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https://www.readbyqxmd.com/read/28537750/detection-of-microrna-by-electrocatalytic-amplification-a-general-approach-for-single-particle-biosensing
#1
Alma D Castañeda, Nicholas J Brenes, Aditya Kondajji, Richard M Crooks
Here we report a sensing scheme for detection of microRNA (miRNA) using electrocatalytic amplification (ECA). ECA is a method in which nanoparticles (NPs) that are catalytic for a specific electrochemical reaction collide with an inert electrode surface. Each collision results in a detectable current transient. In the present article, we show that this general approach can be extended to detection of miRNA. Specifically, PtNPs are modified with a single-strand DNA (ssDNA) shell that is complementary to the miRNA target...
May 24, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28535585/good-laboratory-standards-for-clinical-next-generation-sequencing-cancer-panel-tests
#2
REVIEW
Jihun Kim, Woong-Yang Park, Nayoung K D Kim, Se Jin Jang, Sung-Min Chun, Chang-Ohk Sung, Jene Choi, Young-Hyeh Ko, Yoon-La Choi, Hyo Sup Shim, Jae-Kyung Won
Next-generation sequencing (NGS) has recently emerged as an essential component of personalized cancer medicine due to its high throughput and low per-base cost. However, no sufficient guidelines for implementing NGS as a clinical molecular pathology test are established in Korea. To ensure clinical grade quality without inhibiting adoption of NGS, a taskforce team assembled by the Korean Society of Pathologists developed laboratory guidelines for NGS cancer panel testing procedures and requirements for clinical implementation of NGS...
May 2017: Journal of Pathology and Translational Medicine
https://www.readbyqxmd.com/read/28534707/type-ia-topoisomerases-can-be-magicians-for-both-dna-and-rna-in-all-domains-of-life
#3
Muzammil Ahmad, Dongyi Xu, Weidong Wang
Topoisomerases solve critical topological problems in DNA metabolism and have long been regarded as the "magicians" of the DNA world. Here we present views from two of our recent studies indicating that Type IA topoisomerases from all domains of life often possess dual topoisomerase activities for both DNA and RNA. In animals, one of the two Type IA topoisomerases, Top3β, contains an RNA-binding domain, possesses RNA topoisomerase activity, binds mRNAs, interacts with mRNA-binding proteins, and associates with active mRNA translation machinery...
May 23, 2017: RNA Biology
https://www.readbyqxmd.com/read/28532812/the-occurrence-of-biofilm-in-an-equine-experimental-wound-model-of-healing-by-secondary-intention
#4
E Jørgensen, L Bay, T Bjarnsholt, L Bundgaard, M A Sørensen, S Jacobsen
In humans, biofilm is a well-known cause of delayed healing and low-grade inflammation of chronic wounds. In horses, biofilm formation in wounds has been studied to a very limited degree. The objective of this study was thus to investigate the occurrence of biofilm in equine experimental wounds healing by secondary intention. Tissue biopsies from non-contaminated, experimental excisional shoulder and limb wounds were obtained on day 1-2, day 7-10 and day 14-15 post-wounding. Limb wounds were either un-bandaged or bandaged to induce exuberant granulation tissue (EGT) formation and thereby impaired healing...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28532300/engineered-polymeric-amphiphiles-self-assembling-into-nanostructures-and-acting-as-efficient-gene-and-drug-carriers
#5
Ruby Bansal, Pradeep Kumar
Nonviral gene delivery systems are finding widespread use due to their safety, rapid and economical production, and ease of modification. In this work, series of N-alkyl-substituted linear polyethylenimine (CP) polymers have been synthesized, characterized, and investigated about how degree of substitution (hydrophobic-hydrophilic balance) (i.e. N-alkylation) influenced the transfection efficiency. Mobility shift assay demonstrated efficient binding of plasmid DNA (pDNA). Transfection efficiency and cytotoxicity of CP polymers were assessed in vitro, which revealed that all the formulations exhibited higher transfection activity than linear polyethylenimine (lPEI) and commercial transfection reagents, Lipofectamine and Superfect, with negligible toxicity (MTT assay)...
