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https://www.readbyqxmd.com/read/28921812/evaluation-of-air-samplers-and-filter-materials-for-collection-and-recovery-of-airborne-norovirus
#1
Katrine Uhrbrand, Ismo K Koponen, Anna Charlotte Schultz, Anne Mette Madsen
AIMS: The aim of this study was to identify the most efficient sampling method for quantitative PCR-based detection of airborne human norovirus (NoV). METHODS AND RESULTS: A comparative experiment was conducted in an aerosol chamber using aerosolised murine norovirus (MNV) as a surrogate for NoV. Sampling was performed using a nylon (NY) filter in conjunction with four kinds of personal samplers; Gesamtstaubprobenahme sampler (GSP), Triplex-cyclone sampler (TC), 3-piece closed-faced Millipore cassette (3P) and a 2-stage NIOSH cyclone sampler (NIO)...
September 18, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28920942/exponential-growth-and-selection-in-self-replicating-materials-from-dna-origami-rafts
#2
Xiaojin He, Ruojie Sha, Rebecca Zhuo, Yongli Mi, Paul M Chaikin, Nadrian C Seeman
Self-replication and evolution under selective pressure are inherent phenomena in life, and but few artificial systems exhibit these phenomena. We have designed a system of DNA origami rafts that exponentially replicates a seed pattern, doubling the copies in each diurnal-like cycle of temperature and ultraviolet illumination, producing more than 7 million copies in 24 cycles. We demonstrate environmental selection in growing populations by incorporating pH-sensitive binding in two subpopulations. In one species, pH-sensitive triplex DNA bonds enable parent-daughter templating, while in the second species, triplex binding inhibits the formation of duplex DNA templating...
September 18, 2017: Nature Materials
https://www.readbyqxmd.com/read/28905972/red-emissive-triplex-forming-pna-probes-carrying-cyanine-base-surrogates-for-fluorescence-sensing-of-double-stranded-rna
#3
Toshiki Chiba, Takaya Sato, Yusuke Sato, Seiichi Nishizawa
Red-emissive fluorescent probes have been developed by integration of quinoline blue or thiazole red as the base surrogate into triplex-forming PNAs, allowing selective sensing of a sequence of double-stranded RNA.
September 14, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28887512/lna-effects-on-dna-binding-and-conformation-from-single-strand-to-duplex-and-triplex-structures
#4
Y Vladimir Pabon-Martinez, You Xu, Alessandra Villa, Karin E Lundin, Sylvain Geny, Chi-Hung Nguyen, Erik B Pedersen, Per T Jørgensen, Jesper Wengel, Lennart Nilsson, C I Edvard Smith, Rula Zain
The anti-gene strategy is based on sequence-specific recognition of double-strand DNA by triplex forming (TFOs) or DNA strand invading oligonucleotides to modulate gene expression. To be efficient, the oligonucleotides (ONs) should target DNA selectively, with high affinity. Here we combined hybridization analysis and electrophoretic mobility shift assay with molecular dynamics (MD) simulations to better understand the underlying structural features of modified ONs in stabilizing duplex- and triplex structures...
September 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28875701/effect-of-loop-length-and-sequence-on-the-stability-of-dna-pyrimidine-triplexes-with-tat-base-triplets
#5
Hui-Ting Lee, Carolyn E Carr, Irine Khutsishvili, Luis A Marky
We report the thermodynamic contributions of loop length and loop sequence on the overall stability of DNA intramolecular pyrimidine triplexes. Two sets of triplexes were designed, with both sets based on 7TAT, which has a 5' to 3' sequence of d(A7C5T7C5T7); in the first set, the loop closing the triplex-stem was replaced with 5'-CTnC loops (n = 1-5), while in the second set both the duplex and triplex loop were replaced with a 5'-GCAA (7TAT-GCAA and GCAA-7TAT) or 5'-AACG (7TAT-AACG and AACG-7TAT) tetraloop...
