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https://www.readbyqxmd.com/read/28530559/meat-species-identification-by-two-direct-triplex-real-time-pcr-assays-using-low-resolution-melting
#1
Phuvadol Thanakiatkrai, Thitika Kitpipit
We developed and validated the first direct multiplex real-time PCR assay with melt curve analysis for the identification of different types of meat. The assay detects six commonly eaten meat species and provides the following benefits: ease of use, shortened analysis time, and decreased analysis cost. Species-specific primers were designed from cytochrome b, cytochrome oxidase I, and 16S rRNA genes to generate PCR products with specific melting peaks that differentiate pork, beef, horsemeat, duck meat, ostrich meat, and chicken...
October 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28528442/herpesvirus-capsid-assembly-and-dna-packaging
#2
Jason D Heming, James F Conway, Fred L Homa
Herpes simplex virus type I (HSV-1) is the causative agent of several pathologies ranging in severity from the common cold sore to life-threatening encephalitic infection. During productive lytic infection, over 80 viral proteins are expressed in a highly regulated manner, resulting in the replication of viral genomes and assembly of progeny virions. The virion of all herpesviruses consists of an external membrane envelope, a proteinaceous layer called the tegument, and an icosahedral capsid containing the double-stranded linear DNA genome...
2017: Advances in Anatomy, Embryology, and Cell Biology
https://www.readbyqxmd.com/read/28522581/conformational-dynamics-of-the-frameshift-stimulatory-structure-in-hiv-1
#3
Dustin B Ritchie, Tonia R Cappellano, Collin Tittle, Negar Rezajooei, Logan Rouleau, William Ka Sikkema, Michael T Woodside
Programmed ribosomal frameshifting (PRF) in HIV-1 is thought to be stimulated by a hairpin in the mRNA, although a pseudoknot-like triplex has also been proposed. Because the conformational dynamics of the stimulatory structure under tension applied by the ribosomal helicase during translation may play an important role in PRF, we used optical tweezers to apply tension to the HIV stimulatory structure and monitor its unfolding and refolding dynamics. The folding and unfolding kinetics and energy landscape of the hairpin were measured by ramping the force on the hairpin up and down, providing a detailed biophysical characterisation...
May 18, 2017: RNA
https://www.readbyqxmd.com/read/28515050/the-mapping-of-predicted-triplex-dna-rna-in-the-drosophila-genome-reveals-a-prominent-location-in-development-and-morphogenesis-related-genes
#4
Claude Pasquier, Sandra Agnel, Alain Robichon
Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand. A nucleic acid triplex occurs according to Hoogsteen rules that predict the stability and affinity of the third strand bound to the Watson-Crick duplex. The "triplex-forming oligonucleotide" (TFO) can be a short sequence of RNA that binds to the major groove of the targeted duplex only when this duplex presents a sequence of purine or pyrimidine bases in one of the DNA strands. Many nuclear proteins are known to bind triplex DNA or DNA:RNA, but their biological functions are unexplored...
May 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28512543/tensile-strength-and-impact-strength-of-color-modified-acrylic-resin-reinforced-with-titanium-dioxide-nanoparticles
#5
Loghman Ghahremani, Saeed Shirkavand, Faezeh Akbari, Niloofar Sabzikari
BACKGROUND: Poor mechanical properties are among the main limitations of acrylic resins. Addition of titanium dioxide (TiO2) nanoparticles to acrylic resin has been shown to improve its mechanical properties with an adverse effect on its color. Thus, this study sought to assess the tensile and impact strength of a color modified heat cure acrylic resin reinforced with TiO2 nanoparticles. MATERIAL AND METHODS: In this in vitroexperimental study, 1wt% TiO2 nanoparticles were added to SR Triplex Hot heat-cure acrylic resin powder and mixed...
