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https://www.readbyqxmd.com/read/27916934/immune-related-gene-expression-patterns-in-gpv-or-h9n2-infected-goose-spleens
#1
Shun Chen, Anqi Wang, Lipei Sun, Fei Liu, Mingshu Wang, Renyong Jia, Dekang Zhu, Mafeng Liu, Qiao Yang, Ying Wu, Kunfeng Sun, Xiaoyue Chen, Anchun Cheng
Goose parvovirus (GPV) and avian influenza virus subtype H9N2 are single-stranded DNA (ssDNA) and single-stranded RNA (ssRNA) viruses, respectively, both of which can spread in goslings and cause a significant economic loss. To explore the comprehensive transcriptome of GPV- or H9N2-infected goose spleens and to understand the immune responses induced by a DNA virus (GPV) or a RNA virus (H9N2), RNA-seq was performed on the spleens of goslings at the fifth day post infection. In the present study, 2604 and 2409 differentially expressed unigenes were identified in the GPV- and H9N2-infected groups, respectively...
December 1, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27911492/rolling-circle-amplification-with-chemically-modified-nucleoside-triphosphates
#2
Marcel Hollenstein, Masad J Damha
Modified nucleoside triphosphates (dN*TPs) represent facile and versatile precursors for the introduction of chemical diversity into nucleic acids. While dN*TPs have been utilized in a plethora of practical applications, very little attention has been devoted to the assessment of their compatibility with isothermal amplification strategies. In this context, rolling circle amplification (RCA) is a wide-spread enzymatic replication method in which small single-stranded DNA (ssDNA) circles serve as templates in primer extension reactions yielding very long, ssDNA products...
December 1, 2016: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/27909845/a-fluorescence-sensor-for-lead-ii-ions-determination-based-on-label-free-gold-nanoparticles-gnps-dnazyme-using-time-gated-mode-in-aqueous-solution
#3
Xiao-Yu Wang, Cheng-Gang Niu, Li-Juan Guo, Liu-Yin Hu, Sheng-Quan Wu, Guang-Ming Zeng, Fei Li
This paper describes a label-free 17E DNAzyme-based time-gated fluorescence sensor for Pb(2+) detection by unmodified gold nanoparticles (GNPs) and a terbium ternary complex. The fluorophore that used in this paper is a terbium ternary complex. Its signal can be measured in a time-gated manner which could eliminate most of the unspecific fluorescent background. It is well known that unfolded single-stranded DNA (ssDNA) could be adsorbed on GNPs while double-stranded DNA could not. The cleavage of the substrate by the 17E DNAzyme in the presence of Pb(2+) causes the release of ssDNA from the 17E-17S duplex to be absorbed onto GNPs, preventing the aggregation of GNPs and then leading to a fluorescence decrease of terbium ternary complex...
December 1, 2016: Journal of Fluorescence
https://www.readbyqxmd.com/read/27905816/cementocyte-cell-death-occurs-in-rat-cellular-cementum-during-orthodontic-tooth-movement
#4
Humihiro Matsuzawa, Naoko Toriya, Yuya Nakao, Moe Konno-Nagasaka, Toshiya Arakawa, Miki Okayama, Itaru Mizoguchi
OBJECTIVE: To clarify the mechanism of root resorption during orthodontic treatment, we examined cementocyte cell death and root resorption in the cellular cementum on the pressure side during experimental tooth movement. MATERIALS AND METHODS: Using 8-week-old male Wistar rats, the right first molar was pushed mesiobuccally with a force of 40 g by a Ni-Ti alloy wire while the contralateral first molar was used as a control. Localization and number of cleaved caspase-3-positive and single-stranded DNA (ssDNA) - positive cells were evaluated using dual-label immunohistochemistry with anticleaved caspase-3 and anti-ssDNA antibodies...
