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nucleic acids

Ranjan Basak, Naveen Kumar Nair, Indraneel Mittra
There is extensive literature to show that nucleic acids can be taken up by cells under experimental conditions and that foetal DNA can be detected in maternal tissues. The uptaken DNA can integrate into host cell genomes and can be transcribed and translated into proteins. They can also cause chromosomal damage and karyotype alterations. Cell-free nucleic acids (cfNAs)-based non-invasive DNA diagnostic techniques are being extensively researched in the field of cancer with the potential to advance new prognostic parameters and direct treatment decisions...
October 12, 2016: Mutation Research
Adrian R Ferré-D'Amaré
Sequence-specific nucleic acid binding proteins do not recognize one sequence out of all possibilities; rather, they bind to many sequences with a range of affinities. In this issue of Cell Chemical Biology, Lin et al. (2016), describe the entire landscape of affinities between different RNA molecules and an RNA-binding protein, thus providing a comprehensive description of the factors affecting specificity.
October 20, 2016: Cell Chemical Biology
Jean-Rene Arseneau, Royce Steeves, Mark Laflamme
The increasing use of high-throughput sequencing platforms has made the isolation of pure, high molecular weight DNA a primary concern for studies of a diverse range of organisms. Purification of DNA remains a significant challenge in many tissue and sample types due to various organic and inorganic molecules that co-precipitate with nucleic acids. Molluscs, for example, contain high concentrations of polysaccharides which often co-precipitate with DNA and can inhibit downstream enzymatic reactions. We modified a low-salt CTAB (MoLSC) extraction protocol to accommodate contaminant rich animal tissues and compared this method to a standard CTAB extraction protocol and two commercially available animal tissue DNA extraction kits using oyster adductor muscle...
October 21, 2016: Molecular Ecology Resources
Paolo Gabrieli, Francesca Scolari
The Mediterranean fruit fly (medfly) Ceratitis capitata (Wiedemann) (Diptera: Tephritidae) is a pest species with extremely high agricultural relevance. This is due to its reproductive behavior: females damage the external surface of fruits and vegetables when they lay eggs and the hatched larvae feed on their pulp. Wild C. capitata populations are traditionally controlled through insecticide spraying and/or eco-friendly approaches, the most successful being the Sterile Insect Technique (SIT). The SIT relies on mass-rearing, radiation-based sterilization and field release of males that retain their capacity to mate but are not able to generate fertile progeny...
October 1, 2016: Journal of Visualized Experiments: JoVE
Pavel Damborský, Katarzyna M Koczula, Andrea Gallotta, Jaroslav Katrlík
Lateral flow assays (LFAs) enable the simple and rapid detection and quantification of analytes and is popular for point-of-care (PoC), point-of-use and outdoor testing applications. LFAs typically depend on antibody or nucleic acid based recognition. We present the innovative concept of a LFA using lectins in the role of the biorecognition element. Lectins are a special kind of glycan-binding protein and the lectin-based LFA herein described was developed for the determination of the glycosylation of free prostate specific antigen (PSA)...
October 21, 2016: Analyst
Elizabeth A Neuner, Andrea M Pallotta, Simon W Lam, David Stowe, Steven M Gordon, Gary W Procop, Sandra S Richter
OBJECTIVE To describe the impact of rapid diagnostic microarray technology and antimicrobial stewardship for patients with Gram-positive blood cultures. DESIGN Retrospective pre-intervention/post-intervention study. SETTING A 1,200-bed academic medical center. PATIENTS Inpatients with blood cultures positive for Staphylococcus aureus, Enterococcus faecalis, E. faecium, Streptococcus pneumoniae, S. pyogenes, S. agalactiae, S. anginosus, Streptococcus spp., and Listeria monocytogenes during the 6 months before and after implementation of Verigene Gram-positive blood culture microarray (BC-GP) with an antimicrobial stewardship intervention...
November 2016: Infection Control and Hospital Epidemiology
Sonja Obersteller, Heinrich Neubauer, Ralf Matthias Hagen, Hagen Frickmann
The extraction and further processing of nucleic acids (NA) from formalin-fixed paraffin-embedded (FFPE) tissues for microbiological diagnostic polymerase chain reaction (PCR) approaches is challenging. Here, we assessed the effects of five different commercially available nucleic acid extraction kits on the results of real-time PCR. FFPE samples from organs of Burkholderia pseudomallei-infected Swiss mice were subjected to processing with five different extraction kits from QIAGEN (FFPE DNA Tissue Kit, EZ1 DNA Tissue Kit, DNA Mini Kit, DNA Blood Mini Kit, and FlexiGene DNA Kit) in combination with three different real-time PCRs targeting B...