January 1, 2017: Journal of Biomaterials Applications
https://www.readbyqxmd.com/read/28531186/parvovirus-b19-induced-vascular-damage-in-the-heart-is-associated-with-elevated-circulating-endothelial-microparticles
#6
Katrin Bachelier, Susanne Biehl, Viktoria Schwarz, Ingrid Kindermann, Reinhard Kandolf, Martina Sauter, Christian Ukena, Ali Yilmaz, Karen Sliwa, Claus-Thomas Bock, Karin Klingel, Michael Böhm
BACKGROUND: Diagnosis of viral myocarditis is difficult by clinical criteria but facilitated by detection of inflammation and viral genomes in endomyocardial biopsies. Parvovirus B19 (B19V) targets endothelial cells where viral nucleic acid is exclusively detected in the heart. Microparticles (MPs) are released after cell damage or activation of specific cells. We aimed to investigate whether circulating endothelial MPs (EMPs) in human and experimental models of myocarditis are associated with B19V myocarditis...
2017: PloS One
https://www.readbyqxmd.com/read/28530287/microfluidic-self-assembly-of-folate-targeted-monomolecular-sirna-lipid-nanoparticles
#7
R Krzysztoń, B Salem, D J Lee, G Schwake, E Wagner, J O Rädler
Non-viral delivery of nucleic acids for therapies based on RNA interference requires a rational design and optimal self-assembly strategies. Nucleic acid particles need to be small, stable and functional in terms of selective cell uptake and controlled release of encapsulated nucleic acids. Here we report on small (∼38 nm) monomolecular nucleic acid/lipid particles (mNALPs) that contain single molecules of short double-stranded oligonucleotides covered by a tight, highly curved lipid bilayer. The particles consist of DOPE, DOTAP, DOPC and DSPE-PEG(2000) and are assembled with 21 bp double-stranded DNA or small interfering RNA by solvent exchange on a hydrodynamic-focusing microfluidic chip...
May 22, 2017: Nanoscale
https://www.readbyqxmd.com/read/28529978/emerging-applications-of-exosomes-in-cancer-therapeutics-and-diagnostics
#8
REVIEW
Sahil Inamdar, Rajeshwar Nitiyanandan, Kaushal Rege
Exosomes are nanoscale extracellular vesicles that are shed from different cells in the body. Exosomes encapsulate several biomolecules including lipids, proteins, and nucleic acids, and can therefore play a key role in cellular communication. These vesicles can be isolated from different body fluids and their small sizes make them attractive in various biomedical applications. Here, we review state-of-the art approaches in exosome isolation and purification, and describe their potential use in cancer vaccines, drug delivery, and diagnostics...
March 2017: Bioengineering & Translational Medicine
https://www.readbyqxmd.com/read/28528575/characterization-of-a-cyclic-olefin-polymer-microcentrifuge-tube
#9
Lloyd Waxman, Rachel L Erwin, Vinod D Vilivalam
Here, we describe the properties of a prototype microcentrifuge tube made from the plastic cyclic olefin polymer (COP). This material has been used in the manufacture of primary containers including syringes and vials for the storage, shipment, and delivery of biotherapeutics, vaccines, and cell therapy products. Its low level of extractable substances and metals along with its glass-like clarity make COP an attractive material for the fabrication of microcentrifuge tubes and other consumable laboratory plasticware where contamination is an important consideration, such as in the storage and analysis of labile proteins, nucleic acids, and metabolites...
May 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28526032/multiplex-dnase-free-one-step-reverse-transcription-pcr-for-plasmodium-18s-rrna-and-spliced-gametocyte-specific-mrnas
#10
Amelia E Hanron, Zachary P Billman, Annette M Seilie, Tayla M Olsen, Matthew Fishbaugher, Ming Chang, Thomas Rueckle, Nicole Andenmatten, Bryan Greenhouse, Emmanuel Arinaitwe, John Rek, Smita Das, Gonzalo J Domingo, Kelly Shipman, Stefan H Kappe, James G Kublin, Sean C Murphy
BACKGROUND: Plasmodium gametocytes are sexual stages transmitted to female Anopheles mosquitoes. While Plasmodium parasites can be differentiated microscopically on Giemsa-stained blood smears, molecular methods are increasingly used because of their increased sensitivity. Molecular detection of gametocytes requires methods that discriminate between asexual and sexual stage parasites. Commonly tested gametocyte-specific mRNAs are pfs25 and pfs230 detected by reverse transcription polymerase chain reaction (RT-PCR)...
