keyword
MENU ▼
Read by QxMD icon Read
search

DNase

keyword
https://www.readbyqxmd.com/read/27911030/acellular-endocardium-as-a-novel-biomaterial-for-the-intima-of-tissue-engineered-small-caliber-vascular-grafts
#1
Feng Wang, Xin Guan, TianYi Wu, JianOu Qiao, ZhaoQing Han, JinLong Wu, XiaoWei Yu, QingJun You
We aimed to investigate whether acellular endocardium can be used as a useful biomaterial for the intima of engineered small-caliber vascular grafts. Fresh endocardium was harvested from the swine left atrium and was decellularized by digestion with the decellularization solution of Triton X-100 and SDS containing DNase I and RNase A. Surface morphological characteristics and Young's modulus were evaluated. To analyze the effect of mechanical characteristics on cell adhesion, the decellularized endocardium was stiffened with 2...
December 2016: Artificial Organs
https://www.readbyqxmd.com/read/27907104/a-new-member-of-the-growing-family-of-contact-dependent-growth-inhibition-systems-in-xenorhabdus-doucetiae
#2
Jean-Claude Ogier, Bernard Duvic, Anne Lanois, Alain Givaudan, Sophie Gaudriault
Xenorhabdus is a bacterial symbiont of entomopathogenic Steinernema nematodes and is pathogenic for insects. Its life cycle involves a stage inside the insect cadaver, in which it competes for environmental resources with microorganisms from soil and the insect gut. Xenorhabdus is, thus, a useful model for identifying new interbacterial competition systems. For the first time, in an entomopathogenic bacterium, Xenorhabdus doucetiae strain FRM16, we identified a cdi-like locus. The cdi loci encode contact-dependent inhibition (CDI) systems composed of proteins from the two-partner secretion (TPS) family...
2016: PloS One
https://www.readbyqxmd.com/read/27905545/on-the-ability-of-molecular-dynamics-simulation-and-continuum-electrostatics-to-treat-interfacial-water-molecules-in-protein-protein-complexes
#3
Guillaume Copie, Fabrizio Cleri, Ralf Blossey, Marc F Lensink
Interfacial waters are increasingly appreciated as playing a key role in protein-protein interactions. We report on a study of the prediction of interfacial water positions by both Molecular Dynamics and explicit solvent-continuum electrostatics based on the Dipolar Poisson-Boltzmann Langevin (DPBL) model, for three test cases: (i) the barnase/barstar complex (ii) the complex between the DNase domain of colicin E2 and its cognate Im2 immunity protein and (iii) the highly unusual anti-freeze protein Maxi which contains a large number of waters in its interior...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27903897/combining-atac-seq-with-nuclei-sorting-for-discovery-of-cis-regulatory-regions-in-plant-genomes
#4
Zefu Lu, Brigitte T Hofmeister, Christopher Vollmers, Rebecca M DuBois, Robert J Schmitz
: Chromatin structure plays a pivotal role in facilitating proper control of gene expression. Transcription factor (TF) binding of cis-elements is often associated with accessible chromatin regions. Therefore, the ability to identify these accessible regions throughout plant genomes will advance understanding of the relationship between TF binding, chromatin status and the regulation of gene expression. Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) is a recently developed technique used to map open chromatin zones in animal genomes...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27901386/comparison-of-four-methods-for-generating-decellularized-equine-synovial-extracellular-matrix
#5
Nathalie A Reisbig, Hayam A Hussein, Erin Pinnell, Alicia L Bertone
OBJECTIVE To evaluate 4 methods for generating decellularized equine synovial extracellular matrix. SAMPLE Villous synovium harvested from the femoropatellar and medial femorotibial joints of 4 healthy adult horses < 7 years of age. Synovial samples were frozen (-80°C) until used. PROCEDURES Synovial samples were thawed and left untreated (control) or decellularized with 1 of 4 methods (15 samples/horse/method): incubation in 0.1% peracetic acid (PAA), incubation in 0.1% PAA twice, incubation in 1% Triton X-100 followed by incubation in DNase, and incubation in 2M NaCl followed by incubation in DNase...
