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Łukasz Rajski, Francisco José Díaz Galiano, Víctor Cutillas, Amadeo R Fernández-Alba
Ion chromatography coupled to a quadrupole Orbitrap mass analyzer was used to develop a multiresidue method for the determination of highly polar pesticides and their metabolites (chlorate, perchlorate, fosetyl-aluminum, glyphosate, aminomethylphosphonic acid (AMPA), phosphonic acid, N-acetyl AMPA, and N-acetyl glyphosate) in fruits and vegetables. After extraction with methanol, samples were diluted 5× with water. No derivatization was applied. Pesticides were separated in an anion-exchange column. Water was used as the ion chromatography mobile phase...
November 15, 2017: Journal of AOAC International
Katherine E Berry, Ann Hochschild
The interaction of RNA molecules with proteins is a critical aspect of gene regulation across all domains of life. Here, we report the development of a bacterial three-hybrid (B3H) assay to genetically detect RNA-protein interactions. The basis for this three-hybrid assay is a transcription-based bacterial two-hybrid assay that has been used widely to detect and dissect protein-protein interactions. In the three-hybrid assay, a DNA-bound protein with a fused RNA-binding moiety (the coat protein of bacteriophage MS2 (MS2CP)) is used to recruit a hybrid RNA upstream of a test promoter...
November 11, 2017: Nucleic Acids Research
Sivaranjani Devarakonda, Renu Singh, Jyoti Bhardwaj, Jaesung Jang
Although many studies concerning the detection of influenza virus have been published, a paper-based, label-free electrochemical immunosensor has never been reported. Here, we present a cost-effective, handmade paper-based immunosensor for label-free electrochemical detection of influenza virus H1N1. This immunosensor was prepared by modifying paper with a spray of hydrophobic silica nanoparticles, and using stencil-printed electrodes. We used a glass vaporizer to spray the hydrophobic silica nanoparticles onto the paper, rendering it super-hydrophobic...
November 11, 2017: Sensors
Evelina Tutucci, Maria Vera, Jeetayu Biswas, Jennifer Garcia, Roy Parker, Robert H Singer
The MS2-MCP system enables researchers to image multiple steps of the mRNA life cycle with high temporal and spatial resolution. However, for short-lived mRNAs, the tight binding of the MS2 coat protein (MCP) to the MS2 binding sites (MBS) protects the RNA from being efficiently degraded, and this confounds the study of mRNA regulation. Here, we describe a reporter system (MBSV6) with reduced affinity for the MCP, which allows mRNA degradation while preserving single-molecule detection determined by single-molecule FISH (smFISH) or live imaging...
November 13, 2017: Nature Methods
Tim Walker, Melisa Canales, Sacha Noimark, Kristopher Page, Ivan Parkin, Jane Faull, Manni Bhatti, Lena Ciric
Evidence has shown that environmental surfaces play an important role in the transmission of nosocomial pathogens. Deploying antimicrobial surfaces in hospital wards could reduce the role environmental surfaces play as reservoirs for pathogens. Herein we show a significant reduction in viable counts of Staphylococcus epidermidis, Saccharomyces cerevisiae, and MS2 Bacteriophage after light treatment of a medical grade silicone incorporating crystal violet, methylene blue and 2 nm gold nanoparticles. Furthermore, a migration assay demonstrated that in the presence of light, growth of the fungus-like organism Pythium ultimum and the filamentous fungus Botrytis cinerea was inhibited...
November 10, 2017: Scientific Reports
Christoph Bauer, Eugenia Niculescu-Morzsa, Stefan Nehrer
RNA isolation from human or animal cartilage tissue is necessary when performing mechanical or biotribological applications. Despite no influence on the cells and no alterations in gene expression patterns, enzymatic digestion of tissues should be avoided as it's known that the expression of collagen 2 can be effected (Hayman et al., 2006 [1]). After mechanical or biotribological tests alternative options with an immediate disruption of the tissue should be contemplated. To obtain RNA, different tissue homogenization and disruption methods are available on the market (Yu et al...
2017: MethodsX
Huaming Sheng, Weijuan Tang, Jinshan Gao, James Steven Riedeman, Guannan Li, Tiffany Mae Jarrell, Matthew R Hurt, Linan Yang, Priya Murria, Xin Ma, John Joseph Nash, Hilkka I Kenttamaa
Seven synthesized G-lignin oligomer model compounds (ranging in size from dimers to an octamer) with 5-5 and/or β-O-4 linkag-es, and three synthesized S-lignin model compounds (a dimer, trimer and tetramer) with β-O-4 linkages, were evaporated and deprotonated using negative-ion mode ESI in a linear quadrupole ion trap/Fourier transform ion cyclotron resonance mass spec-trometer. The collision-activated dissociation (CAD) fragmentation patterns (obtained in MS2 and MS3 experiments, respectively) for the negative ions were studied in order to develop a procedure for sequencing unknown lignin oligomers...