May 19, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28524845/divergent-prebiotic-synthesis-of-pyrimidine-and-8-oxo-purine-ribonucleotides
#11
Shaun Stairs, Arif Nikmal, Dejan-Krešimir Bučar, Shao-Liang Zheng, Jack W Szostak, Matthew W Powner
Understanding prebiotic nucleotide synthesis is a long standing challenge thought to be essential to elucidating the origins of life on Earth. Recently, remarkable progress has been made, but to date all proposed syntheses account separately for the pyrimidine and purine ribonucleotides; no divergent synthesis from common precursors has been proposed. Moreover, the prebiotic syntheses of pyrimidine and purine nucleotides that have been demonstrated operate under mutually incompatible conditions. Here, we tackle this mutual incompatibility by recognizing that the 8-oxo-purines share an underlying generational parity with the pyrimidine nucleotides...
May 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28524366/contrasting-hcv-and-hiv-seroepidemiology-in-11-years-of-blood-donors-screening-in-brazil
#12
J E Levi, S M Lira, C B Bub, M B Polite, C C Terzian, J M Kutner
BACKGROUND: Blood donors are, in principle, healthy individuals who may be revealed as infectious for blood-borne agents by the laboratory screening process, depicting the asymptomatic burden of the disease. Therefore, monitoring hepatitis C virus (HCV)-infected donor and human immunodeficiency virus (HIV)-infected donor and associating to their demographical and behavioural characteristics may shed light on the dynamics and contemporary changes in these viruses' epidemiology. METHODS: Donors presenting repeatedly reactive HCV or HIV serology/nucleic acid testing (NAT) screening results were submitted to confirmatory testing...
May 19, 2017: Transfusion Medicine
https://www.readbyqxmd.com/read/28524007/the-proinflammatory-cytokine-gitrl-contributes-to-trail-mediated-neurotoxicity-in-the-hcn-2-human-neuronal-cell-line
#13
Giulia Di Benedetto, Salvatore Saccone, Laurence Lempereur, Nicole Ronsisvalle, Giuseppe Nocentini, Rodolfo Bianchini, Carlo Riccardi, Renato Bernardini, Giuseppina Cantarella
Cytokines belonging to the TNF superfamily play a relevant role in neurodegenerative processes. Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand (TRAIL), released during neuronal injury, has proven to potently mediate and sustain neurotoxic processes leading to neuronal death. Similarly to TRAIL, the cytokine Glucocorticoid-induced TNF receptor ligand (GITRL) is able to transduce proapoptotic signals. In spite of the array of reports suggesting relationships between TRAIL and other cytokines, scanty data are, so far, available about a GITRL/TRAIL crosstalk...
May 18, 2017: Current Alzheimer Research
https://www.readbyqxmd.com/read/28523956/pathogen-reduction-technologies-the-pros-and-cons-for-platelet-transfusion
#14
Audrey Magron, Jonathan Laugier, Patrick Provost, Eric Boilard
The transfusion of platelets is essential for diverse pathological conditions associated with thrombocytopenia or platelet disorders. To maintain optimal platelet quality and functions, platelets are stored as platelet concentrates (PCs) at room temperature under continuous agitation-conditions that are permissive for microbial proliferation. In order to reduce these contaminants, pathogen reduction technologies (PRTs) were developed by the pharmaceutical industry and subsequently implemented by blood banks...
May 19, 2017: Platelets
https://www.readbyqxmd.com/read/28522948/evaluation-of-xpert-mtb-rif-assay-performance-in-the-diagnosis-of-abdominal-tuberculosis
#15
Suraj Kumar, Sawan Bopanna, Saurabh Kedia, Pratap Mouli, Rajan Dhingra, Rajesh Padhan, Mikashmi Kohli, Jigyasa Chaubey, Rohini Sharma, Prasenjit Das, S Dattagupta, Govind Makharia, S K Sharma, Vineet Ahuja
BACKGROUND/AIMS: The use of genetic probes for the diagnosis of pulmonary tuberculosis (TB) has been well described. However, the role of these assays in the diagnosis of intestinal tuberculosis is unclear. We therefore assessed the diagnostic utility of the Xpert Mycobacterium tuberculosis/rifampicin (MTB/RIF) assay, and estimated the prevalence of multidrug-resistant (MDR) TB in the Indian population. METHODS: Of 99 patients recruited, 37 had intestinal TB; two control groups comprised 43 with Crohn's disease (CD) and 19 with irritable bowel syndrome...
