jana Wobst, Bernhard Wolf, Juliane Eckhold, Baiba Vilne, Ronja Hollstein, Simon von Ameln, Tan An Dang, Hendrik B Sager, Philipp Moritz Rumpf, Redouane Aherrahrou, Adnan Kastrati, Johan L M Bjoerkegren, Jeanette Erdmann, Aldons J Lusis, Mete Civelek, Frank J Kaiser, Heribert Schunkert
Background -A chromosomal locus at 4q32.1 has been genome-wide significantly associated with coronary artery disease risk. The locus encompasses GUCY1A3, which encodes the α1-subunit of the soluble guanylyl cyclase (sGC), a key enzyme in the nitric oxide (NO)/cyclic guanosine monophosphate (cGMP) signaling pathway. The mechanism linking common variants in this region with coronary risk is not known. Methods -Gene and protein expression were analyzed using quantitative polymerase chain reaction (qPCR) and immunoblotting, respectively...
May 9, 2017: Circulation
https://www.readbyqxmd.com/read/28485798/immune-complexes-induce-tnf-%C3%AE-and-baff-production-from-u937-cells-by-hmgb1-and-rage
#20
X-J Gao, Y-Y Qu, X-W Liu, M Zhu, C-Y Ma, Y-L Jiao, B Cui, Z-J Chen, Y-R Zhao
OBJECTIVE: This study investigated the effects of immune complexes (ICs) on tumor necrosis factor α (TNF-α) and B cell-activating factor (BAFF) production from U937 cells and further explored the mechanism. MATERIALS AND METHODS: U937 cells were incubated with necrosis supernatant or systemic lupus erythematosus (SLE) sera alone, or their combination. The expression of TNF-α and BAFF was determined by Real-time polymerase chain reaction and enzyme-linked immunosorbent assay...
April 2017: European Review for Medical and Pharmacological Sciences
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