November 8, 2017: Analytical Chemistry
Robert J Millikin, Stefan K Solntsev, Michael R Shortreed, Lloyd M Smith
The rapid and accurate quantification of peptides is a critical element of modern proteomics that has become increasingly challenging as proteomic data sets grow in size and complexity. We present here FlashLFQ, a computer program for high-speed label-free quantification of peptides following a search of bottom-up mass spectrometry data. FlashLFQ is approximately an order of magnitude faster than established label-free quantification methods. The increased speed makes it practical to base quantification upon all of the charge states for a given peptide rather than solely upon the charge state that was selected for MS2 fragmentation...
November 8, 2017: Journal of Proteome Research
Luis A Ramón-Núñez, Laura Martos, Álvaro Fernández-Pardo, Julia Oto, Pilar Medina, Francisco España, Silvia Navarro
microRNAs are promising biomarkers in biological fluids in several diseases. Different plasma RNA isolation protocols and carriers are available, but their efficiencies have been scarcely compared. Plasma microRNAs were isolated using a phenol and column-based procedure and a column-based procedure, in the presence or absence of two RNA carriers (yeast RNA and MS2 RNA). We evaluated the presence of PCR inhibitors and the relative abundance of certain microRNAs by qRT-PCR. Furthermore, we analyzed the association between different isolation protocols, the relative abundance of the miRNAs in the sample, the GC content and the free energy of microRNAs...
2017: PloS One
Guillaume Sautrey, Adrien Brié, Christophe Gantzer, Alain Walcarius
SDS is commonly employed as BGE additive in CZE analysis of non-enveloped icosahedral viruses. But the way by which SDS interacts with the surface of such viruses remains to date poorly known, making complicate to understand their behavior during a run. In this article, two related bacteriophages, MS2 and Qβ, are used as model to investigate the migration mechanism of non-enveloped icosahedral viruses in SDS-based CZE. Both phages are characterized by similar size and surface charge but significantly different surface hydrophobicity (Qβ > MS2, where '>' means 'more hydrophobic than')...
October 26, 2017: Electrophoresis
Roland Bruderer, Oliver M Bernhardt, Tejas Gandhi, Yue Xuan, Julia Sondermann, Manuela Schmidt, David Gomez-Varela, Lukas Reiter
Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key objectives of quantitative proteomics. Here, we present an implementation of data-independent acquisition using its parallel acquisition nature that surpasses the limitation of serial MS2 acquisition of data-dependent acquisition on a quadrupole ultra-high field Orbitrap mass spectrometer. In deep single shot data-independent acquisition, we identified and quantified 6,383 proteins in human cell lines using 2-or-more peptides/protein and over 7,100 proteins when including the 717 proteins that were identified on the basis of a single peptide sequence...
October 25, 2017: Molecular & Cellular Proteomics: MCP
Jin-Xian Feng, Jin-Qi Wu, Yexiang Tong, Gao-Ren Li
Low-cost transition-metal dichalcogenides (MS2) have attracted great interest as alternative catalysts for hydrogen evolution. However, a significant challenge is the formation of sulfur-hydrogen bonds on MS2 (S-Hads), which will severely suppress hydrogen evolution reaction (HER). Here we report Cu nanodots (NDs)-decorated Ni3S2 nanotubes (NTs) supported on carbon fibers (CFs) (Cu NDs/Ni3S2 NTs-CFs) as efficient electrocatalysts for HER in alkaline media. The electronic interactions between Cu and Ni3S2 make that Cu NDs are positively charged and can promote water adsorption and activation...
October 23, 2017: Journal of the American Chemical Society
Grace Logan, Joseph Newman, Caroline F Wright, Lidia Lasecka-Dykes, Daniel T Haydon, Eleanor M Cottam, Tobias J Tuthill
Non-enveloped viruses protect their genomes by packaging them into an outer shell or capsid of virus-encoded proteins. Packaging and capsid assembly in RNA viruses can involve interactions between capsid proteins and secondary structures in the viral genome as exemplified by the RNA bacteriophage MS2 and as proposed for other RNA viruses of plants, animals and human. In the picornavirus family of non-enveloped RNA viruses, the requirements for genome packaging remain poorly understood. Here we show a novel and simple approach to identify predicted RNA secondary structures involved in genome packaging in the picornavirus foot-and-mouth disease virus (FMDV)...