April 2017: Intestinal Research
https://www.readbyqxmd.com/read/28522842/cryo-electron-microscopy-structure-of-the-macrobrachium-rosenbergii-nodavirus-capsid-at-7-angstroms-resolution
#16
Kok Lian Ho, Chare Li Kueh, Poay Ling Beh, Wen Siang Tan, David Bhella
White tail disease in the giant freshwater prawn Macrobrachium rosenbergii causes significant economic losses in shrimp farms and hatcheries and poses a threat to food-security in many developing countries. Outbreaks of Macrobrachium rosenbergii nodavirus (MrNV), the causative agent of white tail disease (WTD) are associated with up to 100% mortality rates. There are no interventions available to treat or prevent MrNV disease however. Here we show the structure of MrNV virus-like particles (VLPs) produced by recombinant expression of the capsid protein, using cryogenic electron microscopy...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522818/efficient-modification-of-%C3%AE-dna-substrates-for-single-molecule-studies
#17
Yoori Kim, Armando de la Torre, Andrew A Leal, Ilya J Finkelstein
Single-molecule studies of protein-nucleic acid interactions frequently require site-specific modification of long DNA substrates. The bacteriophage λ is a convenient source of high quality long (48.5 kb) DNA. However, introducing specific sequences, tertiary structures, and chemical modifications into λ-DNA remains technically challenging. Most current approaches rely on multi-step ligations with low yields and incomplete products. Here, we describe a molecular toolkit for rapid preparation of modified λ-DNA...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522639/definition-of-a-rack1-interaction-network-in-drosophila-melanogaster-using-swath-ms
#18
Lauriane Kuhn, Karim Majzoub, Evelyne Einhorn, Johana Chicher, Pompon Julien, Jean-Luc Imler, Philippe Hammann, Carine Meignin
Receptor for Activated C kinase 1 (RACK1) is a scaffold protein that has been found in association with several signaling complexes, and with the 40S subunit of the ribosome. Using the model organism Drosophila melanogaster, we recently showed that RACK1 is required at the ribosome for IRES-mediated translation of viruses. Here, we report a proteomic characterization of the interactome of RACK1 in Drosophila S2 cells. We carried out Label-Free quantitation using both Data-Dependent and Data-Independent Acquisition and observed a significant advantage for the Sequential Window Acquisition of all THeoretical fragment-ion spectra (SWATH) method both in terms of identification of interactants and quantification of low abundance proteins...
May 18, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28521053/compaction-and-condensation-of-dna-mediated-by-the-c-terminal-domain-of-hfq
#19
Antoine Malabirade, Kai Jiang, Krzysztof Kubiak, Alvaro Diaz-Mendoza, Fan Liu, Jeroen A van Kan, Jean-François Berret, Véronique Arluison, Johan R C van der Maarel
Hfq is a bacterial protein that is involved in several aspects of nucleic acids metabolism. It has been described as one of the nucleoid associated proteins shaping the bacterial chromosome, although it is better known to influence translation and turnover of cellular RNAs. Here, we explore the role of Escherichia coli Hfq's C-terminal domain in the compaction of double stranded DNA. Various experimental methodologies, including fluorescence microscopy imaging of single DNA molecules confined inside nanofluidic channels, atomic force microscopy, isothermal titration microcalorimetry and electrophoretic mobility assays have been used to follow the assembly of the C-terminal and N-terminal regions of Hfq on DNA...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28521002/changes-in-microbiome-during-and-after-travellers-diarrhea-what-we-know-and-what-we-do-not
#20
David A Rasko
The study of bacterial pathogens has advanced from culture on plates to basic biochemical studies; to sequencing reference genomes and attempting to ascribe those qualities to the whole species; to evaluating complete communities based on the universal marker of the 16S rRNA gene; to now sequencing all available nucleic acids in any sample to characterize the community as a whole. These types of scientific advances highlight that there are multiple layers of information within any sample, and to some extent we are only now beginning to be able to identify, categorize and understand the complex interactions of the host, pathogen and microbiome...
April 1, 2017: Journal of Travel Medicine
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