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https://www.readbyqxmd.com/read/29447396/rna-dna-hybrids-promote-the-expansion-of-friedreich-s-ataxia-gaa-n-repeats-via-break-induced-replication
#1
Alexander J Neil, Miranda U Liang, Alexandra N Khristich, Kartik A Shah, Sergei M Mirkin
Expansion of simple DNA repeats is responsible for numerous hereditary diseases in humans. The role of DNA replication, repair and transcription in the expansion process has been well documented. Here we analyzed, in a yeast experimental system, the role of RNA-DNA hybrids in genetic instability of long (GAA)n repeats, which cause Friedreich's ataxia. Knocking out both yeast RNase H enzymes, which counteract the formation of RNA-DNA hybrids, increased (GAA)n repeat expansion and contraction rates when the repetitive sequence was transcribed...
February 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29445799/dna-nanodevices-monitored-with-fluorogenic-looped-out-2-aminopurine
#2
Pai Peng, Yi Du, Tao Li
We report several DNA nanodevices monitored with fluorogenic looped-out 2-aminopurine. It is found that looped-out 2-AP, an analogue of adenine, in split parallel G-quadruplexes, triplexes and duplexes always shows much higher fluorescence intensity than that in single- or double-stranded DNAs, due to the weaker quenching effects derived from the reduced base stacking environments. Taking advantage of these traits, we introduce a new strategy to monitor the behaviours of DNA nanodevices via the fluorescence signal output by utilizing changes in the base stacking environment of 2-AP...
February 15, 2018: Analyst
https://www.readbyqxmd.com/read/29432899/non-canonical-dna-structures-comparative-quantum-mechanical-study
#3
Stanislav S Bachurin, Mikhail E Kletskii, Oleg N Burov, Sergey V Kurbatov
A study of relative thermodynamic stability of non-canonical DNA structures (triplexes, G-quadruplexes, i-motifs) for the first time was conducted on the basis of quantum chemical DFT/B3LYP/6-31++G (d) calculations. Results of the calculations completely reproduce the experimental data on stability of G-quadruplexes comparatively Watson-Crick B-DNA. It was discovered that combinations of non-canonical DNA structures were energetically more favorable than separated nitrogenous bases. Supramolecular complexes of the non-canonical DNA structures (NSs) can be considered as a biological drug targets in gene regulation (for example in tumor therapy), in contrast to previous works, where NSs were studied independently...
February 8, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29427924/highly-sensitive-electrochemical-assay-for-nosema-bombycis-gene-dna-ptp1-via-conformational-switch-of-dna-nanostructures-regulated-by-h-from-lamp
#4
Jianmin Zhao, Jiaxi Gao, Ting Zheng, Zhehan Yang, Yaqin Chai, Shihong Chen, Ruo Yuan, Wenju Xu
The portable and rapid detection of biomolecules via pH meters to monitor the concentration of hydrogen ions (H+) from biological reactions (e.g. loop-mediated isothermal amplification, LAMP) has attracted research interest. However, this assay strategy suffered from inherent drawback of low sensitivity, resulting in great limitations in practical applications. Herein, a novel electrochemical biosensor was constructed for highly sensitive detection of Nosema bombycis gene DNA (PTP1) through transducing chemical stimuli H+ from PTP1-based LAMP into electrochemical output signal of electroactive ferrocene (Fc)...
February 2, 2018: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29421168/associations-of-urinary-phthalate-metabolites-and-lipid-peroxidation-with-sperm-mitochondrial-dna-copy-number-and-deletions
#5
Alexandra M Huffman, Haotian Wu, Allyson Rosati, Tayyab Rahil, Cynthia K Sites, Brian W Whitcomb, J Richard Pilsner
BACKGROUND: Phthalates, a chemical class of plasticizers, are ubiquitous environmental contaminants that have been associated with oxidative stress. Mitochondria DNA copy number (mtDNAcn) and DNA deletions (mtDNAdel) are emerging biomarkers for cellular oxidative stress and environment exposures. OBJECTIVES: To examine associations of urinary phthalate metabolite and isoprostane concentrations on sperm mtDNAcn and mtDNAdel in male partners undergoing assisted reproductive technologies (ART)...