December 1, 2016: Angle Orthodontist
https://www.readbyqxmd.com/read/27903895/protein-dynamics-of-human-rpa-and-rad51-on-ssdna-during-assembly-and-disassembly-of-the-rad51-filament
#5
Chu Jian Ma, Bryan Gibb, YoungHo Kwon, Patrick Sung, Eric C Greene
Homologous recombination (HR) is a crucial pathway for double-stranded DNA break (DSB) repair. During the early stages of HR, the newly generated DSB ends are processed to yield long single-stranded DNA (ssDNA) overhangs, which are quickly bound by replication protein A (RPA). RPA is then replaced by the DNA recombinase Rad51, which forms extended helical filaments on the ssDNA. The resulting nucleoprotein filament, known as the presynaptic complex, is responsible for pairing the ssDNA with homologous double-stranded DNA (dsDNA), which serves as the template to guide DSB repair...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899634/homologous-recombination-mediated-by-the-mycobacterial-adnab-helicase-without-end-resection-by-the-adnab-nucleases
#6
Richa Gupta, Mihaela-Carmen Unciuleac, Stewart Shuman, Michael S Glickman
Current models of bacterial homologous recombination (HR) posit that extensive resection of a DNA double-strand break (DSB) by a multisubunit helicase-nuclease machine (e.g. RecBCD, AddAB or AdnAB) generates the requisite 3' single-strand DNA substrate for RecA-mediated strand invasion. AdnAB, the helicase-nuclease implicated in mycobacterial HR, consists of two subunits, AdnA and AdnB, each composed of an N-terminal ATPase domain and a C-terminal nuclease domain. DSB unwinding by AdnAB in vitro is stringently dependent on the ATPase activity of the 'lead' AdnB motor translocating on the 3' ssDNA strand, but not on the putative 'lagging' AdnA ATPase...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898377/upconversion-nanoparticles-grafted-molybdenum-disulfide-nanosheets-platform-for-microcystin-lr-sensing
#7
Jiajia Lv, Sen Zhao, Shijia Wu, Zhouping Wang
Water safety is one of the most pervasive problems afflicting people throughout the world. Microcystin-LR (MC-LR), a representative toxin released by cyanobacteria, poses an increasing and serious threat to water safety. In order to develop facile, specific and sensitive detection methods for MC-LR, we fabricated an ultrasensitive fluorescence aptasensor using the enhanced fluorescence of UCNP and the effective quenching ability, high affinity toward single strand DNA (ssDNA) of MoS2 (termed as FAUM). This assay specifically determined MC-LR in the linear range of 0...
October 4, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27895657/implication-of-the-whitefly-bemisia-tabaci-cyclophilin-b-protein-in-the-transmission-of-tomato-yellow-leaf-curl-virus
#8
Surapathrudu Kanakala, Murad Ghanim
Tomato yellow leaf curl virus (TYLCV) is a single-stranded (ssDNA) begomoviruses that causes severe damage to tomato and several other crops worldwide. TYLCV is exclusively transmitted by the sweetpotato whitefly, Bemisia tabaci in a persistent circulative and propagative manner. Previous studies have shown that the transmission, retention, and circulation of TYLCV in its vector involves interaction with insect and endosymbiont proteins, which aid in the transmission of the virus, or have a protective role in response to the presence of the virus in the insect body...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27895165/rats-with-a-missense-mutation-in-atm-display-neuroinflammation-and-neurodegeneration-subsequent-to-accumulation-of-cytosolic-dna-following-unrepaired-dna-damage
#9
Hazel Quek, John Luff, KaGeen Cheung, Sergei Kozlov, Magtouf Gatei, C Soon Lee, Mark C Bellingham, Peter G Noakes, Yi Chieh Lim, Nigel L Barnett, Steven Dingwall, Ernst Wolvetang, Tomoji Mashimo, Tara L Roberts, Martin F Lavin
Mutations in the ataxia-telangiectasia (A-T)-mutated (ATM) gene give rise to the human genetic disorder A-T, characterized by immunodeficiency, cancer predisposition, and neurodegeneration. Whereas a series of animal models recapitulate much of the A-T phenotype, they fail to present with ataxia or neurodegeneration. We describe here the generation of an Atm missense mutant [amino acid change of leucine (L) to proline (P) at position 2262 (L2262P)] rat by intracytoplasmic injection (ICSI) of mutant sperm into oocytes...
November 28, 2016: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/27893356/single-stranded-dna-aptamer-targeting-and-neutralization-of-anti-d-alloantibody-a-potential-therapeutic-strategy-for-haemolytic-diseases-caused-by-rhesus-alloantibody
#10
Yinze Zhang, Fan Wu, Manni Wang, Naibao Zhuang, Huayou Zhou, Hua Xu
BACKGROUND: Rhesus (Rh) D antigen is the most important antigen in the Rh blood group system because of its strong immunogenicity. When RhD-negative individuals are exposed to RhD-positive blood, they may produce anti-D alloantibody, potentially resulting in delayed haemolytic transfusion reactions and Rh haemolytic disease of the foetus and newborn, which are difficult to treat. Inhibition of the binding of anti-D antibody with RhD antigens on the surface of red blood cells may effectively prevent immune haemolytic diseases...