September 6, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28865451/genome-wide-computational-analysis-of-potential-long-noncoding-rna-mediated-dna-dna-rna-triplexes-in-the-human-genome
#6
Saakshi Jalali, Amrita Singh, Souvik Maiti, Vinod Scaria
BACKGROUND: Only a handful of long noncoding RNAs have been functionally characterized. They are known to modulate regulation through interacting with other biomolecules in the cell: DNA, RNA and protein. Though there have been detailed investigations on lncRNA-miRNA and lncRNA-protein interactions, the interaction of lncRNAs with DNA have not been studied extensively. In the present study, we explore whether lncRNAs could modulate genomic regulation by interacting with DNA through the formation of highly stable DNA:DNA:RNA triplexes...
September 2, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28860020/triplex-hrm-assay-for-the-simultaneous-assessment-of-il28b-rs12979860-abcb11-rs2287622-and-rnf7-rs16851720-genotypes-in-chronic-hepatitis-c-patients
#7
Elena Luminita Enache, Anca Sin, Liviu Sorin Enache, Ligia Bancu
Chronic hepatitis C (CHC) is a leading cause of liver disease. Despite the improved efficacy of new antivirals, their high costs preclude their adoption in resource-limited settings, where CHC prevalence is highest. We developed a triplex high resolution melting assay for the simultaneous assessment of three genetic polymorphisms related to the response to treatment and development of advanced fibrosis in CHC: IL28B rs12979860, ABCB11 rs2287622, and RNF7 rs16851720. We validated the assay in clinical samples from 130 CHC patients treated with classical therapy...
August 28, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28839111/super-lncrnas-identification-of-lncrnas-that-target-super-enhancers-via-rna-dna-dna-triplex-formation
#8
Benjamin Soibam
Super-enhancers are characterized by high levels of Mediator binding and are major contributors to the expression of their associated genes. They exhibit high levels of local chromatin interactions and higher order of local chromatin organization. On the other hand, LncRNAs can localize to specific DNA sites by forming a RNA:DNA:DNA triplex, which in turn can contribute to local chromatin organization. In this paper, we characterize a new class of lncRNAs called super-lncRNAs that target super-enhancers and which can contribute to the local chromatin organization of the super-enhancers...
August 24, 2017: RNA
https://www.readbyqxmd.com/read/28828056/autoimmune-hepatitis-with-autoimmune-haemolytic-anemia-triggered-by-varicella-a-rare-presentation
#9
Deepak Jain, Harpreet Singh, Gaganpreet Singh, Promil Jain
Varicella is a common infectious exanthematous disease of children. Infection manifests as polymorphic maculopapulovesicular along with low grade fever, malaise and headache. Adults are less likely to be infected with varicella infection but once infected suffer disproportionately from serious complications like pneumonia, encephalitis, hepatitis and thrombocytopenia. Varicella hepatitis is generally a self-limiting disease with only a temporary subclinical rise in hepatic enzymes and are usually encountered however autoimmune hepatitis (AIH) which is an autoimmune disorder of unknown etiology affecting the liver is a very rare association of Varicella infection ...
December 2016: Mædica
https://www.readbyqxmd.com/read/28806644/effects-of-the-fluorine-substituent-positions-of-the-intercalating-ligands-on-the-binding-behavior-and-third-strand-stabilization-of-two-ru-ii-complexes-toward-poly-u-%C3%A2-poly-a-poly-u-triplex-rna
#10
Mengna Peng, Wen Ni, Lifeng Tan
Two new Ru(II) polypyridyl complexes containing fluorine substituents, [Ru(bpy)2(o-fpip)](2+) (Ru1, bpy=2,2'-bipyridine, o-fpip=2-(2-fluorophenyl)imidazo[4,5-f] [1,10]phenanthroline) and [Ru(bpy)2(p-fpip)](2+) (Ru2, p-fpip=2-(4-fluorophenyl)imidazo[4,5-f] [1,10]phenanthroline) have been synthesized as binders for poly(U)•poly(A)∗poly(U) triplex RNA. The binding of the two complexes with the triplex RNA has been investigated by spectroscopic methods and viscosity measurements. Analysis of the electronic absorption spectra indicates that the association of intercalating Ru2 with the triplex RNA is greater than that of Ru1, which is also supported by spectroscopic titrations and viscosity measurements...
