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R loop

Rajib Deb, Gyanendra Singh Sengar, Umesh Singh, Sushil Kumar, R R Alyethodi, Rani Alex, T V Raja, A K Das, B Prakash
Loop-mediated isothermal amplification (LAMP) is a diagnostic method for amplification of DNA with rapid and minimal equipment requirement. In the present study, we applied the LAMP assay for rapid detection of cow components adulteration in buffalo milk/meat samples. The test can be completed within around 1 h 40 min starting from DNA extraction and can be performed in water bath without requirement of thermocycler. The cow DNA in buffalo samples were identified in the developed LAMP assay by either visualizing with SYBR Green I/HNB dyes or observing the typical ladder pattern on gel electrophoresis...
October 19, 2016: Molecular Biotechnology
Colleen E Dugan, James P Grinias, Sebastian D Parlee, Mahmoud El-Azzouny, Charles R Evans, Robert T Kennedy
Microfluidics is an enabling technology for both cell biology and chemical analysis. We combine these attributes with a microfluidic device for on-line solid-phase extraction (SPE) and mass spectrometry (MS) analysis of secreted metabolites from living cells in culture on the chip. The device was constructed with polydimethylsiloxane (PDMS) and contains a reversibly sealed chamber for perfusing cells. A multilayer design allowed a series of valves to control an on-chip 7.5 μL injection loop downstream of the cell chamber with operation similar to a six-port valve...
October 19, 2016: Analytical and Bioanalytical Chemistry
Tong Liu, Keping Sun, Yung Chul Park, Jiang Feng
The greater horseshoe bat, Rhinolophus ferrumequinum, is an important model organism for studies on chiropteran phylogeographic patterns. Previous studies revealed the population history of R. ferrumequinum from Europe and most Asian regions, yet there continue to be arguments about their evolutionary process in Northeast Asia. In this study, we obtained mitochondrial DNA cyt b and D-loop data of R. ferrumequinum from Northeast China, South Korea and Japan to clarify their phylogenetic relationships and evolutionary process...
2016: PeerJ
Krystal A Morales, Yuan Yang, Taylor R Cole, Tatyana I Igumenova
Ca(2+)-dependent conserved-region 2 (C2) domains target their host signaling proteins to anionic membranes. The Ca(2+)-binding event is a prerequisite for membrane association. Here, we investigate multiscale metal-ion-dependent dynamics of the C2 domain of protein kinase Cα (C2α) using NMR spectroscopy. Interactions with metal ions attenuate microsecond-timescale motions of the loop regions, indicating that preorganization of the metal-binding loops occurs before membrane insertion. Binding of a full complement of Ca(2+) ions has a profound effect on the millisecond-timescale dynamics of the N- and C-terminal regions of C2α...
October 18, 2016: Biophysical Journal
Max C Petersen, Anila K Madiraju, Brandon M Gassaway, Michael Marcel, Ali R Nasiri, Gina Butrico, Melissa J Marcucci, Dongyan Zhang, Abudukadier Abulizi, Xian-Man Zhang, William Philbrick, Stevan R Hubbard, Michael J Jurczak, Varman T Samuel, Jesse Rinehart, Gerald I Shulman
Nonalcoholic fatty liver disease (NAFLD) is a risk factor for type 2 diabetes (T2D), but whether NAFLD plays a causal role in the pathogenesis of T2D is uncertain. One proposed mechanism linking NAFLD to hepatic insulin resistance involves diacylglycerol-mediated (DAG-mediated) activation of protein kinase C-ε (PKCε) and the consequent inhibition of insulin receptor (INSR) kinase activity. However, the molecular mechanism underlying PKCε inhibition of INSR kinase activity is unknown. Here, we used mass spectrometry to identify the phosphorylation site Thr1160 as a PKCε substrate in the functionally critical INSR kinase activation loop...
October 17, 2016: Journal of Clinical Investigation
L J P Xavier, D R da Costa, A Chaves, J M Pereira, G A Farias
We investigate localized states of a quantum ring confinement in monolayer graphene defined by a circular mass-related potential, which can be induced e.g. by interaction with a substrate that breaks the sublattice symmetry, where a circular line defect provides a change in the sign of the induced mass term along the radial direction. Electronic properties are calculated analytically within the Dirac-Weyl approximation in the presence of an external magnetic field. Analytical results are also compared with those obtained by the tight-binding approach...
October 19, 2016: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Carl R May, Mark Johnson, Tracy Finch
BACKGROUND: Context is a problem in research on health behaviour change, knowledge translation, practice implementation and health improvement. This is because many intervention and evaluation designs seek to eliminate contextual confounders, when these represent the normal conditions into which interventions must be integrated if they are to be workable in practice. DISCUSSION: We present an ecological model of the ways that participants in implementation and health improvement processes interact with contexts...
