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https://www.readbyqxmd.com/read/29144729/an-optical-nanoantenna-for-single-molecule-based-detection-of-zika-virus-nucleic-acids-without-molecular-multiplication
#1
Sarah Elisabeth Ochmann, Carolin Vietz, Kateryna Trofymchuk, Guillermo P Acuna, Birka Lalkens, Philip Tinnefeld
Due to the limited signal-to-background ratio, molecular diagnostics requires molecular amplification of the target molecules or molecular signal amplification after target recognition. For direct molecular detection, we demonstrate a purely physical fluorescence enhancement process which can elevate the fluorescence signal of single fluorescent dyes by several orders of magnitude. To this end, DNA origami-based optical antennas with a height of around 125 nm are used, which utilize metallic nanoparticles to create a hotspot where fluorescence signals are enhanced by plasmonic effects...
November 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29144411/nucleic-acid-aptamers-emerging-applications-in-medical-imaging-nanotechnology-neurosciences-and-drug-delivery
#2
REVIEW
Pascal Röthlisberger, Cécile Gasse, Marcel Hollenstein
Recent progresses in organic chemistry and molecular biology have allowed the emergence of numerous new applications of nucleic acids that markedly deviate from their natural functions. Particularly, DNA and RNA molecules-coined aptamers-can be brought to bind to specific targets with high affinity and selectivity. While aptamers are mainly applied as biosensors, diagnostic agents, tools in proteomics and biotechnology, and as targeted therapeutics, these chemical antibodies slowly begin to be used in other fields...
November 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29144379/a-digital-microfluidics-platform-for-loop-mediated-isothermal-amplification-detection
#3
Beatriz Jorge Coelho, Bruno Veigas, Hugo Águas, Elvira Fortunato, Rodrigo Martins, Pedro Viana Baptista, Rui Igreja
Digital microfluidics (DMF) arises as the next step in the fast-evolving field of operation platforms for molecular diagnostics. Moreover, isothermal schemes, such as loop-mediated isothermal amplification (LAMP), allow for further simplification of amplification protocols. Integrating DMF with LAMP will be at the core of a new generation of detection devices for effective molecular diagnostics at point-of-care (POC), providing simple, fast, and automated nucleic acid amplification with exceptional integration capabilities...
November 16, 2017: Sensors
https://www.readbyqxmd.com/read/29143920/distinguishing-the-disease-associated-snps-based-on-composition-frequency-analysis
#4
Wenling Li, Menglong Li, Xuemei Pu, Yanzhi Guo
Single-nucleotide polymorphism (SNP) is a basical variation in genome. When SNPs occur at the binding sites of microRNA, they can influence the binding efficiency, cause a fluctuation of the mRNA in vivo, and thus arouse posttranscriptional level abnormality. Therefore, SNP has a strong correlation with diseases. Although enormous SNPs have been experimentally identified, only a tiny proportion of them are truly disease-associated SNPs (dSNPs) that relate to microRNA modification and then are involved in disease causing process...
November 16, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29143837/development-of-a-label-free-raman-imaging-technique-for-differentiation-of-malaria-parasite-infected-from-non-infected-tissue
#5
Laura Frame, James Brewer, Rebecca Lee, Karen Faulds, Duncan Graham
During malarial infection, the host uses the spleen to clear the malaria parasites, however, the parasites have evolved the ability to bind to endothelial receptors in blood vessels of tissues to avoid removal, known as sequestration, and this is largely responsible for the symptoms and severity of infection. So a technique which could non-invasively diagnose tissue burden could be utilised as an aid for localised malaria diagnosis within tissue. Raman spectroscopy is a label-free imaging technique and can provide unique and chemically specific Raman 'fingerprint' spectrum of biological samples such as tissue...