May 2017: Journal of Clinical and Experimental Dentistry
https://www.readbyqxmd.com/read/28503346/color-stability-of-heat-cure-acrylic-resin-subjected-to-simulated-short-term-immersion-in-fast-acting-denture-cleansers
#6
K Lohitha, M Prakash, A Gopinadh, A J Sai Sankar, C H Sandeep, B Sreedevi
BACKGROUND: Regular usage of denture cleansers is recommended in complete denture wearers for effective plaque control, and these cleansers alter the physical properties of acrylic resin over a period of time. Thus, an in vitro study was carried out to assess the effect of denture cleansers on the color stability of heat-cure denture base resin. AIM: The aim of the present study was to evaluate the effect of commercially available fast-acting denture cleansers on the color stability of heat-cure denture base resin at different time intervals...
September 2016: Annals of Medical and Health Sciences Research
https://www.readbyqxmd.com/read/28487921/triplex-hybridizing-bioconjugated-gold-nanoparticles-for-specific-y-chromosome-sequence-targeting-of-bull-spermatozoa
#7
L Gamrad, R Mancini, D Werner, D Tiedemann, U Taylor, A Ziefuß, C Rehbock, S Klein, W Kues, S Barcikowski, D Rath
Gold nanoparticles (AuNPs) are widely used in biomedical applications for drug targeting and bioimaging. This often neccesitates their functionalization with biomolecules carrying a defined biological function, yielding gold nanoparticle bioconjugates. The utilization of triplex-forming oligonucleotides (TFOs) as ligands gives access to nanoconjugates as tools for specific DNA-related nanotargeting via triplex hybridization. Since triplex hybridization with nanobioconjugates has to date not been shown on biologically relevant samples, sex-specific sperm marking may be an appropriate model system to demonstrate the opportunities of this targeting method in vitro...
May 10, 2017: Analyst
https://www.readbyqxmd.com/read/28468604/simultaneous-detection-of-chikungunya-virus-dengue-virus-and-human-pathogenic-leptospira-genomes-using-a-multiplex-taqman%C3%A2-assay
#8
Claude Giry, Bénédicte Roquebert, Ghislaine Li-Pat-Yuen, Philippe Gasque, Marie-Christine Jaffar-Bandjee
BACKGROUND: In 2005-2006 a major epidemics of Chikungunya disease occurred in South-West Indian Ocean islands. In Reunion Island, the magnitude of Chikungunya infection related symptoms was high and with over 38% of serological prevalence in the population. This epidemics illustrated the potential threat of emerging arboviral diseases for inhabitants of Reunion Island and elsewhere since vectors are worldwide distributed. A sentinel surveillance network was set-up to detect emerging pathogens associated with fever over 38 °C and in the absence of known etiologic causes...
May 3, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28457784/laboratory-validation-of-two-real-time-rt-pcr-methods-with-5-tailed-primers-for-an-enhanced-detection-of-foot-and-mouth-disease-virus
#9
Frank Vandenbussche, David J Lefebvre, Ilse De Leeuw, Steven Van Borm, Kris De Clercq
The 3D and 5UTR real-time RT-PCR assays (RT-qPCR) from Callahan et al. (2002) and Reid et al. (2002) are commonly used reference methods for the detection of foot-and-mouth disease virus (FMDV). For an optimal detection of FMDV in clinical samples, it is advised to use both assays simultaneously (King et al., 2006). Recently, Vandenbussche et al. (2016) showed that the addition of 5'-tails to the FMDV-specific primers enhances the detection of FMDV in both the 3D and the 5UTR RT-qPCR assay. To validate the 3D and 5UTR RT-qPCR assays with 5'-tailed primers for diagnostic purposes, both assays were run in parallel in a triplex one-step RT-qPCR protocol with beta-actin as an internal control and synthetic RNA as an external control...
April 27, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28456575/incorporation-of-the-kaposi-s-sarcoma-associated-herpesvirus-capsid-vertex-specific-component-cvsc-into-self-assembled-capsids
#10
Peter Grzesik, Derek MacMath, Brandon Henson, Sanjana Prasad, Poorval Joshi, Prashant J Desai
Self-assembly of herpesvirus capsids can be accomplished in heterologous expression systems provided all six capsid proteins are present. We have demonstrated the assembly of icosahedral Kaposi's sarcoma-associated herpesvirus (KSHV) capsids in insect cells using the baculovirus expression system. Using this self-assembly system we investigated whether we could add additional capsid associated proteins and determine their incorporation into the assembled capsid. We chose the capsid vertex-specific component (CVSC) proteins encoded by open reading frames (ORFs) 19 and 32 to test this...
