keyword
MENU ▼
Read by QxMD icon Read
search

DNaseI

keyword
https://www.readbyqxmd.com/read/29572206/roles-of-pad4-and-netosis-in-experimental-atherosclerosis-and-arterial-injury-implications-for-superficial-erosion
#1
Grégory Franck, Thomas L Mawson, Eduardo J Folco, Roberto Molinaro, Victoria Ruvkun, Daniel Engelbertsen, Xin Liu, Yevgenia Tesmenitsky, Eugenia Shvartz, Galina K Sukhova, Jean-Baptiste Michel, Antonino Nicoletti, Andrew H Lichtman, Denisa D Wagner, Kevin J Croce, Peter Libby
<u>Rationale:</u> Neutrophils likely contribute to the thrombotic complications of human atheromata. In particular, neutrophil extracellular traps (NETs) could exacerbate local inflammation and amplify and propagate arterial intimal injury and thrombosis. Peptidyl arginine deiminase 4 (PAD4) participates in NET formation, but understanding of this enzyme's role in atherothrombosis remains scant. <u>Objective:</u> This study tested the hypothesis that PAD4 and NETs influence experimental atherogenesis and in processes implicated in superficial erosion, a form of plaque complication we previously associated with NETs...
March 23, 2018: Circulation Research
https://www.readbyqxmd.com/read/29563192/cryo-em-structure-of-the-nucleosome-containing-the-alb1-enhancer-dna-sequence
#2
Yoshimasa Takizawa, Hiroki Tanaka, Shinichi Machida, Masako Koyama, Kazumitsu Maehara, Yasuyuki Ohkawa, Paul A Wade, Matthias Wolf, Hitoshi Kurumizaka
Pioneer transcription factors specifically target their recognition DNA sequences within nucleosomes. FoxA is the pioneer transcription factor that binds to the ALB1 gene enhancer in liver precursor cells, and is required for liver differentiation in embryos. The ALB1 enhancer DNA sequence is reportedly incorporated into nucleosomes in cells, although the nucleosome structure containing the targeting sites for FoxA has not been clarified yet. In this study, we determined the nucleosome structure containing the ALB1 enhancer (N1) sequence, by cryogenic electron microscopy at 4...
March 2018: Open Biology
https://www.readbyqxmd.com/read/29551295/systemic-activation-of-nlrp3-inflammasome-in-patients-with-severe-primary-sj%C3%A3-gren-s-syndrome-fueled-by-inflammagenic-dna-accumulations
#3
Aigli G Vakrakou, Sorina Boiu, Panayiotis D Ziakas, Evangelia Xingi, Haralabia Boleti, Menelaos N Manoussakis
Sjögren's syndrome (SS) patients manifest high cell-free DNA (cf-DNA) levels in serum, associated with impaired DNaseI activity. Undegraded DNA may accumulate in tissues and act as an inflammasome-activating signal. Herein, we investigated the occurrence of aberrant DNA build-up in various biologic compartments of SS patients and its correlation with the activity of NLRP3 and AIM2 inflammasomes. For this purpose, we evaluated sera, PBMC, circulating monocytes and salivary glands (SG) from different SS patient subgroups and controls...
March 16, 2018: Journal of Autoimmunity
https://www.readbyqxmd.com/read/29520342/control-of-hmu-heme-uptake-genes-in-yersinia-pseudotuberculosis-in-response-to-iron-sources
#4
Leah Schwiesow, Erin Mettert, Yahan Wei, Halie K Miller, Natalia G Herrera, David Balderas, Patricia J Kiley, Victoria Auerbuch
Despite the mammalian host actively sequestering iron to limit pathogenicity, heme (or hemin when oxidized) and hemoproteins serve as important sources of iron for many bloodborne pathogens. The HmuRSTUV hemin uptake system allows Yersinia species to uptake and utilize hemin and hemoproteins as iron sources. HmuR is a TonB-dependent outer membrane receptor for hemin and hemoproteins. HmuTUV comprise a inner membrane ABC transporter that transports hemin and hemoproteins from the periplasmic space into the bacterial cytoplasm, where it is degraded by HmuS...
2018: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29451908/cas9-mediated-excision-of-proximal-dnasei-h3k4me3-signatures-confers-robust-silencing-of-microrna-and-long-non-coding-rna-genes
#5
Harshavardhan Janga, Marina Aznaourova, Fabian Boldt, Katrin Damm, Arnold Grünweller, Leon N Schulte
CRISPR/Cas9-based approaches have greatly facilitated targeted genomic deletions. Contrary to coding genes however, which can be functionally knocked out by frame-shift mutagenesis, non-coding RNA (ncRNA) gene knockouts have remained challenging. Here we present a universal ncRNA knockout approach guided by epigenetic hallmarks, which enables robust gene silencing even in provisionally annotated gene loci. We build on previous work reporting the presence of overlapping histone H3 lysine 4 tri-methylation (H3K4me3) and DNaseI hypersensitivity sites around the transcriptional start sites of most genes...