September 29, 2016: European Journal of Microbiology & Immunology
Essowè Palanga, Denis Filloux, Darren P Martin, Emmanuel Fernandez, Daniel Gargani, Romain Ferdinand, Jean Zabré, Zakaria Bouda, James Bouma Neya, Mahamadou Sawadogo, Oumar Traore, Michel Peterschmitt, Philippe Roumagnac
Cowpea, (Vigna unguiculata L. (Walp)) is an annual tropical grain legume. Often referred to as "poor man's meat", cowpea is one of the most important subsistence legumes cultivated in West Africa due to the high protein content of its seeds. However, African cowpea production can be seriously constrained by viral diseases that reduce yields. While twelve cowpea-infecting viruses have been reported from Africa, only three of these have so-far been reported from Burkina Faso. Here we use a virion-associated nucleic acids (VANA)-based metagenomics method to screen for the presence of cowpea viruses from plants collected from the three agro-climatic zones of Burkina Faso...
2016: PloS One
Thomas Briese, David T Williams, Vishal Kapoor, Sinead M Diviney, Andrea Certoma, Jianning Wang, Cheryl A Johansen, Rashmi Chowdhary, John S Mackenzie, W Ian Lipkin
The Mapputta group comprises antigenically related viruses indigenous to Australia and Papua New Guinea that are included in the family Bunyaviridae but not currently assigned to a specific genus. We determined and analyzed the genome sequences of five Australian viruses isolated from mosquitoes collected during routine arbovirus surveillance in Western Australia (K10441, SW27571, K13190, and K42904) and New South Wales (12005). Based on matching sequences of all three genome segments to prototype MRM3630 of Trubanaman virus (TRUV), NB6057 of Gan Gan virus (GGV), and MK7532 of Maprik virus (MPKV), isolates K13190 and SW27571 were identified as TRUV, 12005 as GGV, and K42904 as a Mapputta group virus from Western Australia linking GGV and MPKV...
2016: PloS One
Simnikiwe H Mayaphi, Desmond J Martin, Thomas C Quinn, Oliver Laeyendecker, Steve A S Olorunju, Gregory R Tintinger, Anton C Stoltz
BACKGROUND: Two thirds of the world's new HIV infections are in sub-Saharan Africa. Acute HIV infection (AHI) is the time of virus acquisition until the appearance of HIV antibodies. Early HIV infection, which includes AHI, is the interval between virus acquisition and establishment of viral load set-point. This study aimed to detect acute and early HIV infections in a hyper-endemic setting. METHODS: This was a cross-sectional diagnostic study that enrolled individuals who had negative rapid HIV results in five clinics in South Africa...
2016: PloS One
Marie Louise Landry, Kirsten St George
CONTEXT: -The rapid and accurate diagnosis of Zika virus infection is an international priority. OBJECTIVE: -To review current recommendations, methods, limitations, and priorities for Zika virus testing. DATA SOURCES: -Sources include published literature, public health recommendations, laboratory procedures, and testing experience. CONCLUSIONS: -Until recently, the laboratory diagnosis of Zika infection was confined to public health or research laboratories that prepared their own reagents, and test capacity has been limited...
October 20, 2016: Archives of Pathology & Laboratory Medicine
Alyssa B Chinen, Jennifer R Ferrer, Timothy J Merkel, Chad A Mirkin
Two synthetic approaches that allow one to control PEG content within spherical nucleic acids (SNAs) have been developed. One approach begins with RNA-modified gold nanoparticles followed by a backfill of PEG 2K alkanethiols, and the other involves co-adsorption of the two entities on a gold nanoparticle template. These two methods have been used to explore the role of PEG density on the chemical and biological properties of RNA-SNAs. Such studies show that while increasing the extent of PEGylation within RNA-SNAs extends their blood circulation half-life in mice, it also results in decreased cellular uptake...
October 20, 2016: Bioconjugate Chemistry
Jessalyn M Ubellacker, Sandra S McAllister
Systemic factors including cytokines, cell-free nucleic acids, microvesicles, and platelets are appreciated as important regulators of adenocarcinoma progression. Research findings using pre-clinical mouse models have revealed that many such systemically acting factors are either secreted by or responsive to peripheral tumors and impact bone and bone marrow (collectively referred to as the bone microenvironment) to initiate processes that ultimately govern disease progression, even in the absence of detectable bone metastases...
