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https://www.readbyqxmd.com/read/28738606/a-label-free-fluorometric-assay-for-actin-detection-based-on-enzyme-responsive-dna-templated-copper-nanoparticles
#1
Quanwei Song, Lixia Yang, Hongkun Chen, Rong Zhang, Na Na, Jin Ouyang
Herein, we develop a fluorescent strategy for label-free detection of actin by the in situ formation of double-stranded DNA (dsDNA) templated copper nanoparticles (CuNPs) and the digestion capability of deoxyribonuclease I (DNase I). In this design, the introduction of actin can effectively hinder the enzymic digestion owing to the exceptional target-mediated conformational structure between actin and DNase I. Consequently, the remaining adenine-thymine-rich dsDNA can act as an efficient template for fluorescent CuNPs (λex = 340nm, λem = 585nm) with a Mega-Stokes shifting (245nm)...
November 1, 2017: Talanta
https://www.readbyqxmd.com/read/28738444/protein-coating-of-dna-nanostructures-for-enhanced-stability-and-immunocompatibility
#2
Henni Auvinen, Hongbo Zhang, Nonappa, Alisa Kopilow, Elina H Niemelä, Sami Nummelin, Alexandra Correia, Hélder A Santos, Veikko Linko, Mauri A Kostiainen
Fully addressable DNA nanostructures, especially DNA origami, possess huge potential to serve as inherently biocompatible and versatile molecular platforms. However, their use as delivery vehicles in therapeutics is compromised by their low stability and poor transfection rates. This study shows that DNA origami can be coated by precisely defined one-to-one protein-dendron conjugates to tackle the aforementioned issues. The dendron part of the conjugate serves as a cationic binding domain that attaches to the negatively charged DNA origami surface via electrostatic interactions...
July 24, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28732013/the-kp1_4563-gene-is-regulated-by-the-camp-receptor-protein-and-controls-type-3-fimbrial-function-in-klebsiella-pneumoniae-ntuh-k2044
#3
Mei Luo, Shiya Yang, Xuan Li, Pin Liu, Jian Xue, Xipeng Zhou, Kewen Su, Xuan Xu, Ying Qing, Jingfu Qiu, Yingli Li
Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogen that can adhere to host cells or extracellular matrix via type 1 and type 3 fimbriae. KP1_4563 is a gene encoding a hypothetical protein in K. pneumoniae NTUH-K2044. KP1_4563 is located between the type 1 and type 3 fimbrial gene clusters and is likely associated with fimbrial function given its putative conserved domains of unknown function (DUF1471). Cyclic AMP receptor protein (CRP) regulates virulence-related gene expression and is a crucial transcriptional regulator in many bacteria...
2017: PloS One
https://www.readbyqxmd.com/read/28728145/extracellular-dna-contributes-to-dental-biofilm-stability
#4
Sebastian Schlafer, Rikke L Meyer, Irene Dige, Viduthalai R Regina
Extracellular DNA (eDNA) is a major matrix component of many bacterial biofilms. While the presence of eDNA and its role in biofilm stability have been demonstrated for several laboratory biofilms of oral bacteria, there is no data available on the presence and function of eDNA in in vivo grown dental biofilms. This study aimed to determine whether eDNA was part of the matrix in biofilms grown in situ in the absence of sucrose and whether treatment with DNase dispersed biofilms grown for 2.5, 5, 7.5, 16.5, or 24 h...
July 21, 2017: Caries Research
https://www.readbyqxmd.com/read/28723896/maternal-h3k27me3-controls-dna-methylation-independent-imprinting
#5
Azusa Inoue, Lan Jiang, Falong Lu, Tsukasa Suzuki, Yi Zhang
Mammalian sperm and oocytes have different epigenetic landscapes and are organized in different fashions. After fertilization, the initially distinct parental epigenomes become largely equalized with the exception of certain loci, including imprinting control regions. How parental chromatin becomes equalized and how imprinting control regions escape from this reprogramming is largely unknown. Here we profile parental allele-specific DNase I hypersensitive sites in mouse zygotes and morula embryos, and investigate the epigenetic mechanisms underlying these allelic sites...
July 19, 2017: Nature
https://www.readbyqxmd.com/read/28715766/different-effects-of-matrix-degrading-enzymes-towards-biofilms-formed-by-e-faecalis-and-e-faecium-clinical-isolates
#6
Riccardo Torelli, Margherita Cacaci, Massimiliano Papi, Francesco Paroni Sterbini, Cecilia Martini, Brunella Posteraro, Valentina Palmieri, Marco De Spirito, Maurizio Sanguinetti, Francesca Bugli
E. faecalis and E. faecium cause urinary tract infections highly resistant to therapies due to a protective extracellular matrix. To exploit a new strategy able to treat infections without increasing antibiotic doses, we used enzymes targeting specific biofilm matrix components in combination with Vancomycin. We investigated the activity of Vancomycin combined with two matrix-degrading enzymes, Alginate Lyase (AlgL) and Deoxyribonuclease I (DNase I) against in vitro biofilm of E. faecalis and E. faecium clinical isolates...