February 5, 2018: Environmental Research
https://www.readbyqxmd.com/read/29414077/triplex%C3%A2-waveguide-based-fluorescence-biosensor-for-multichannel-environmental-contaminants-detection
#6
Lanhua Liu, Didi Shan, Xiaohong Zhou, Hanchang Shi, Baodong Song, Floris Falke, Arne Leinse, René Heideman
In order to realize the multi-analyte assays for environmental contaminants, an optical biosensor utilizing laser-induced fluorescence-based detection via the binding of biomolecules to the surface of an integrated TriPleX™ waveguide chip on a glass substrate (fused silica, FS) is described. As far as we know, this is the first demonstration of using the TriPleX™ technology to fabricate the waveguide chip on a FS substrate. The sensor consists of 32 individually addressable sensor patches, which were formed on the chip surface by exploiting 3 Y-junction splitters, creating four equal rows of eight evanescently excited windows in parallel...
February 1, 2018: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29410302/the-blackfly-vectors-and-transmission-of-onchocerca-volvulus-in-mahenge-south-eastern-tanzania
#7
Adam Hendy, Andreas Krüger, Kenneth Pfarr, Jacobus De Witte, Addow Kibweja, Upendo Mwingira, Jean-Claude Dujardin, Rory Post, Robert Colebunders, Sarah O'Neill, Akili Kalinga
The Mahenge Mountains onchocerciasis focus in south eastern Tanzania was historically one of the most heavily infected areas in the country. The vectors of Onchocerca volvulus are mainly Simulium damnosum complex blackflies, but a species of the Simulium neavei group may also contribute to transmission in some areas. The only detailed studies of parasite transmission in Mahenge were conducted in the late 1960s. The taxonomy of the S. damnosum complex has since been revised and onchocerciasis control through annual community directed treatment with ivermectin (CDTI) commenced in 1997...
February 1, 2018: Acta Tropica
https://www.readbyqxmd.com/read/29396020/low-intensity-shockwave-therapy-for-erectile-dysfunction-a-randomized-clinical-trial-comparing-2-treatment-protocols-and-the-impact-of-repeating-treatment
#8
Dimitrios Kalyvianakis, Evangelos Memmos, Ioannis Mykoniatis, Paraskevi Kapoteli, Dimitrios Memmos, Dimitrios Hatzichristou
BACKGROUND: There is lack of evidence-based optimization of the protocol for low-intensity shockwave therapy for erectile dysfunction. Furthermore, the safety and efficacy of repeating shockwave therapy have not been explored. AIM: To compare the efficacy and safety of 6 and 12 treatment sessions within a 6-week treatment period and investigate the effect of repeat treatment after a 6-month period in a 2-phase study. METHODS: Patients with vasculogenic erectile dysfunction that responded to phosphodiesterase type 5 inhibitors were randomized into 2 groups: low-intensity shockwave therapy sessions once (group A, n = 21) or twice (group B, n = 21) per week for 6 consecutive weeks (phase 1)...
January 27, 2018: Journal of Sexual Medicine
https://www.readbyqxmd.com/read/29395166/usefulness-of-fc-triplex-chagas-leish-igg1-as-confirmatory-assay-for-non-negative-results-in-blood-bank-screening-of-chagas-disease
#9
Fernanda Magalhães Freire Campos, Laura Cotta Repoles, Fernanda Fortes de Araújo, Vanessa Peruhype-Magalhães, Marcelo Antônio Pascoal Xavier, Ester Cerdeira Sabino, Anna Bárbara de Freitas Carneiro Proietti, Mariléia Chaves Andrade, Andréa Teixeira-Carvalho, Olindo Assis Martins-Filho, Célia Maria Ferreira Gontijo
A relevant issue in Chagas disease serological diagnosis regards the requirement of using several confirmatory methods to elucidate the status of non-negative results from blood bank screening. The development of a single reliable method may potentially contribute to distinguish true and false positive results. Our aim was to evaluate the performance of the multiplexed flow-cytometry anti-T. cruzi/Leishmania IgG1 serology/(FC-TRIPLEX Chagas/Leish IgG1) with three conventional confirmatory criteria (ELISA-EIA, Immunofluorescence assay-IIF and EIA/IIF consensus criterion) to define the final status of samples with actual/previous non-negative results during anti-T...
January 30, 2018: Journal of Immunological Methods
https://www.readbyqxmd.com/read/29391178/triplex-real-time-pcr-method-for-the-qualitative-detection-of-european-and-american-foulbrood-in-honeybee
#10
Benjamin Dainat, Daniela Grossar, Brigitte Ecoffey, Christoph Haldemann
The bacteria Melissococcus plutonius and Paenibacillus larvae, causative agents of respectively European and American foulbrood, damage honeybee health worldwide. Here, we present a specific and sensitive qualitative triplex real-time PCR method to detect simultaneously those microbial agents and a honeybee gene, validated through a study involving 7 laboratories through Europe.