November 16, 2017: Analyst
https://www.readbyqxmd.com/read/29143619/diagnostic-accuracy-of-tests-to-detect-hepatitis-b-surface-antigen-a-systematic-review-of-the-literature-and-meta-analysis
#6
Ali Amini, Olivia Varsaneux, Helen Kelly, Weiming Tang, Wen Chen, Debrah I Boeras, Jane Falconer, Joseph D Tucker, Roger Chou, Azumi Ishizaki, Philippa Easterbrook, Rosanna W Peeling
BACKGROUND: Chronic Hepatitis B Virus (HBV) infection is characterised by the persistence of hepatitis B surface antigen (HBsAg). Expanding HBV diagnosis and treatment programmes into low resource settings will require high quality but inexpensive rapid diagnostic tests (RDTs) in addition to laboratory-based enzyme immunoassays (EIAs) to detect HBsAg. The purpose of this review is to assess the clinical accuracy of available diagnostic tests to detect HBsAg to inform recommendations on testing strategies in 2017 WHO hepatitis testing guidelines...
November 1, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29143615/diagnostic-accuracy-of-tests-to-detect-hepatitis-c-antibody-a-meta-analysis-and-review-of-the-literature
#7
Weiming Tang, Wen Chen, Ali Amini, Debi Boeras, Jane Falconer, Helen Kelly, Rosanna Peeling, Olivia Varsaneux, Joseph D Tucker, Philippa Easterbrook
BACKGROUND: Although direct-acting antivirals can achieve sustained virological response rates greater than 90% in Hepatitis C Virus (HCV) infected persons, at present the majority of HCV-infected individuals remain undiagnosed and therefore untreated. While there are a wide range of HCV serological tests available, there is a lack of formal assessment of their diagnostic performance. We undertook a systematic review and meta-analysis to evaluate he diagnostic accuracy of available rapid diagnostic tests (RDT) and laboratory based EIA assays in detecting antibodies to HCV...
November 1, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29143609/survey-of-programmatic-experiences-and-challenges-in-delivery-of-hepatitis-b-and-c-testing-in-low-and-middle-income-countries
#8
Azumi Ishizaki, Julie Bouscaillou, Niklas Luhmann, Stephanie Liu, Raissa Chua, Nick Walsh, Sarah Hess, Elena Ivanova, Teri Roberts, Philippa Easterbrook
BACKGROUND: There have been few reports on programmatic experience of viral hepatitis testing and treatment in resource-limited settings. To inform the development of the 2017 World Health Organization (WHO) viral hepatitis testing guidance and in particular the feasibility of proposed recommendations, we undertook a survey across a range of organisations engaged with hepatitis testing in low- and middle-income countries (LMICs). Our objective was to describe current hepatitis B and C testing practices across a range of settings in different countries, as well as key barriers or challenges encountered and proposed solutions to promote testing scale-up...
November 1, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29143069/hemin-g-quadruplex-horseradish-peroxidase-mimicking-dnazyme-principle-and-biosensing-application
#9
Negar Alizadeh, Abdollah Salimi, Rahman Hallaj
Enzymes are macromolecular biological catalysts that accelerate chemical reactions. Enzyme labels are commonly used to obtain signal amplification in sensors and biosensors on the basis of reactions of some enzymes such as horseradish peroxidase (HRP). However, use of natural enzymes can encounter some challenges. Lately, nucleic acids that exhibit catalytic properties have attracted growing interest because they have certain advantages in comparison with traditional protein enzymes. DNAzymes are DNA-based catalysts, representing an important class of functional DNA, which have been widely used because of their excellent activity, programmability, signal amplification through catalytic turnover, high chemical stability, simple synthesis, and easy modification...
November 16, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/29142748/intraoperative-prediction-of-the-two-axillary-lymph-node-macrometastases-threshold-in-patients-with-breast-cancer-using-a-one-step-nucleic-acid-cytokeratin-19-amplification-assay
#10
Victoria Fung, Stan Kohlhardt, Patricia Vergani, Gregory J Zardin, Norman R Williams
The aim of the present study was to assess the sensitivity, specificity and practicality of using a one-step nucleic acid amplification (OSNA) assay during breast cancer staging surgery to predict and discriminate between at least 2 involved nodes and more than 2 involved nodes and facilitate the decision to provide axillary conservation in the presence of a low total axillary node tumour burden. A total of 700 consecutive patients, not treated with neo-adjuvant chemotherapy, received intraoperative sentinel lymph node (SLN) analysis using OSNA for cT1-T3 cN0 invasive breast cancer...