November 11, 2016: Blood Transfusion, Trasfusione del Sangue
https://www.readbyqxmd.com/read/27886773/a-novel-aptameric-biosensor-based-on-the-self-assembled-dna-ws2-nanosheet-architecture
#11
Aixue Li, Jian Zhang, Jichuan Qiu, Zhenhuan Zhao, Cheng Wang, Chunjiang Zhao, Hong Liu
It has been reported that tungsten disulfide (WS2) can bind single-stranded DNA (ssDNA) with high affinity while it has less affinity toward double stranded DNA (dsDNA). In this work, for the first time, the high affinity between WS2 and ssDNA was used to construct stable sensing interface for ATP detection. A DNA sequence with -SH at one end was first immobilized on Au electrode. WS2 nanosheets were immobilized on the SH-DNA/Au electrode surface due to the strong affinity between WS2 and ssDNA. Then the WS2 nanosheets were used to immobilize ATP binding aptamer (ABA) through the high affinity between WS2 and ssDNA, too...
January 15, 2017: Talanta
https://www.readbyqxmd.com/read/27881299/transient-rna-dna-hybrids-are-required-for-efficient-double-strand-break-repair
#12
Corina Ohle, Rafael Tesorero, Géza Schermann, Nikolay Dobrev, Irmgard Sinning, Tamás Fischer
RNA-DNA hybrids are a major internal cause of DNA damage within cells, and their degradation by RNase H enzymes is important for maintaining genomic stability. Here, we identified an unexpected role for RNA-DNA hybrids and RNase H enzymes in DNA repair. Using a site-specific DNA double-strand break (DSB) system in Schizosaccharomyces pombe, we showed that RNA-DNA hybrids form as part of the homologous-recombination (HR)-mediated DSB repair process and that RNase H enzymes are essential for their degradation and efficient completion of DNA repair...
November 3, 2016: Cell
https://www.readbyqxmd.com/read/27880870/formation-and-processing-of-dna-damage-substrates-for-the-hneil-enzymes
#13
Aaron M Fleming, Cynthia J Burrows
Reactive oxygen species (ROS) are harnessed by the cell for signaling at the same time as being detrimental to cellular components such as DNA. The genome and transcriptome contain instructions that can alter cellular processes when oxidized. The guanine (G) heterocycle in the nucleotide pool, DNA, or RNA is the base most prone to oxidation. The oxidatively-derived products of G consistently observed in high yields from hydroxyl radical, carbonate radical, or singlet oxygen oxidations under conditions modeling the cellular reducing environment are discussed...
November 20, 2016: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/27878582/chilli-leaf-curl-virus-based-vector-for-phloem-specific-silencing-of-endogenous-genes-and-overexpression-of-foreign-genes
#14
Nirbhay Kumar Kushwaha, Supriya Chakraborty
Geminiviruses are the largest and most devastating group of plant viruses which contain ssDNA as a genetic material. Geminivirus-derived virus-induced gene silencing (VIGS) vectors have emerged as an efficient and simple tool to study functional genomics in various plants. However, previously developed VIGS vectors have certain limitations, owing to their inability to be used in tissue-specific functional study. In the present study, we developed a Chilli leaf curl virus (ChiLCV)-based VIGS vector for its tissue-specific utilization by replacing the coat protein gene (open reading frame (ORF) AV1) with the gene of interest for phytoene desaturase (PDS) of Nicotiana benthamiana...
November 23, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27878460/comparative-analysis-of-common-regions-found-in-babuviruses-and-alphasatellite-molecules
#15
Daisy Stainton, Darren P Martin, David A Collings, Arvind Varsani
Viruses in the genus Babuvirus have multi-component ssDNA genomes and often associate with alphasatellite molecules containing two common motifs, a common-region stem-loop (CR-SL) involved in initiation of rolling-circle replication and a common-region major (CR-M) motif involved in secondary-strand synthesis. We compared known babuvirus genome components and alphasatellite CR-SL and CR-M sequences, defining five divergent CR-SL sequence classes. We identified iterated sequence elements in babuvirus genome components that have particularly conserved sequences and spatial arrangements between known babuviruses...