January 29, 2018: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29378390/a-stable-and-label-free-fluorescent-probe-based-on-g-triplex-dna-and-thioflavin-t
#11
Hui Zhou, Qian-Jin Han, Zhi-Fang Wu, Hong-Mei Zhong, Jun-Bin Peng, Xun Li, Xiao-Lin Fan
G-triplexes have recently been identified as a new kind of DNA structures. They perhaps possess specific biological and chemical functions similar as identified G-quardruplex, but can be formed by shorter G-rich sequences with only three G-tracts. However, till now, limited G-triplexes sequences have been reported, which might be due to the fact that their stability is one of the biggest concerns during their functional studies and application researches. Herein, we found a G-rich sequence (5'-TGGGTAGGGCGGG-3') which can form a stable G-triplex (Tm ~ 60 °C) at room temperature...
January 30, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29376179/kinetic-and-thermodynamic-analysis-of-triplex-formation-between-peptide-nucleic-acid-and-double-stranded-rna
#12
Takaya Sato, Naonari Sakamoto, Seiichi Nishizawa
Kinetics and thermodynamics of triplex formation between 9-mer homopyrimidine PNA (H2N-Lys-TCTCCTCCC-CONH2) and double-stranded RNA (dsRNA, 5'-AGAGGAGGG-3'/3'-UCUCCUCCC-5') at acidic pH were studied by means of a stopped-flow technique and isothermal titration calorimetry (ITC). These results revealed the following main findings: (i) the stable PNA-dsRNA triplex formation mostly originated from the large association rate constant (kon), which was dominated by both the charge neutral PNA backbone and the protonation level of the PNA cytosine...
January 29, 2018: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29372182/stereochemistry-and-amyloid-inhibition-asymmetric-triplex-metallohelices-enantioselectively-bind-to-a%C3%AE-peptide
#13
Yijia Guan, Zhi Du, Nan Gao, Yue Cao, Xiaohui Wang, Peter Scott, Hualong Song, Jinsong Ren, Xiaogang Qu
Stereochemistry is vital for pharmaceutical development and can determine drug efficacy. Herein, 10 pairs of asymmetric triplex metallohelix enantiomers as a library were used to screen inhibitors of amyloid β (Aβ) aggregation via a fluorescent cell-based high-throughput method. Intriguingly, Λ enantiomers show a stronger inhibition effect than Δ enantiomers. In addition, the metallohelices with aromatic substituents are more effective than those without, revealing that these groups play a key role in the Aβ interaction...
January 2018: Science Advances
https://www.readbyqxmd.com/read/29370166/expanding-molecular-diagnostics-of-helminthiasis-piloting-use-of-the-gpln-platform-for-surveillance-of-soil-transmitted-helminthiasis-and-schistosomiasis-in-ghana
#14
Lucas J Cunningham, John Odoom, Deborah Pratt, Linda Boatemaa, Nana Asante-Ntim, Keren Attiku, Bismarck Banahene, Mike Osei-Atweneboana, Jaco J Verweij, David Molyneux, Russell J Stothard, Emily R Adams
The efforts to control and eradicate polio as a global health burden have been successful to the point where currently only three countries now report endemic polio, and the number of cases of polio continues to decrease. The success of the polio programme has been dependant on a well-developed network of laboratories termed the global polio laboratory network (GPLN). Here we explore collaborative opportunities with the GPLN to target two of the 18 diseases listed as a neglected tropical diseases (NTD) namely soil transmitted helminthiasis (STH) and Schistosomiasis (SCH)...
January 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29367517/one-step-triplex-pcr-rt-pcr-to-detect-canine-distemper-virus-canine-parvovirus-and-canine-kobuvirus
#15
Dafei Liu, Fei Liu, Dongchun Guo, Xiaoliang Hu, Zhijie Li, Zhigang Li, Jianzhang Ma, Chunguo Liu
To rapidly distinguish Canine distemper virus (CDV), canine parvovirus (CPV), and canine kobuvirus (CaKoV) in practice, a one-step multiplex PCR/RT-PCR assay was developed, with detection limits of 102.1 TCID50 for CDV, 101.9 TCID50 for CPV and 103 copies for CaKoV. This method did not amplify nonspecific DNA or RNA from other canine viruses. Therefore, the assay provides a sensitive tool for the rapid clinical detection and epidemiological surveillance of CDV, CPV and CaKoV in dogs.