December 2016: American Journal of Veterinary Research
https://www.readbyqxmd.com/read/27899572/c3-symmetric-opioid-scaffolds-are-ph-responsive-dna-condensation-agents
#6
Natasha McStay, Zara Molphy, Alan Coughlan, Attilio Cafolla, Vickie McKee, Nicholas Gathergood, Andrew Kellett
Herein we report the synthesis of tripodal C3-symmetric opioid scaffolds as high-affinity condensation agents of duplex DNA. Condensation was achieved on both supercoiled and canonical B-DNA structures and identified by agarose electrophoresis, viscosity, turbidity and atomic force microscopy (AFM) measurements. Structurally, the requirement of a tris-opioid scaffold for condensation is demonstrated as both di- (C2-symmetric) and mono-substituted (C1-symmetric) mesitylene-linked opioid derivatives poorly coordinate dsDNA...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899335/design-and-characterization-of-plasmids-encoding-antigenic-peptides-of-aha1-from-aeromonas-hydrophila-as-prospective-fish-vaccines
#7
Pradipta R Rauta, Bismita Nayak, Gabriel A Monteiro, Marília Mateus
The current investigation aimed at designing DNA vaccines against Aeromonas hydrophila infections. The DNA vaccine candidates were designed to express two antigenic outer membrane protein (Aha1) peptides and to be delivered by a nanoparticle-based delivery system. Gene sequences of conserved regions of antigenic Aha1 [aha1(211-381), aha1(211-381)opt, aha1(703-999) and aha1(703-999)opt] were cloned into pVAX-GFP expression vector. The selected DNA vaccine candidates were purified from E. coli DH5α and transfected into Chinese hamster ovary cells...
November 26, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27898729/rna-contaminates-glycosaminoglycans-extracted-from-cells-and-tissues
#8
Jasper J van Gemst, Markus A Loeven, Mark J J de Graaf, Jo H M Berden, Ton J Rabelink, Cornelis H Smit, Johan van der Vlag
Glycosaminoglycans (GAGs) are linear negatively charged polysaccharides and important components of extracellular matrices and cell surface glycan layers such as the endothelial glycocalyx. The GAG family includes sulfated heparin, heparan sulfate (HS), dermatan sulfate (DS), chondroitin sulfate (CS), keratan sulfate, and non-sulfated hyaluronan. Because relative expression of GAGs is dependent on cell-type and niche, isolating GAGs from cell cultures and tissues may provide insight into cell- and tissue-specific GAG structure and functions...
2016: PloS One
https://www.readbyqxmd.com/read/27895039/region-specific-effect-of-the-decellularized-meniscus-extracellular-matrix-on-mesenchymal-stem-cell-based-meniscus-tissue-engineering
#9
Kazunori Shimomura, Benjamin B Rothrauff, Rocky S Tuan
BACKGROUND: The meniscus is the most commonly injured knee structure, and surgical repair is often ineffective. Tissue engineering-based repair or regeneration may provide a needed solution. Decellularized, tissue-derived extracellular matrices (ECMs) have received attention for their potential use as tissue-engineered scaffolds. In considering meniscus-derived ECMs (mECMs) for meniscus tissue engineering, it is noteworthy that the inner and outer regions of the meniscus have different structural and biochemical features, potentially directing the differentiation of cells toward region-specific phenotypes...
November 28, 2016: American Journal of Sports Medicine
https://www.readbyqxmd.com/read/27884105/structural-features-of-dna-that-determine-rna-polymerase-ii-core-promoter
#10
Irina A Il'icheva, Mingian V Khodikov, Maria S Poptsova, Dmitry Yu Nechipurenko, Yury D Nechipurenko, Sergei L Grokhovsky
BACKGROUND: The general structure and action of all eukaryotic and archaeal RNA polymerases machinery have an astonishing similarity despite the diversity of core promoter sequences in different species. The goal of our work is to find common characteristics of DNA region that define it as a promoter for the RNA polymerase II (Pol II). RESULTS: The profiles of a large number of physical and structural characteristics, averaged over representative sets of the Pol II minimal core promoters of the evolutionary divergent species from animals, plants and unicellular fungi were analysed...