November 2017: Molecular and Clinical Oncology
https://www.readbyqxmd.com/read/29142313/effects-of-exosome-on-the-activation-of-cd4-t-cells-in-rhesus-macaques-a-potential-application-for-hiv-latency-reactivation
#11
Xiaowu Hong, Blake Schouest, Huanbin Xu
Exosomes are small extracellular vesicles (EVs), released by a wide variety of cell types, carry donor origin-proteins, cytokines, and nucleic acids, transport these cargos to adjacent or distant specific recipient cells, and thereby regulate gene expression and activation of target cells. In this study, we isolated and identified exosomes in rhesus macaques, and investigated their effects on cell tropism and activation, especially their potential to reactivate HIV latency. The results indicated that plasma-derived exosomes preferentially fuse to TCR-activated T cells and autologous parent cells...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142018/terahertz-dictating-the-frequency-of-life-do-macromolecular-vibrational-modes-impose-thermal-limitations-on-terrestrial-life
#12
Kieran Hand, Edwin Yates
Conditions on exoplanets include elevated temperatures and pressures. The response of carbon-based biological macromolecules to such conditions is then relevant to the viability of life. The capacity of proteins and ribozymes to catalyse reactions or bind receptors, and nucleic acids to convey information, depends on them sampling different conformational states. These are determined by macromolecular vibrational states, or phonon modes, accessible using terahertz (THz: 10(12)Hz) absorption spectroscopy. THz spectra of biological macromolecules exhibit broad absorption at approximately 6 THz (equating to approx...
November 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29141709/rapid-diagnostic-testing-of-hospitalized-malawian-children-reveals-opportunities-for-improved-hiv-diagnosis-and-treatment
#13
Theresa F Madaline, Sarah E Hochman, Karl B Seydel, Alice Liomba, Alex Saidi, Grace Matebule, Wenzhu B Mowrey, Bernadette O'Hare, Danny A Milner, Kami Kim
Recent World Health Organization (WHO) guidelines recommend antiretroviral therapy (ART) for all HIV-infected people; previously CD4+ T lymphocyte quantification (CD4 count) or clinical staging determined eligibility for children ≥ 5 years old in low- and middle-income countries. We examined positive predictive value (PPV) of a rapid diagnostic test (RDT) algorithm and ART eligibility for hospitalized children with newly diagnosed HIV infection. We enrolled 363 hospitalized Malawian children age 2 months to 16 years with two serial positive HIV RDT from 2013 to 2015...
October 16, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29141408/accurate-quantification-of-nucleic-acids-using-hypochromicity-measurements-in-conjunction-with-uv-spectrophotometry
#14
Alison Nwokeoji, Peter M Kilby, David Portwood, Mark J Dickman
UV absorbance spectrophotometry is widely used for the quantification of nucleic acids. For accurate quantification it is important to determine the hypochromocity of the oligonucleotide or complex nucleic acid structure. The use of thermal denaturation studies in conjunction with UV spectrophotometry to determine hypochromicity requires prolonged, elevated temperatures, which may cause partial hydrolysis of RNA. In addition, dsRNA is difficult to denature even at elevated temperature and the extinction coefficients of nucleic acids are also affected by temperature, which makes it difficult to accurately determine the nucleic acid concentration...
November 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29141138/differential-effects-of-strand-asymmetry-on-the-energetics-and-structural-flexibility-of-dna-internal-loops
#15
Thao Tran, Brian Cannon
Internal loops within structured nucleic acids disrupt local base-stacking and destabilize neighboring helical domains; however, these structural motifs also expand the conformational and functional capabilities for structured nucleic acids. Variations in size, distribution of loop nucleotides on opposing strands (strand asymmetry), and sequence alter their biophysical properties. Here, the thermodynamics and structural flexibility of poly(T)-rich DNA internal loops were systematically investigated in terms of loop size and strand asymmetry...