August 8, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28800432/linear-and-circular-dichroism-characterization-of-thionine-binding-mode-with-dna-polynucleotides
#11
Eimer Mary Tuite, Bengt Nordén
The binding mode of thionine (3,7-diamino-5-phenothiazinium) with alternating and non-alternating DNA polynucleotides at low binding ratios was conclusively determined using linear and circular dichroism spectroscopies. The binding to [poly(dG-dC)]2 and poly(dG)·poly(dC) was purely intercalative and was insensitive to ionic strength. Intercalative binding to [poly(dA-dT)]2 is observed at low ionic strength, but a shift of some dye to an non-intercalative mode is observed as the background salt concentration increases...
August 1, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28795795/mass-defect-based-dimethyl-pyrimidinyl-ornithine-dipyro-tags-for-multiplex-quantitative-proteomics
#12
Dustin C Frost, Amanda R Buchberger, Lingjun Li
We have developed a novel amine-reactive mass defect-based chemical tag, dimethyl pyrimidinyl ornithine (DiPyrO), that is compact in size, is suitable for various biological samples, and enables highly multiplexed quantification of peptides at the MS(1) level without increasing mass spectral complexity. The DiPyrO tag structure incorporates heavy isotopes in a variety of configurations to impart as much as 45.3 mDa or as little as 5.8 mDa per tag between labeled peptides. Notably, peptides containing lysine are labeled with two tags, doubling the imparted mass defect to up to 90...
August 28, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28793207/divalent-ion-mediated-dna-dna-interactions-a%C3%A2-comparative-study-of-triplex-and-duplex
#13
COMPARATIVE STUDY
Zhong-Liang Zhang, Yuan-Yan Wu, Kun Xi, Jian-Ping Sang, Zhi-Jie Tan
Ion-mediated interaction between DNAs is essential for DNA condensation, and it is generally believed that monovalent and nonspecifically binding divalent cations cannot induce the aggregation of double-stranded (ds) DNAs. Interestingly, recent experiments found that alkaline earth metal ions such as Mg(2+) can induce the aggregation of triple-stranded (ts) DNAs, although there is still a lack of deep understanding of the surprising findings at the microscopic level. In this work, we employed all-atom dynamic simulations to directly calculate the potentials of mean force (PMFs) between tsDNAs, between dsDNAs, and between tsDNA and dsDNA in Mg(2+) solutions...
August 8, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28769061/particle-triplexes-cluster-in-the-tumor-suppressor-wwox-and-may-extend-throughout-the-human-genome
#14
Valerie Bríd O'Leary, Jan Smida, Fabian Andreas Buske, Laura Garcia Carrascosa, Omid Azimzadeh, Doris Maugg, Sarah Hain, Soile Tapio, Wolfgang Heidenreich, James Kerr, Matt Trau, Saak Victor Ovsepian, Michael John Atkinson
The long non-coding RNA PARTICLE (Gene PARTICL- 'Promoter of MAT2A-Antisense RadiaTion Induced Circulating LncRNA) partakes in triple helix (triplex) formation, is transiently elevated following low dose irradiation and regulates transcription of its neighbouring gene - Methionine adenosyltransferase 2A. It now emerges that PARTICLE triplex sites are predicted in many different genes across all human chromosomes. In silico analysis identified additional regions for PARTICLE triplexes at >1600 genomic locations...
August 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28764969/peptide-nucleic-acids-advanced-tools-for-biomedical-applications
#15
REVIEW
Anjali Gupta, Anuradha Mishra, Nidhi Puri
Peptide Nucleic Acids (PNAs) are the DNA/RNA analogues in which sugar-phosphate backbone is replaced by N-2-aminoethylglycine repeating units. PNA contains neutral backbone hence due to the absence of electrostatic repulsion, its hybridization shows remarkable stability towards complementary oligonucleotides. PNAs are highly resistant to cleavage by chemicals and enzymes due to the substrate specific nature of enzymes and therefore not degraded inside the cells. PNAs are emerging as new tools in the market due to their applications in antisense and antigene therapies by inhibiting translation and transcription respectively...