November 25, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27878922/a-nodd-like-protein-activates-transcription-of-genes-involved-with-naringenin-degradation-in-a-flavonoid-dependent-manner-in-herbaspirillum-seropedicae
#11
R Wassem, A M Marin, A Daddaoua, R A Monteiro, L S Chubatsu, J L Ramos, W J Deakin, W J Broughton, F O Pedrosa, E M Souza
Herbaspirillum seropedicae is an associative, endophytic non-nodulating diazotrophic bacterium that colonises several grasses. An ORF encoding a LysR-type transcriptional regulator, very similar to NodD proteins of rhizobia, was identified in its genome. This nodD-like gene, named fdeR, is divergently transcribed from an operon encoding enzymes involved in flavonoid degradation (fde operon). Apigenin, chrysin, luteolin and naringenin strongly induce transcription of the fde operon, but not that of the fdeR, in an FdeR-dependent manner...
November 23, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27875544/extensive-association-of-common-disease-variants-with-regulatory-sequence
#12
Michal Mokry, Magdalena Harakalova, Folkert W Asselbergs, Paul I W de Bakker, Edward E S Nieuwenhuis
Overlap between non-coding DNA regulatory sequences and common variant associations can help to identify specific cell and tissue types that are relevant for particular diseases. In a systematic manner, we analyzed variants from 94 genome-wide association studies (reporting at least 12 loci at p<5x10-8) by projecting them onto 466 epigenetic datasets (characterizing DNase I hypersensitive sites; DHSs) derived from various adult and fetal tissue samples and cell lines including many biological replicates...
2016: PloS One
https://www.readbyqxmd.com/read/27866707/a-functional-variant-associated-with-atrial-fibrillation-regulates-pitx2c-expression-through-tfap2a
#13
Jiangchuan Ye, Nathan R Tucker, Lu-Chen Weng, Sebastian Clauss, Steven A Lubitz, Patrick T Ellinor
The most significantly associated genetic locus for atrial fibrillation (AF) is in chromosomal region 4q25, where four independent association signals have been identified. Although model-system studies suggest that altered PITX2c expression might underlie the association, the link between specific variants and the direction of effect on gene expression remains unknown for all four signals. In the present study, we analyzed the AF-associated region most proximal to PITX2 at 4q25. First, we identified candidate regulatory variants that might confer AF risk through a combination of mammalian conservation, DNase hypersensitivity, and histone modification from ENCODE and the Roadmap Epigenomics Project, as well as through in vivo analysis of enhancer activity in embryonic zebrafish...
December 1, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27865056/the-caspase-activated-dnase-apoptosis-and-beyond
#14
REVIEW
Brian D Larsen, Claus S Sørensen
Organismal development and function requires multiple and accurate signal transduction pathways to ensure that proper balance between cell proliferation, differentiation, inactivation, and death is achieved. Cell death via apoptotic caspase signal transduction is extensively characterized and integral to this balance. Importantly, the view of apoptotic signal transduction has expanded over the previous decades. Sub-apoptotic caspase signaling has surfaced as mechanism that can promote the adoption of a range of cellular fates...
November 19, 2016: FEBS Journal
https://www.readbyqxmd.com/read/27856755/controlling-dna-nanoparticle-serum-interactions
#15
Kyryl Zagorovsky, Leo Y T Chou, Warren C W Chan
Understanding the interaction of molecularly assembled nanoparticles with physiological fluids is critical to their use for in vivo delivery of drugs and contrast agents. Here, we systematically investigated the factors and mechanisms that govern the degradation of DNA on the nanoparticle surface in serum. We discovered that a higher DNA density, shorter oligonucleotides, and thicker PEG layer increased protection of DNA against serum degradation. Oligonucleotides on the surface of nanoparticles were highly resistant to DNase I endonucleases, and degradation was carried out exclusively by protein-mediated exonuclease cleavage and full-strand desorption...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27851974/eforge-a-tool-for-identifying-cell-type-specific-signal-in-epigenomic-data
#16
Charles E Breeze, Dirk S Paul, Jenny van Dongen, Lee M Butcher, John C Ambrose, James E Barrett, Robert Lowe, Vardhman K Rakyan, Valentina Iotchkova, Mattia Frontini, Kate Downes, Willem H Ouwehand, Jonathan Laperle, Pierre-Étienne Jacques, Guillaume Bourque, Anke K Bergmann, Reiner Siebert, Edo Vellenga, Sadia Saeed, Filomena Matarese, Joost H A Martens, Hendrik G Stunnenberg, Andrew E Teschendorff, Javier Herrero, Ewan Birney, Ian Dunham, Stephan Beck
Epigenome-wide association studies (EWAS) provide an alternative approach for studying human disease through consideration of non-genetic variants such as altered DNA methylation. To advance the complex interpretation of EWAS, we developed eFORGE (http://eforge.cs.ucl.ac.uk/), a new standalone and web-based tool for the analysis and interpretation of EWAS data. eFORGE determines the cell type-specific regulatory component of a set of EWAS-identified differentially methylated positions. This is achieved by detecting enrichment of overlap with DNase I hypersensitive sites across 454 samples (tissues, primary cell types, and cell lines) from the ENCODE, Roadmap Epigenomics, and BLUEPRINT projects...