April 26, 2017: Virus Research
https://www.readbyqxmd.com/read/28444822/triplex-dna-nanostructures-from-basic-properties-to-applications
#11
Yuwei Hu, Alessandro Cecconello, Andrea Idili, Francesco Ricci, Itamar Willner
Triplex nucleic acids attract recent interest as part of the rich "tool-box" of structures used to develop DNA-based nanostructures and materials. This review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles and the reversible oligomerization of "origami" tiles or DNA circles are described. Also, the use of triplex-DNA structures as functional units to assemble pH-responsive systems and materials are presented...
April 26, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28433533/corrigendum-to-development-of-sers-substrate-using-phage-based-magnetic-template-for-triplex-assay-in-sepsis-diagnosis-biosens-bioelectron-%C3%A2-85-2016-522-528
#12
Anh H Nguyen, Yesol Shin, Sang Jun Sim
No abstract text is available yet for this article.
September 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28425774/profile-of-the-triplex-assay-for-detection-of-chlamydia-gonorrhea-and-trichomonas-using-the-bd-max%C3%A2-system
#13
Barbara Van Der Pol
Chlamydia, gonorrhea and trichomonas are the most common curable STI. improved access to testing could reduce infection rates and prevent sequelae. nucleic acid amplification tests are the recommend class of diagnostic assay for these infections which are often asymptomatic. Areas covered: A description of the BD MAX™ System (MAX) and the BD MAX CT/GC/TV assay is provided along with data from a large US clinical trial. The capacity of the system for other tests and for lab developed assays is also described...
April 27, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28391510/evaluation-of-two-triplex-one-step-qrt-pcr-assays-for-the-quantification-of-human-enteric-viruses-in-environmental-samples
#14
Kata Farkas, Dafydd E Peters, James E McDonald, Alexis de Rougemont, Shelagh K Malham, Davey L Jones
Human enteric viruses are responsible for waterborne and shellfish-associated disease outbreaks worldwide. Quantitative reverse transcription PCR (qRT-PCR) is often used to assess the health risks associated with shellfish and environmental water, but viral titres in sediments are less commonly investigated. In this study, we developed and validated two multiplex qRT-PCR assays for aquatic sediment and shellfish samples targeting viruses that are a common cause of gastroenteritis (norovirus GI, GII and hepatitis A virus), two emerging viruses (sapovirus and hepatitis E virus), along with mengovirus (MgV), which is often used as a sample process control for the assessment of RNA extraction efficiency...
April 8, 2017: Food and Environmental Virology
https://www.readbyqxmd.com/read/28390431/mycoplasma-detection-by-triplex-real-time-pcr-in-bronchoalveolar-lavage-fluid-from-bovine-respiratory-disease-complex-cases
#15
Jan B W J Cornelissen, Freddy M de Bree, Fimme J van der Wal, Engbert A Kooi, Miriam G J Koene, Alex Bossers, Bregtje Smid, Adriaan F Antonis, Henk J Wisselink
BACKGROUND: In this study we evaluated the RespoCheck Mycoplasma triplex real-time PCR for the detection in bronchoalveolar lavage fluid (BALF) of Mycoplasma (M.) dispar, M. bovis and M. bovirhinis, all three associated with bovine respiratory disease (BRD). Primers and probes of the RespoCheck Mycoplasma triplex real-time PCR are based on the V3/V4 region of the 16S rRNA gene of the three Mycoplasma species. RESULTS: The analytical sensitivity of the RespoCheck triplex real-time PCR was, as determined by spiking experiments of the Mycoplasma strains in Phosphate Buffered Saline, 300 colony forming units (cfu)/mL for M...
April 8, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28383784/folding-topology-of-a-short-coiled-coil-peptide-structure-templated-by-an-oligonucleotide-triplex
#16
Chenguang Lou, Niels Johan Christensen, Manuel C Martos-Maldonado, Søren Roi Midtgaard, Maria Ejlersen, Peter W Thulstrup, Kasper K Sørensen, Knud J Jensen, Jesper Wengel
The rational design of a well-defined protein-like tertiary structure formed by small peptide building blocks is still a formidable challenge. Using peptide-oligonucleotide conjugates (POC) as building blocks, we here present the self-assembly of miniature coiled coil α-helical peptides guided by oligonucleotide duplex and triplex formation. POC synthesis was achieved by copper-free alkyne-azide cycloaddition between three oligonucleotides and a 23-mer peptide, which by itself exhibited multiple oligomeric states in solution...