November 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/29140681/orthogonal-operation-of-constitutional-dynamic-networks-consisting-of-dna-tweezer-machines
#16
Liang Yue, Shan Wang, Alessandro Cecconello, Jean-Marie Lehn, Itamar Willner
Overexpression or down-regulation of cellular processes are often controlled by dynamic chemical networks. Bioinspired by nature, we introduce constitutional dynamic networks (CDNs) as systems that emulate principle of the nature processes. The CDNs comprise of dynamically exchangeable equilibrated constituents that respond to external triggers by adapting the composition of the dynamic mixture to the energetic stabilization of the constituents. We introduce a nucleic acid-based CDN that includes four exchangeable and mechanically-triggered tweezers AA', BB', AB' and BA' existing in close, close, open and open configurations, respectively...
November 15, 2017: ACS Nano
https://www.readbyqxmd.com/read/29140470/database-resources-of-the-national-center-for-biotechnology-information
#17
(no author information available yet)
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 39 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets...
November 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29139616/raft-polymerization-for-the-synthesis-of-tertiary-amine-based-diblock-copolymer-nucleic-acid-delivery-vehicles
#18
Annie K McClellan, Taisen Hao, Tracy A Brooks, Adam E Smith
The synthesis and characterization of a family of nine pH-responsive, diblock copolymers designed to effectively deliver nucleic acids are reported. The stabilizing A block is comprised of an oligo(ethylene glycol) methyl ether methacrylate to impart water solubility. The cationic blocks of varying degrees of polymerization (DPs) are derived from three pH responsive, tertiary amine-containing methacrylates capable of complexing negatively charged nucleic acids. The cytotoxicity studies utilizing human embryonic kidney cells (HEK-293) and Michigan Cancer Foundation-7 (MCF-7) breast cancer cells indicate no decrease of cell viability with the diblock copolymers, with the exception of the two highest DPs of the cationic blocks with ethyl-substitutes tertiary amine...
November 15, 2017: Macromolecular Bioscience
https://www.readbyqxmd.com/read/29139533/at-the-very-beginning-of-life-on-earth-the-thiol-rich-peptide-trp-world-hypothesis
#19
Yannick Vallee, Ibrahim Shalayel, Kieu-Dung Ly, K V Raghavendra Rao, Gael De Paëpe, Katharina Märker, Anne Milet
Life developed on Earth probably about 3.8 billion years ago, on a planet that was already largely covered by oceans and where the atmosphere was very humid. The reactions, which may have led to the formation of the first polymers, particularly to the first peptides and nucleic acids, must have been compatible with these conditions. This is the case of the reaction of nitriles with aminothiols, such as cysteine and homocysteine. Since aminonitriles are the probable precursors of amino acids, this condensation reaction has been able to rapidly yield dipeptides, tripeptides, oligomers and even true polymers, each containing thiol functions...
2017: International Journal of Developmental Biology
https://www.readbyqxmd.com/read/29139529/lab-on-capillary-a-rapid-simple-and-quantitative-genetic-analysis-platform-integrating-nucleic-acid-extraction-amplification-and-detection
#20
Yu Fu, Xiaoming Zhou, Da Xing
In this work, we describe for the first time a genetic diagnosis platform employing a polydiallyldimethylammonium chloride (PDDA)-modified capillary and a liquid-based thermalization system for rapid, simple and quantitative DNA analysis with minimal user interaction. Positively charged PDDA is modified on the inner surface of the silicon dioxide capillary by using an electrostatic self-assembly approach that allows the negatively charged DNA to be separated from the lysate in less than 20 seconds. The capillary loaded with the PCR mix is incorporated in the thermalization system, which can achieve on-site real-time PCR...
November 15, 2017: Lab on a Chip
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