July 29, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28755398/microfluidic-lithography-of-bioinspired-helical-micromotors
#16
Yunru Yu, Luoran Shang, Wei Gao, Ze Zhao, Huan Wang, Yuanjin Zhao
Considerable efforts have been devoted to developing artificial micro/nanomotors that can convert energy into movement. A flow lithography integrated microfluidic spinning and spiraling system is developed for the continuous generation of bioinspired helical micromotors. Because the generation processes could be precisely tuned by adjusting the flow rates and the illuminating frequency, the length, diameter, and pitch of the helical micromotors were highly controllable. Benefiting from the fast online gelation and polymerization, the resultant helical micromotors could be imparted with Janus, triplex, and core-shell cross-sectional structures that have never been achieved by other methods...
July 29, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28709087/novel-electrochemiluminescence-of-silver-nanoclusters-fabricated-on-triplex-dna-scaffolds-for-label-free-detection-of-biothiols
#17
Lingyan Feng, Li Wu, Feifei Xing, Lianzhe Hu, Jinsong Ren, Xiaogang Qu
Electrochemiluminescence (ECL) of metal nanoclusters and their application have been widely reported due to the good biocompatibility, fascinating electrocatalytic activity and so on. Using DNA as synthesis template opens new opportunities to modulate the physical properties of AgNCs. Triplex DNA has been reported for the site-specific, homogeneous and highly stable silver nanoclusters (AgNCs) fabrication from our recent research. Here we further explore their extraordinary ECL properties and applications in biosensor utilization...
July 6, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28686662/comparison-of-a-new-multiplex-real-time-pcr-with-the-kato-katz-thick-smear-and-copro-antigen-elisa-for-the-detection-and-differentiation-of-taenia-spp-in-human-stools
#18
COMPARATIVE STUDY
Dinh Ng-Nguyen, Mark A Stevenson, Pierre Dorny, Sarah Gabriël, Tinh Van Vo, Van-Anh Thi Nguyen, Trong Van Phan, Sze Fui Hii, Rebecca J Traub
BACKGROUND: Taenia solium, the cause of neurocysticercosis (NCC), has significant socioeconomic impacts on communities in developing countries. This disease, along with taeniasis is estimated to infect 2.5 to 5 million people globally. Control of T. solium NCC necessitates accurate diagnosis and treatment of T. solium taeniasis carriers. In areas where all three species of Taenia tapeworms (T. solium, Taenia saginata and Taenia asiatica) occur sympatrically, conventional microscope- and copro-antigen based diagnostic methods are unable to distinguish between these three Taenia species...
July 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28681829/molecular-characterisation-of-uropathogenic-escherichia-coli-isolates-at-a-tertiary-care-hospital-in-south-india
#19
Arindam Chakraborty, Prabha Adhikari, Shalini Shenoy, Vishwas Saralaya
Uropathogenic Escherichia coli (UPEC) express a multitude of virulence factors (VFs) to break the inertia of the mucosal barrier of the urinary tract. The aim of the present study was undertaken to characterised the UPEC strains and to correlate carriage of specific virulence markers with different phylogroups and also to correlate these findings with clinical outcome of patients. A total of 156 non-repeated, clinically significant UPEC isolates were studied. Virulent genes were determined by two set of multiplex polymerase chain reaction (PCR)...
April 2017: Indian Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28674450/triplex-dna-based-bioanalytical-platform-for-highly-sensitive-homogeneous-electrochemical-detection-of-melamine
#20
Xiaojuan Liu, Mengmeng Song, Feng Li
Melamine detection has attracted much attention since the discovery of the damage of melamine to human health. Herein, we have developed a sensitive homogeneous electroanalytical platform for melamine detection, which is relied on the formation of triplex molecular beacon integrated with exonuclease III (Exo III)-mediated signal amplification. The formation of triplex molecular beacon was triggered by the recognition and incorporation of melamine to the abasic (AP) site contained in the triplex stem. The stem of the triplex molecular beacon was designed to have a protruding double-strand DNA, which can be recognized and hydrolyzed by Exo III for releasing methylene blue (MB)-labeled mononucleotide...
July 3, 2017: Scientific Reports
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