2018: PloS One
https://www.readbyqxmd.com/read/29425920/sting-signaling-promotes-inflammation-in-experimental-acute-pancreatitis
#6
Qinglan Zhao, Yi Wei, Stephen J Pandol, Lingyin Li, Aida Habtezion
BACKGROUND & AIMS: Acute pancreatitis (AP) is characterized by severe inflammation and acinar cell death. Transmembrane protein 173 (TMEM173 or STING) is a DNA sensor adaptor protein on immune cells that recognizes cytosolic nucleic acids and transmits signals that activate production of interferons and the innate immune response. We investigated whether leukocyte STING signaling mediates inflammation in mice with AP. METHODS: We induced AP in C57BL/6J mice (control) and C57BL/6J-Tmem173gt/J mice (STING-knockout mice) by injection of cerulein or placement on choline-deficient DL-ethionine supplemented diet...
May 2018: Gastroenterology
https://www.readbyqxmd.com/read/29023490/network-modeling-of-kinase-inhibitor-polypharmacology-reveals-pathways-targeted-in-chemical-screens
#7
Oana Ursu, Sara J C Gosline, Neil Beeharry, Lauren Fink, Vikram Bhattacharjee, Shao-Shan Carol Huang, Yan Zhou, Tim Yen, Ernest Fraenkel
Small molecule screens are widely used to prioritize pharmaceutical development. However, determining the pathways targeted by these molecules is challenging, since the compounds are often promiscuous. We present a network strategy that takes into account the polypharmacology of small molecules in order to generate hypotheses for their broader mode of action. We report a screen for kinase inhibitors that increase the efficacy of gemcitabine, the first-line chemotherapy for pancreatic cancer. Eight kinase inhibitors emerge that are known to affect 201 kinases, of which only three kinases have been previously identified as modifiers of gemcitabine toxicity...
2017: PloS One
https://www.readbyqxmd.com/read/28694794/antivirulent-properties-of-underexplored-cinnamomum-tamala-essential-oil-and-its-synergistic-effects-with-dnase-against-pseudomonas-aeruginosa-biofilms-an-in-vitro-study
#8
Sanaulla Farisa Banu, Durairajan Rubini, Sairam Rakshitaa, Kamaraj Chandrasekar, Ramar Murugan, Aruni Wilson, Shanmugaraj Gowrishankar, Shunmugiah Karutha Pandian, Paramasivam Nithyanand
Pseudomonas aeruginosa is a nosocomial pathogen colonizing patients with chronic infectious diseases and has gained resistance to all the known broad spectrum antibiotics available today. The present study showcases the antibiofilm potential of an essential oil (EO) from an underexplored Cinnamomum species namely, C. tamala, against P. aeruginosa biofilms. Furthermore, the synergistic effects of the EO along with a commercially available DNase (DNaseI) and a DNase (MBD) isolated from a marine bacterium were explored for its antibiofilm activity...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28642863/friends-enemies-endogenous-retroviruses-are-major-transcriptional-regulators-of-human-dna
#9
REVIEW
Anton A Buzdin, Vladimir Prassolov, Andrew V Garazha
Endogenous retroviruses are mobile genetic elements hardly distinguishable from infectious, or "exogenous," retroviruses at the time of insertion in the host DNA. Human endogenous retroviruses (HERVs) are not rare. They gave rise to multiple families of closely related mobile elements that occupy ~8% of the human genome. Together, they shape genomic regulatory landscape by providing at least ~320,000 human transcription factor binding sites (TFBS) located on ~110,000 individual HERV elements. The HERVs host as many as 155,000 mapped DNaseI hypersensitivity sites, which denote loci active in the regulation of gene expression or chromatin structure...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28642500/genome-wide-mapping-of-dnase-i-hypersensitive-sites-reveals-chromatin-accessibility-changes-in-arabidopsis-euchromatin-and-heterochromatin-regions-under-extended-darkness
#10
Yue Liu, Wenli Zhang, Kang Zhang, Qi You, Hengyu Yan, Yuannian Jiao, Jiming Jiang, Wenying Xu, Zhen Su
Light, as the energy source in photosynthesis, is essential for plant growth and development. Extended darkness causes dramatic gene expression changes. In this study, we applied DNase-seq (DNase I hypersensitive site sequencing) to study changes of chromatin accessibility in euchromatic and heterochromatic regions under extended darkness in Arabidopsis. We generated 27 Gb DNase-seq and 67.6 Gb RNA-seq data to investigate chromatin accessibility changes and global gene expression under extended darkness and control condition in Arabidopsis...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28619820/soxf-factors-induce-notch1-expression-via-direct-transcriptional-regulation-during-early-arterial-development
#11
Ivy Kim-Ni Chiang, Martin Fritzsche, Cathy Pichol-Thievend, Alice Neal, Kelly Holmes, Anne Lagendijk, Jeroen Overman, Donatella D'Angelo, Alice Omini, Dorien Hermkens, Emmanuelle Lesieur, Ke Liu, Indrika Ratnayaka, Monica Corada, George Bou-Gharios, Jason Carroll, Elisabetta Dejana, Stefan Schulte-Merker, Benjamin Hogan, Monica Beltrame, Sarah De Val, Mathias Francois
Arterial specification and differentiation are influenced by a number of regulatory pathways. While it is known that the Vegfa-Notch cascade plays a central role, the transcriptional hierarchy controlling arterial specification has not been fully delineated. To elucidate the direct transcriptional regulators of Notch receptor expression in arterial endothelial cells, we used histone signatures, DNaseI hypersensitivity and ChIP-seq data to identify enhancers for the human NOTCH1 and zebrafish notch1b genes. These enhancers were able to direct arterial endothelial cell-restricted expression in transgenic models...