April 6, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28380870/high-performance-refractive-index-sensor-based-on-low-q-factor-ring-resonators-and-fft-processing-of-wavelength-scanning-data
#17
Lefteris Gounaridis, Panos Groumas, Erik Schreuder, George Tsekenis, Athanasios Marousis, Rene Heideman, Hercules Avramopoulos, Christos Kouloumentas
We extend our previous simulation study and we present experimental results regarding our Fast Fourier Transform method for the calculation of the resonance shifts in biosensors based on micro-ring resonators (MRRs). For the simulation study, we use a system model with a tunable laser at 850 nm, an MRR with 1.5∙10<sup>4</sup> quality factor, and a detection system with 50 dB maximum signal-to-noise ratio, and investigate the impact on the system performance of factors like the number of the resonance peaks inside the scanning window, the wavelength dependence of the laser power, and the asymmetry of the transfer functions of the MRRs...
April 3, 2017: Optics Express
https://www.readbyqxmd.com/read/28372729/development-of-a-thermostabilised-triplex-lamp-assay-with-dry-reagent-four-target-lateral-flow-dipstick-for-detection-of-entamoeba-histolytica-and-non-pathogenic-entamoeba-spp
#18
Phiaw Chong Foo, Yean Yean Chan, Maizan Mohamed, Weng Kin Wong, A B Nurul Najian, Boon Huat Lim
This study highlighted the development of a four target nitrocellulose-based nucleic acid lateral flow immunoassay biosensor in a dry-reagent strip format for interpretation of double-labelled double-stranded amplicons from thermostabilised triplex loop-mediated isothermal amplification assay. The DNA biosensor contained two test lines which captured biotin and texas red labelled amplicons; a LAMP internal amplification control line that captured digoxigenin labelled amplicon; and a chromatography control line that validated the functionality of the conjugated gold nanoparticles and membrane...
May 8, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28371376/a-smart-responsive-dual-aptamers-targeted-bubble-generating-nanosystem-for-cancer-triplex-therapy-and-ultrasound-imaging
#19
Feifei Zhao, Jie Zhou, Xiangjie Su, Yuhui Wang, Xiaosa Yan, Shaona Jia, Bin Du
The absence of targeted, single treatment methods produces low therapeutic value for treating cancers. To increase the accumulation of drugs in tumors and improve the treatment effectiveness, near-infrared 808 nm photothermal responsive dual aptamers-targeted docetaxel (DTX)-containing nanoparticles is proposed. In this system, DTX and NH4 HCO3 are loaded in thermosensitive liposomes. The surface of liposomes is coated with gold nanoshells and connected with sulfydryl (SH) modified AS1411 and S2.2 aptamers...
March 30, 2017: Small
https://www.readbyqxmd.com/read/28370485/19f-nmr-spectroscopic-analysis-of-the-binding-modes-in-triple-helical-pna-microrna-complexes
#20
Pasi Markus Virta, Ville Tähtinen, Lotta Granqvist, Merita Murtola, Roger Strömberg
Triplex-forming peptide nucleic acids (TFPNAs) were targeted to double helical regions of 19F-labelled RNA hairpin models (a UA-rich duplex with a hexaethylene glycol (heg) loop and a miR-215 model). In addition to the conventional UV- and CD-based detection, the binding was monitored by 19F NMR spectroscopy. Detailed information considering the stoichiometry and transition between the triple helical PNA/RNA- and (PNA)2/RNA-binding modes could be obtained. γ-(R)-hydroxymethyl-modified (thymine-1-yl- and 2-aminopyridin-3-yl-acetyl derivatives) TFPNAs were additionally synthesized, targeted to the same RNA models and the effect of the γ-(R)-hydroxymethyl group on the binding was studied...
March 28, 2017: Chemistry: a European Journal
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