November 22, 2016: Archives of Virology
https://www.readbyqxmd.com/read/27876150/coupling-hybridization-chain-reaction-with-dnazyme-recycling-for-enzyme-free-and-dual-amplified-sensitive-fluorescent-detection-of-methyltransferase-activity
#16
Bingying Jiang, Yulian Wei, Junqiang Xu, Ruo Yuan, Yun Xiang
Aberrant DNA methylation originated from changes in DNA methyltransferase activity can lead to many genetic diseases and tumor types, and the monitoring of methyltransferase activity is thus of great importance in disease diagnosis and drug screening. In this work, by combing hybridization chain reaction (HCR) and metal ion-dependent DNAzyme recycling, we have developed a convenient enzyme-free signal amplification strategy for highly sensitive detection of DNA adenine methyltransferase (Dam MTase) activity and its inhibitors...
January 1, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/27867009/a-polar-and-nucleotide-dependent-mechanism-of-action-for-rad51-paralogs-in-rad51-filament-remodeling
#17
Martin R G Taylor, Mário Špírek, Chu Jian Ma, Raffaella Carzaniga, Tohru Takaki, Lucy M Collinson, Eric C Greene, Lumir Krejci, Simon J Boulton
Central to homologous recombination in eukaryotes is the RAD51 recombinase, which forms helical nucleoprotein filaments on single-stranded DNA (ssDNA) and catalyzes strand invasion with homologous duplex DNA. Various regulatory proteins assist this reaction including the RAD51 paralogs. We recently discovered that a RAD51 paralog complex from C. elegans, RFS-1/RIP-1, functions predominantly downstream of filament assembly by binding and remodeling RAD-51-ssDNA filaments to a conformation more proficient for strand exchange...
December 1, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27866079/multimodal-plasmonic-biosensing-nanostructures-prepared-by-dna-directed-immobilization-of-multifunctional-dna-gold-nanoparticles
#18
Nuria Tort, J-Pablo Salvador, M-Pilar Marco
Biofunctional multimodal plasmonic nanostructures suitable for multiplexed localized surface plasmon resonance (LSPR) biosensing have been created by DNA-directed immobilization (DDI) of two distinct multifunctional biohybrid gold nanoparticles. Gold nanoparticles (AuNP) of distinct sizes, and therefore showing distinct plasmon resonant peaks (RP), have been biofunctionalized and codified with two different single stranded-DNA (ssDNA) chains. One of these oligonucleotide chains has been specifically designed to direct each AuNP to a distinct location of the surface of a DNA microarray chip through specific hybridization with complementary oligonucleotide strands...
November 11, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27863397/targeting-gli-by-gant61-involves-mechanisms-dependent-on-inhibition-of-both-transcription-and-dna-licensing
#19
Ruowen Zhang, Jiahui Wu, Sylvain Ferrandon, Katie J Glowacki, Janet A Houghton
The GLI genes are transcription factors and in cancers are oncogenes, aberrantly and constitutively activated. GANT61, a specific GLI inhibitor, has induced extensive cytotoxicity in human models of colon cancer. The FOXM1 promoter was determined to be a transcriptional target of GLI1. In HT29 cells, inhibition of GLI1 binding at the GLI consensus sequence by GANT61 led to inhibited binding of Pol II, the pause-release factors DSIF, NELF and p-TEFb. The formation of R-loops (RNA:DNA hybrids, ssDNA), were reduced by GANT61 at the FOXM1 promoter...
November 15, 2016: Oncotarget
https://www.readbyqxmd.com/read/27861980/bringing-it-all-together-coupling-excision-repair-to-the-dna-damage-checkpoint
#20
Laura A Lindsey-Boltz
Nucleotide excision repair and the ATR-mediated DNA damage checkpoint are two critical cellular responses to the genotoxic stress induced by ultraviolet (UV) light and are important for cancer prevention. In vivo genetic data indicate that these global responses are coupled. Aziz Sancar and colleagues developed an in vitro coupled repair-checkpoint system to analyze the basic steps of these DNA damage stress responses in a biochemically defined system. The minimum set of factors essential for repair-checkpoint coupling include damaged DNA, the excision repair factors (XPA, XPC, XPF-ERCC1, XPG, TFIIH, RPA), the 5'-3' exonuclease EXO1, and the damage checkpoint proteins ATR-ATRIP and TopBP1...
November 14, 2016: Photochemistry and Photobiology
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