July 15, 2017: Development
https://www.readbyqxmd.com/read/28593035/smchd1-regulates-a-limited-set-of-gene-clusters-on-autosomal-chromosomes
#12
Amanda G Mason, Roderick C Slieker, Judit Balog, Richard J L F Lemmers, Chao-Jen Wong, Zizhen Yao, Jong-Won Lim, Galina N Filippova, Enrico Ne, Rabi Tawil, Bas T Heijmans, Stephen J Tapscott, Silvère M van der Maarel
BACKGROUND: Facioscapulohumeral muscular dystrophy (FSHD) is in most cases caused by a contraction of the D4Z4 macrosatellite repeat on chromosome 4 (FSHD1) or by mutations in the SMCHD1 or DNMT3B gene (FSHD2). Both situations result in the incomplete epigenetic repression of the D4Z4-encoded retrogene DUX4 in somatic cells, leading to the aberrant expression of DUX4 in the skeletal muscle. In mice, Smchd1 regulates chromatin repression at different loci, having a role in CpG methylation establishment and/or maintenance...
2017: Skeletal Muscle
https://www.readbyqxmd.com/read/28587678/smchd1-regulates-a-limited-set-of-gene-clusters-on-autosomal-chromosomes
#13
Amanda G Mason, Roderick C Slieker, Judit Balog, Richard J L F Lemmers, Chao-Jen Wong, Zizhen Yao, Jong-Won Lim, Galina N Filippova, Enrico Ne, Rabi Tawil, Bas T Heijmans, Stephen J Tapscott, Silvère M van der Maarel
BACKGROUND: Facioscapulohumeral muscular dystrophy (FSHD) is in most cases caused by a contraction of the D4Z4 macrosatellite repeat on chromosome 4 (FSHD1) or by mutations in the SMCHD1 or DNMT3B gene (FSHD2). Both situations result in the incomplete epigenetic repression of the D4Z4-encoded retrogene DUX4 in somatic cells, leading to the aberrant expression of DUX4 in the skeletal muscle. In mice, Smchd1 regulates chromatin repression at different loci, having a role in CpG methylation establishment and/or maintenance...
June 6, 2017: Skeletal Muscle
https://www.readbyqxmd.com/read/28428090/preparation-and-characterization-of-lipid-nanoparticle-pdna-complexes-for-stat3-downregulation-and-overcoming-chemotherapy-resistance-in-lung-cancer-cells
#14
Mustafa Kotmakçı, Vildan Bozok Çetintaş, A Gülten Kantarcı
Developments in the field of molecular oncology have revealed that resistance to chemotherapeutics is acqured through several mechanisms including overexpression of common oncogenic proteins. Signal Transducer and Activator of Transcription 3 (STAT3) is one of these oncogenes that is overexpressed in many cancer types. RNA interference (RNAi) is proven powerful tool for downregulating STAT3, allowing re-sensitization of resistant cancer cells. However, delivery of RNA interference-mediating molecules for STAT3 downregulation in lung cancer cells is limited to a small number of studies most of which employ commercially available transfection kits...
June 15, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28426246/biofilm-characteristics-and-evaluation-of-the-sanitation-procedures-of-thermophilic-aeribacillus-pallidus-e334-biofilms
#15
Tugba Kilic, Basar Karaca, Beste Piril Ozel, Birgul Ozcan, Cumhur Cokmus, Arzu Coleri Cihan
The ability of Aeribacillus pallidus E334 to produce pellicle and form a biofilm was studied. Optimal biofilm formation occurred at 60 °C, pH 7.5 and 1.5% NaCl. Extra polymeric substances (EPS) were composed of proteins and eDNA (21.4 kb). E334 formed biofilm on many surfaces, but mostly preferred polypropylene and glass. Using CLSM analysis, the network-like structure of the EPS was observed. The A. pallidus biofilm had a novel eDNA content. DNaseI susceptibility (86.8% removal) of eDNA revealed its importance in mature biofilms, but the purified eDNA was resistant to DNaseI, probably due to its extended folding outside the matrix...