July 9, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28715365/analysis-of-the-c-kit-ligand-promoter-using-chromatin-immunoprecipitation
#7
Pingyu Zhang, Andres Rojas, Boris Blechacz
Multiple cellular processes, including DNA replication and repair, DNA recombination, and gene expression, require interactions between proteins and DNA. Therefore, DNA-protein interactions regulate multiple physiological, pathophysiological, and biological functions, such as cell differentiation, cell proliferation, cell cycle control, chromosome stability, epigenetic gene regulation, and cell transformation. In eukaryotic cells, the DNA interacts with histone and nonhistone proteins and is condensed into chromatin...
June 27, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28714845/bacillus-mangrovi-sp-nov-isolated-from-a-sediment-sample-from-a-mangrove-forest
#8
Vasundhera Gupta, Pradip Kumar Singh, Suresh Korpole, Naga Radha Srinivas Tanuku, Anil Kumar Pinnaka
A facultatively anaerobic, endospore forming, alkali-tolerant, Gram-stain-positive, motile, rod-shaped bacterium, designated strain AK61T, was isolated from a sediment sample collected from Coringa mangrove forest, India. Colonies were circular, 1.5 mm in diameter, shiny, smooth, yellowish and convex with entire margins after 48 h growth at 30 °C. Growth occurred at 15-42 °C, with 0-3 % (w/v) NaCl and at pH 6-9. AK61T was positive for amylase activity and negative for oxidase, catalase, aesculinase, caseinase, cellulase, DNase, gelatinase, lipase and urease activities...
July 17, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28713353/functional-characterization-of-novel-faecalibacterium-prausnitzii-strains-isolated-from-healthy-volunteers-a-step-forward-in-the-use-of-f-prausnitzii-as-a-next-generation-probiotic
#9
Rebeca Martín, Sylvie Miquel, Leandro Benevides, Chantal Bridonneau, Véronique Robert, Sylvie Hudault, Florian Chain, Olivier Berteau, Vasco Azevedo, Jean M Chatel, Harry Sokol, Luis G Bermúdez-Humarán, Muriel Thomas, Philippe Langella
Faecalibacterium prausnitzii is a major member of the Firmicutes phylum and one of the most abundant bacteria in the healthy human microbiota. F. prausnitzii depletion has been reported in several intestinal disorders, and more consistently in Crohn's disease (CD) patients. Despite its importance in human health, only few microbiological studies have been performed to isolate novel F. prausnitzii strains in order to better understand the biodiversity and physiological diversity of this beneficial commensal species...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28710778/a-detection-method-for-the-rash-and-fever-illness-associated-viruses-using-multiplex-rt-pcr
#10
Yuki Matsushima, Tomomi Shimizu, Ikuko Doi, Fuminori Mizukoshi, Koo Nagasawa, Akihide Ryo, Hideaki Shimizu, Masae Kobayashi, Keiji Funatogawa, Noriko Nagata, Mariko Ishikawa, Ayako Komane, Nobuhiko Okabe, Yoshio Mori, Makoto Takeda, Hirokazu Kimura
To detect various viral genes in the patients with rash and fever illness (RFI), a new multiplex (reverse transcription) polymerase chain reaction [(RT)-PCR] method was constructed. New primer sets were designed for the detection of herpes simplex viruses 1 and 2 (HSV1 and 2), and Epstein-Barr virus (EBV). The newly designed and previously reported primer sets were used to detect 13 types of RFI-associated viruses by multiplex (RT)-PCR assay systems. Moreover, to eliminate non-specific PCR products, a double-stranded specific DNase was used for the digestion of double-stranded DNA derived from the templates in clinical specimens...
July 15, 2017: Microbiology and Immunology
https://www.readbyqxmd.com/read/28710757/quick-detection-of-dnase-ii-type-breaks-in-formalin-fixed-tissue-sections
#11
Candace L Minchew, Vladimir V Didenko
Blunt-ended DNase II-type breaks with 5' hydroxyls are generated in phagocytic cells of any lineage during digestion of the engulfed DNA. These breaks indicate the ongoing active phagocytic reaction. They are produced by the acid deoxyribonuclease-DNase II which is the primary endonuclease responsible for DNA degradation after its engulfment.Here, we present an express approach that detects blunt-ended 5' OH DNA breaks in fixed tissue sections. The technique is simple to perform and takes only 60 min to complete...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28710749/express-fret-labeling-and-analysis-of-phagocytic-clearance
#12
Vladimir V Didenko
Lysosomal DNase II in phagocytic digestion produces DNA ends with 3'PO4/5'OH, which differ from those created in apoptotic DNA fragmentation, and can be used to label phagocytic clearance of cell death. Here, we describe the use of these specific DNA ends as selective markers of phagocytic reaction in cell suspensions. The approach does not require cell fixation. It selectively labels blunt-ended DNA breaks with terminal 5'OH. The detection is performed by ultra-fast FRET probes in a single step, closed-tube procedure...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28710125/visualization-of-extracellular-dna-released-during-border-cell-separation-from-the-root-cap
#13
Fushi Wen, Gilberto Curlango-Rivera, David A Huskey, Zhongguo Xiong, Martha C Hawes
PREMISE OF THE STUDY: Root border cells are programmed to separate from the root cap as it penetrates the soil environment, where the cells actively secrete >100 extracellular proteins into the surrounding mucilage. The detached cells function in defense of the root tip by an extracellular trapping process that also requires DNA, as in mammalian white blood cells. Trapping in animals and plants is reversed by treatment with DNase, which results in increased infection. The goal of this study was to evaluate the role of DNA in the structural integrity of extracellular structures released as border cells disperse from the root tip upon contact with water...