October 18, 2017: Journal of Virology
Maria Alcocer Alkureishi, Wei Wei Lee, Maureen Lyons, Kristen Wroblewski, Jeanne M Farnan, Vineet M Arora
INTRODUCTION: Electronic Health Record (EHR) use can enhance or weaken patient-provider communication. Despite EHR adoption, no validated tool exists to assess EHR communication skills. We aimed to develop and validate such a tool. METHODS: Electronic-Clinical Evaluation Exercise (e-CEX) is a 10-item-tool based on systematic literature review and pilot-testing. Second-year (MS2s) students participated in an EHR-use lecture and structured Clinical Examination (OSCE)...
October 10, 2017: Patient Education and Counseling
Ekaterina Christensen, Vegard Nilsen, Tor Håkonsen, Arve Heistad, Christophe Gantzer, Lucy J Robertson, Mette Myrmel
The present work evaluates the effect of contact filtration, preceded by coagulation with zirconium (Zr) and chitosan coagulants, on model microorganisms and waterborne pathogens. River water intended for potable water production was spiked with MS2 and Salmonella Typhimurium 28B bacteriophages, Escherichia coli, and Cryptosporidium parvum oocysts prior to coagulation. The hygienic performance demonstrated by Zr comprised 3.0-4.0 log10 removal of viruses and 5.0-6.0 log10 removal of E. coli and C. parvum oocysts...
October 2017: Journal of Water and Health
Morten Lundh, Kaja Pluciñska, Marie S Isidor, Patricia S S Petersen, Brice Emanuelli
OBJECTIVE: Functional investigation of novel gene/protein targets associated with adipocyte differentiation or function heavily relies on efficient and accessible tools to manipulate gene expression in adipocytes in vitro. Recent advances in gene-editing technologies such as CRISPR-Cas9 have not only eased gene editing but also greatly facilitated modulation of gene expression without altering the genome. Here, we aimed to develop and validate a competent in vitro adipocyte model of controllable functionality as well as multiplexed gene manipulation in adipocytes, using the CRISPRa "SAM" system and siRNAs to simultaneously overexpress and silence selected genes in the same cell populations...
October 2017: Molecular Metabolism
Yi Guo, Chen-Xi Liu, Li-Sheng Zhang, Meng-Qing Wang, Hong-Yin Chen
Insects cannot synthesize sterols and must obtain them from plants. Therefore, reducing plant sterol content or changing sterol type might be an effective pest control strategy. However, the impacts of these changes on pests' natural predators remain unknown. Here, we fed artificial diets with reduced sterol content to Mythimna separata (Walker) (Lepidoptera: Noctuidae) and investigated the effects on its natural predator, Arma chinensis (Fallou) (Hemiptera: Pentatomidae). Reduced sterol content in M. separata (MS1, MS2, and MS5) was achieved by feeding them artificial diets prepared from a feed base subjected to one, two, or five cycles of sterol extractions, respectively...
October 11, 2017: Archives of Insect Biochemistry and Physiology
Jacob Waldbauer, Lichun Zhang, Adriana Rizzo, Daniel Muratore
We present an analytical strategy, dimethylation-deuteration and oxygen-exchange IPTL (diDO-IPTL), for high-precision, broad-coverage quantitative proteomics. The diDO-IPTL approach combines two advances in isobaric peptide terminal labeling (IPTL) methodology: first, a one-pot chemical labeling strategy for attaching isotopic tags to both the N- and C-termini of tryptic peptides, and second, a search engine (based on the Morpheus algorithm) optimized for identification and quantification of twinned peaks from peptide fragment ions in MS(2) spectra...
November 7, 2017: Analytical Chemistry
J Shim, D S Stewart, A D Nikolov, D T Wasan, R Wang, R Yan, Y C Shieh
Enteric viruses are recognized as a major etiology for U.S. foodborne infections. These viruses are easily transmitted via food contact surfaces. Understanding virus interactions with surfaces may facilitate developing improved means for their removal thus reducing transmission. Using MS2 coliphage as a virus surrogate, the strength of virus adhesion onto common food processing and preparation surfaces of polyvinyl chloride (PVC) and glass were assessed by atomic force microscopy (AFM) and virus recovery assays...
October 6, 2017: Applied and Environmental Microbiology
T A Azad, S Bhakta, T Tsukahara
Site-directed RNA editing is an important technique for correcting gene sequences and ultimately tuning protein function. In this study, we engineered the deaminase domain of adenosine deaminase acting on RNA (ADAR1) and the MS2 system to target specific adenosines, with the goal of correcting G-to-A mutations at the RNA level. For this purpose, the ADAR1 deaminase domain was fused downstream of the RNA-binding protein MS2, which has affinity for the MS2 RNA. To direct editing to specific targets, we designed guide RNAs complementary to target RNAs...
October 6, 2017: Gene Therapy
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