September 2016: Journal of Bone Oncology
Agnes Gardet, Wei C Chou, Taylor L Reynolds, Diana B Velez, Kai Fu, Julia M Czerkowicz, Jeffrey Bajko, Ann M Ranger, Normand Allaire, Hannah M Kerns, Sarah Ryan, Holly M Legault, Robert W Dunstan, Robert Lafyatis, Matvey Lukashev, Joanne L Viney, Jeffrey L Browning, Dania Rabah
Mouse models lupus nephritis (LN) have provided important insights into disease pathogenesis, although none have been able to recapitulate all features of the human disease. Using comprehensive longitudinal analyses, we characterized a novel accelerated mouse model of lupus using pristane treatment in SNF1 (SWR X NZB F1) lupus prone mice (pristane-SNF1 mice). Pristane treatment in SNF1 mice accelerated the onset and progression of proteinuria, autoantibody production, immune complex deposition and development of renal lesions...
2016: PloS One
Da Zhou, Bing-Hang Li, Jing Wang, Yong-Nian Ding, Yan Dong, Yuan-Wen Chen, Jian-Gao Fan
BACKGROUND: Prolyl oligopeptidase (POP) is a serine endopeptidase that is widely distributed in vivo, particularly in the liver. Significant changes in functional mitochondrial proteins involved with mitochondrial oxidoreductases/transporters and nucleic acid binding proteins were observed after POP inhibition in the liver, which suggested a role of POP in regulating liver energy metabolism. Steatosis in nonalcoholic fatty liver disease (NAFLD) is associated with disturbances in lipid and energy metabolism in hepatocytes...
2016: PloS One
David A Selck, Rustem F Ismagilov
Nucleic acid amplification tests that are coupled with a digital readout enable the absolute quantification of single molecules, even at ultralow concentrations. Digital methods are robust, versatile and compatible with many amplification chemistries including isothermal amplification, making them particularly invaluable to assays that require sensitive detection, such as the quantification of viral load in occult infections or detection of sparse amounts of DNA from forensic samples. A number of microfluidic platforms are being developed for carrying out digital amplification...
2016: PloS One
Lars Hahn, Chris-André Leimeister, Rachid Ounit, Stefano Lonardi, Burkhard Morgenstern
Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set...
October 2016: PLoS Computational Biology
Justin A Lemkul, Alexander D MacKerell
Mg2+ ions are important in biological systems, particularly in stabilizing compact RNA folds. Mg2+ is strongly polarizing, and representing its interactions in heterogeneous environments is a challenge for empirical force field development. To date, the most commonly used force fields in molecular dynamics simulations utilize a pairwise-additive approximation for electrostatic interactions, which cannot account for the significant polarization response in systems containing Mg2+. In the present work, we refine the interactions of Mg2+ with water, Cl- ions, and nucleic acid moieties using a polarizable force field based on the classical Drude oscillator model...
October 19, 2016: Journal of Physical Chemistry. B
Junyi Che, Anqi Tao, Shun Chen, Xiaoming Li, Yi Zhao, Weien Yuan
Small interfering RNA (siRNA) has increased the hope for highly-efficient treatment of gene-related diseases. However, the stable and efficient delivery of therapeutic nucleic acids is a prerequisite for the successful clinical translation of RNA interfering therapy. To achieve this, we condensed the low molecular weight polyethyleneimine (PEI, Mw < 2000) with 2,6-pyridinedicarboxaldehyde (PDA) to synthesize a biologically responsive and degradable cationic polymer (abbreviated to PDAPEI) which was utilized as a gene vector for the delivery of a VEGF-A shRNA expression plasmid DNA (pDNA)...
October 19, 2016: Scientific Reports
Heiko Ihmels, Katy Schäfer, Giampietro Viola, Elena Porcu
The interactions of 8-hydroxybenzo[b]quinolizinium and 9-hydroxy-benzo[b]quinolizinium with DNA are investigated in detail. Specifically, spectro¬photometric and spectrofluorimetric titrations, thermal DNA-de¬na¬turation experiments as well as CD- and LD-spectroscopic ana¬lysis show that a pH shift by just one or two orders of magnitude has a significant impact on the interactions of the acidic ligands with the nucleic acid. Both ligands bind with high affinity to DNA at pH = 6 (Kb ≈ 105 M-1). At pH = 7 or 8, however, the binding interactions are much weaker because of the formation of the corresponding charge neutral conjugate bases whose affinity to DNA is reduced due to the resulting lack of a positive charge...
October 19, 2016: Chemistry: a European Journal
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