July 14, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28709908/variable-rna-expression-from-recently-acquired-endogenous-viral-elements-eve-of-white-spot-syndrome-virus-wssv-in-shrimp
#14
Heny Budi Utari, Chumporn Soowannayan, Timothy W Flegel, Boonsirm Whityachumnarnkul, Maleeya Kruatrachue
The viral accommodation hypothesis proposes that endogenous viral elements (EVE) from both RNA and DNA viruses are being continually integrated into the shrimp genome by natural host processes and that they can result in tolerance to viral infection by fortuitous production of antisense, immunospecific RNA (imRNA). Thus, we hypothesized that previously reported microarray results for the presence of white spot syndrome virus (WSSV) open reading frames (ORFs) formerly called 151, 366 and 427 in a domesticated giant tiger shrimp (Penaeus monodon) breeding stock might have represented expression from EVE, since the stock had shown uninterrupted freedom from white spot disease (WSD) for many generations...
July 11, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28704389/differential-chromatin-profiles-partially-determine-transcription-factor-binding
#15
Rujian Chen, David K Gifford
We characterize how genomic variants that alter chromatin accessibility influence regulatory factor binding with a new method called DeltaBind that predicts condition specific factor binding more accurately than other methods based on DNase-seq data. Using DeltaBind and DNase-seq experiments we predicted the differential binding of 18 factors in K562 and GM12878 cells with an average precision of 28% at 10% recall, with the prediction of individual factors ranging from 5% to 65% precision. We further found that genome variants that alter chromatin accessibility are not necessarily predictive of altering proximal factor binding...
2017: PloS One
https://www.readbyqxmd.com/read/28698277/deep-sea-hydrothermal-vent-viruses-compensate-for-microbial-metabolism-in-virus-host-interactions
#16
Tianliang He, Hongyun Li, Xiaobo Zhang
Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation...
July 11, 2017: MBio
https://www.readbyqxmd.com/read/28696508/neutrophil-extracellular-traps-in-ischemic-stroke-thrombi
#17
Elodie Laridan, Frederik Denorme, Linda Desender, Olivier François, Tommy Andersson, Hans Deckmyn, Karen Vanhoorelbeke, Simon F De Meyer
OBJECTIVE: Neutrophil extracellular traps (NETs) have been shown to promote thrombus formation. Little is known about the exact composition of thrombi that cause ischemic stroke. In particular no information is yet available on the presence of NETs in cerebral occlusions. Such information is however essential to improve current thrombolytic therapy with t-PA. This study aimed at investigating the presence of neutrophils and more specifically NETs in ischemic stroke thrombi. METHODS: Sixty-eight thrombi retrieved from ischemic stroke patients undergoing endovascular treatment were characterized by immunostaining using neutrophil markers (CD66b and neutrophil elastase) and NETs markers (citrullinated histones H3 (H3Cit) and extracellular DNA)...
July 11, 2017: Annals of Neurology
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
#18
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/28692404/one-step-hot-formamide-extraction-of-rna-from-saccharomyces-cerevisiae
#19
Daniel Shedlovskiy, Natalia Shcherbik, Dimitri G Pestov
Current methods for isolating RNA from budding yeast require lengthy and laborious steps such as freezing and heating with phenol, homogenization with glass beads, or enzymatic digestion of the cell wall. Here, extraction with a solution of formamide and EDTA was adapted to isolate RNA from whole yeast cells through a rapid and easily scalable procedure that does not require mechanical cell lysis, phenol, or enzymes. RNA extracted with formamide-EDTA can be directly loaded on gels for electrophoretic analysis without alcohol precipitation...
July 10, 2017: RNA Biology
https://www.readbyqxmd.com/read/28686857/integrative-genetic-and-epigenetic-analysis-uncovers-regulatory-mechanisms-of-autoimmune-disease
#20
Parisa Shooshtari, Hailiang Huang, Chris Cotsapas
Genome-wide association studies in autoimmune and inflammatory diseases (AID) have uncovered hundreds of loci mediating risk. These associations are preferentially located in non-coding DNA regions and in particular in tissue-specific DNase I hypersensitivity sites (DHSs). While these analyses clearly demonstrate the overall enrichment of disease risk alleles on gene regulatory regions, they are not designed to identify individual regulatory regions mediating risk or the genes under their control, and thus uncover the specific molecular events driving disease risk...
July 6, 2017: American Journal of Human Genetics
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