January 23, 2018: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/29367472/-host-symbiont-cospeciation-of-termite-gut-cellulolytic-protists-of-the-genera-teranympha-and-eucomonympha-and-their-treponema-endosymbionts
#16
Satoko Noda, Daichi Shimizu, Masahiro Yuki, Osamu Kitade, Moriya Ohkuma
Cellulolytic flagellated protists inhabit the hindgut of termites. They are unique and essential to termites and related wood-feeding cockroaches, enabling host feeding on cellulosic matter. Protists of two genera in the family Teranymphidae (phylum Parabasalia), Eucomonympha and Teranympha, are phylogenetically closely related and harbor intracellular endosymbiotic bacteria from the genus Treponema. In order to obtain a clearer understanding of the evolutionary history of this triplex symbiotic relationship, the molecular phylogenies of the three symbiotic partners, the Teranymphidae protists, their Treponema endosymbionts, and their host termites, were inferred and compared...
January 24, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29355159/colour-doppler-sonography-of-the-penis-in-the-evaluation-of-erectile-dysfunction-our-experience-in-abuja-nigeria
#17
Joshua Oluwafemi Aiyekomogbon, Joseph Bako Igashi, Reuben Omokafe Lawan, Muftau Jimoh Bioku, Musa Ameadaji
BACKGROUND: Erectile dysfunction (ED) is an inability to achieve and maintain erectile rigidity sufficient for satisfactory sexual performance. It is either organic or psychogenic in origin. This study was aimed at establishing vasculogenic causes among patients being evaluated for ED using triplex Doppler Ultrasound. PATIENTS AND METHODS: This study was conducted at the Department of Radiology, Federal Medical Centre, Abuja, Nigeria from July 2015 to January 2017...
October 2017: Nigerian Postgraduate Medical Journal
https://www.readbyqxmd.com/read/29342139/structure-and-mutagenesis-reveal-essential-capsid-protein-interactions-for-kshv-replication
#18
Xinghong Dai, Danyang Gong, Hanyoung Lim, Jonathan Jih, Ting-Ting Wu, Ren Sun, Z Hong Zhou
Kaposi's sarcoma-associated herpesvirus (KSHV) causes Kaposi's sarcoma, a cancer that commonly affects patients with AIDS and which is endemic in sub-Saharan Africa. The KSHV capsid is highly pressurized by its double-stranded DNA genome, as are the capsids of the eight other human herpesviruses. Capsid assembly and genome packaging of herpesviruses are prone to interruption and can therefore be targeted for the structure-guided development of antiviral agents. However, herpesvirus capsids-comprising nearly 3,000 proteins and over 1,300 Å in diameter-present a formidable challenge to atomic structure determination and functional mapping of molecular interactions...
January 17, 2018: Nature
https://www.readbyqxmd.com/read/29323070/is-diabetes-mellitus-an-important-risk-factor-for-the-antibiotic-resistance-in-extraintestinal-pathogenic-escherichia-coli
#19
Arindam Chakraborty, Shalini Shenoy, Prabha Adhikari, Vishwas Saralaya, Satish Rao
Escherichia coli is a major cause of extraintestinal infections in all age group. However, the infection becomes more severe when patients have some underlying condition such as Diabetes Mellitus. The aim of the study was to determine whether diabetic mellitus may act as an important risk factor for the E. coli to express drug resistance property. This descriptive study was carried out in a multi-specialty tertiary care hospital. One hundred and twenty-seven E. coli isolates from diabetic patients, and one hundred seventy-three isolates from nondiabetic patients were studied...
October 2017: Indian Journal of Pathology & Microbiology
https://www.readbyqxmd.com/read/29282526/triplex-real-time-pcr-for-detection-of-crithidia-mellificae-and-lotmaria-passim-in-honey-bees
#20
Guang Xu, Evan Palmer-Young, Kim Skyrm, Timothy Daly, Martha Sylvia, Anne Averill, Stephen Rich
Currently, light microscopic examination of cell morphology cannot discriminate Crithidia mellificae and Lotmaria passim with 100% certainty. Here, a minor groove-binding (MGB) probe-based multiplex real-time PCR assay was developed for the simultaneous and quantitative detection of C. mellificae and L. passim in honey bees. A conserved Hymenoptera 18S rRNA gene was built in as an internal control that allows accurate detection of PCR inhibition and failure of DNA extraction. The newly developed assay was also applied to field samples...
December 27, 2017: Parasitology Research
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