November 15, 2016: Cell Reports
https://www.readbyqxmd.com/read/27851146/1510-resolvin-d2-and-dnase-minimize-secondary-wound-necrosis
#17
Masayuki Otawara, Yoshitaka Inoue, Yuk Liu, Benjamin Vakoc, Jeremy Goverman, Yong-Ming Yu, Daniel Irimia
No abstract text is available yet for this article.
December 2016: Critical Care Medicine
https://www.readbyqxmd.com/read/27849031/neutrophil-extracellular-traps-are-indirectly-triggered-by-lipopolysaccharide-and-contribute-to-acute-lung-injury
#18
Shuai Liu, Xiaoli Su, Pinhua Pan, Lemeng Zhang, Yongbin Hu, Hongyi Tan, Dongdong Wu, Ben Liu, Haitao Li, Haosi Li, Yi Li, Minhui Dai, Yuanyuan Li, Chengping Hu, Allan Tsung
Neutrophil extracellular traps (NETs) facilitate the extracellular killing of pathogens. However, excessive NETs formation and poor degradation are associated with exacerbated immune responses and tissue injury. In this study, we investigated the role of NETs in lipopolysaccharide (LPS)-mediated acute lung injury (ALI) and assessed the use of DNase I, for the treatment of ALI. Additionally, we focused on the controversial issue of whether LPS directly induces NETs release in vitro. NETs formation was detected in murine ALI tissue in vivo and was associated with increased NETs markers, citrullinated-histone H3 tissue levels and NET-DNA levels in BALF...
November 16, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27847224/tetraiodothyroacetic-acid-conjugated-polyethylenimine-for-integrin-receptor-mediated-delivery-of-the-plasmid-encoding-il-12-gene
#19
Fatemeh Sheikhsaran, Hossein Sadeghpour, Bahman Khalvati, Elaheh Entezar-Almahdi, Ali Dehshahri
Targeted delivery by polymer-based nanoparticles has been considered as an efficient approach to transfer genetic materials into cells. Considering the over expression of integrin αVβ3 receptor on tumor cells and the presence of the binding site for tetraiodothyroacetic acid (tetrac) on integrin receptor, we hypothesized that the conjugation of tetrac to polyethylenimine (PEI) might be an effective strategy for pDNA delivery into the cells over-expressing integrins on their surfaces. In order to test the hypothesis, tetrac conjugated PEI/plasmid DNA complexes were prepared and their ability in the delivery of plasmid encoding IL-12 gene was investigated...
November 5, 2016: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/27846892/choosing-panels-of-genomics-assays-using-submodular-optimization
#20
Kai Wei, Maxwell W Libbrecht, Jeffrey A Bilmes, William Stafford Noble
Due to the high cost of sequencing-based genomics assays such as ChIP-seq and DNase-seq, the epigenomic characterization of a cell type is typically carried out using a small panel of assay types. Deciding a priori which assays to perform is, thus, a critical step in many studies. We present the submodular selection of assays (SSA), a method for choosing a diverse panel of genomic assays that leverages methods from submodular optimization. More generally, this application serves as a model for how submodular optimization can be applied to other discrete problems in biology...
November 15, 2016: Genome Biology
keyword
keyword
12981
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"