April 2017: Biofouling
https://www.readbyqxmd.com/read/28379368/scode-an-efficient-regulatory-network-inference-algorithm-from-single-cell-rna-seq-during-differentiation
#16
Hirotaka Matsumoto, Hisanori Kiryu, Chikara Furusawa, Minoru S H Ko, Shigeru B H Ko, Norio Gouda, Tetsutaro Hayashi, Itoshi Nikaido
Motivation: The analysis of RNA-Seq data from individual differentiating cells enables us to reconstruct the differentiation process and the degree of differentiation (in pseudo-time) of each cell. Such analyses can reveal detailed expression dynamics and functional relationships for differentiation. To further elucidate differentiation processes, more insight into gene regulatory networks is required. The pseudo-time can be regarded as time information and, therefore, single-cell RNA-Seq data are time-course data with high time resolution...
August 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28351714/evaluation-of-environmental-and-nutritional-factors-and-sua-gene-on-in%C3%A2-vitro-biofilm-formation-of-streptococcus-uberis-isolates
#17
Melina Vanesa Moliva, Florencia Cerioli, Elina Beatriz Reinoso
The pathogenesis of Streptococcus uberis is attributed to a combination of extracellular factors and properties such as adherence and biofilm formation. The aim of this work was to evaluate the influence of different factors, additives and bovine milk compounds on S. uberis biofilm formation, as the presence of the sua gene by PCR. Additionally, extracellular DNA and the effect of DNaseI were evaluated in the biofilms yielded. Optimal biofilm development was observed when the pH was adjusted to 7.0 and 37 °C...
June 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28218056/regulation-of-the-escherichia-coli-ydhy-t-operon-in-the-presence-of-alternative-electron-acceptors
#18
Naji Awad A Al Ibrahim, Jeffrey Green
The Escherichia coli K-12 ydhY-T operon, coding for a predicted oxidoreductase complex, is activated under anaerobic conditions and repressed in the presence of nitrate or nitrite. Anaerobic activation is mediated by the transcription factor FNR, and nitrate/nitrite repression is mediated by NarXL and NarQP. In vitro transcription reactions revealed that the DNA upstream of ydhY-T contains sufficient information for RNA polymerase alone to initiate transcription from five locations. FNR severely inhibited synthesis of two of these transcripts (located upstream of, and within, the FNR binding site) and activated the FNR-dependent promoter previously identified in vivo...
April 2017: Microbiology
https://www.readbyqxmd.com/read/28160363/establishment-of-a-tobacco-by2-cell-line-devoid-of-plant-specific-xylose-and-fucose-as-a-platform-for-the-production-of-biotherapeutic-proteins
#19
Uri Hanania, Tami Ariel, Yoram Tekoah, Liat Fux, Maor Sheva, Yehuda Gubbay, Mara Weiss, Dina Oz, Yaniv Azulay, Albina Turbovski, Yehava Forster, Yoseph Shaaltiel
Plant-produced glycoproteins contain N-linked glycans with plant-specific residues of β(1,2)-xylose and core α(1,3)-fucose, which do not exist in mammalian-derived proteins. Although our experience with two enzymes that are used for enzyme replacement therapy does not indicate that the plant sugar residues have deleterious effects, we made a conscious decision to eliminate these moieties from plant-expressed proteins. We knocked out the β(1,2)-xylosyltranferase (XylT) and the α(1,3)-fucosyltransferase (FucT) genes, using CRISPR/Cas9 genome editing, in Nicotiana tabacum L...
September 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28087634/genome-wide-identification-of-regulatory-elements-in-sertoli-cells
#20
Danielle M Maatouk, Anirudh Natarajan, Yoichiro Shibata, Lingyun Song, Gregory E Crawford, Uwe Ohler, Blanche Capel
A current goal of molecular biology is to identify transcriptional networks that regulate cell differentiation. However, identifying functional gene regulatory elements has been challenging in the context of developing tissues where material is limited and cell types are mixed. To identify regulatory sites during sex determination, we subjected Sertoli cells from mouse fetal testes to DNaseI-seq and ChIP-seq for H3K27ac. DNaseI-seq identified putative regulatory sites around genes enriched in Sertoli and pregranulosa cells; however, active enhancers marked by H3K27ac were enriched proximal to only Sertoli-enriched genes...
February 15, 2017: Development
keyword
keyword
51261
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"