October 19, 2016: Implementation Science: IS
Airek R Mathews, Shane S Que Hee
The aim was to develop a whole glove permeation method for cyclohexanol to generate permeation parameter data for a non-moving dextrous robot hand (normalized breakthrough time tb, standardized breakthrough time ts, steady state permeation rate Ps, and diffusion coefficient D). Four types of disposable powderless, unsupported and unlined nitrile gloves from the same producer were investigated: Safeskin Blue, and Kimtech Science Blue, Purple, and Sterling. The whole glove method developed involved a peristaltic pump for water circulation through chemically resistant Viton tubing to continually wash the inner surface of the test glove via holes in the tubing, a dextrous robot hand operated by a microprocessor, a chemically protective nitrile glove to protect the robot hand, an incubator to maintain 35°C temperature, and a hot plate to maintain 35°C at the sampling point of the circulating water...
October 18, 2016: Journal of Occupational and Environmental Hygiene
Shazia Nafis, Kalaiarasan Ponnusamy, Mohammad Husain, R K Brojen Singh, Rameshwar N K Bamezai
An experimentally validated set of apoptosis-regulatory proteins was subjected to network analysis, depicting a scale-free hierarchical fractal network. The power-law distribution of the various topological properties of the network revealed the fractal nature of the network, a signature of self-organization of the network where the network maintained the democratic constitution of nodes at various levels and showed the absence of the centrality-lethality control system. Even though network breakdown under the absence of the centrality-lethality rule of hub removal did not happen, the change in the topological properties of the network could be observed...
October 18, 2016: Molecular BioSystems
Christina R Tyler, Matthew T Labrecque, Elizabeth R Solomon, Xun Guo, Andrea M Allan
Exposure to arsenic, a common environmental toxin found in drinking water, leads to a host of neurological pathologies. We have previously demonstrated that developmental exposure to a low level of arsenic (50ppb) alters epigenetic processes that underlie deficits in adult hippocampal neurogenesis leading to aberrant behavior. It is unclear if arsenic impacts the programming and regulation of embryonic neurogenesis during development when exposure occurs. The master negative regulator of neural-lineage, REST/NRSF, controls the precise timing of fate specification and differentiation of neural stem cells (NSCs)...
October 14, 2016: Neurotoxicology and Teratology
Rane A Harrison, Jia Lu, Martin Carrasco, John Hunter, Anuj Manandhar, Sudershan Gondi, Kenneth D Westover, John R Engen
Structural dynamics of Ras proteins contribute to their activity in signal transduction cascades. Directly targeting Ras proteins with small molecules may rely on movement of a conserved structural motif, switch II. To understand Ras signaling and advance Ras targeting strategies, experimental methods to measure Ras dynamics are required. Here we demonstrate the utility of hydrogen-deuterium exchange mass spectrometry to measure Ras dynamics by studying representatives from two branches of the Ras superfamily, Ras and Rho...
October 14, 2016: Journal of Molecular Biology
Peter Sadowski, David R Fooshee, Niranjan Subrahmanya, Pierre Baldi
We demonstrate how machine learning (ML) and quantum mechanical (QM) methods can be used in two-way synergy to build chemical reaction expert systems. The proposed ML approach to reaction prediction identifies electron sources and sinks among the reactants, and then ranks all source-sink pairs. This is used to address a major bottleneck of QM calculations by providing a prioritized list of mechanistic reaction steps. QM modeling can then be used to compute the transition states and activation energies of the top-ranked reactions, providing additional or improved examples of ranked source-sink pairs...
October 17, 2016: Journal of Chemical Information and Modeling
Michael J Feldman, Saman Sizdahkhani, Nancy A Edwards, Marsha J Merrill, Abhik Ray-Chaudhury, Zhengping Zhuang, Russell R Lonser, Edward H Oldfield, Prashant Chittiboina
von Hippel-Lindau (VHL) patients develop multiple central nervous system hemangioblastomas (HB). Some HBs become symptomatic with exponential growth or cyst formation following long periods of quiescence. Understanding the factors underlying growth in hemangioblastoma may lead to better strategies to arrest or prevent tumor growth. In 5 VHL patients, we resected quiescent hemangioblastomas (Q-HB) that were en-route during surgical access to symptomatic hemangioblastomas (S-HB), for matched tumor analysis. Quantitative reverse transcriptase analysis demonstrated a 2-fold increase in EPO expression in all S-HB, while 4/5 showed either Hypoxia Inducible Factor-1α or 2α upregulation...
October 17, 2016: Scientific Reports
Guy Herv Eacute, Hedeel Guy Evans, Roshini Fernado, Chandni Patel, Fatme Hachem, David R Evans
Elevated hydrostatic pressure was used to probe conformational changes of Aquifex aeolicus dihydroorotase (DHO) which catalyzes the third step in de novo pyrimidine biosynthesisis. The isolated protein, a 45 kDa monomer, lacks catalytic activity but becomes active upon formation of a dodecameric complex with aspartate transcarbamoylase (ATC). X-ray crystallographic studies of the isolated DHO and of the complex showed that association induces several major conformational changes in the DHO structure. In the isolated DHO, a flexible loop occludes the active site blocking the access of substrates...
October 16, 2016: Journal of Biological Chemistry
Yonatan Kahn, Benjamin R Safdi, Jesse Thaler
When ultralight axion dark matter encounters a static magnetic field, it sources an effective electric current that follows the magnetic field lines and oscillates at the axion Compton frequency. We propose a new experiment to detect this axion effective current. In the presence of axion dark matter, a large toroidal magnet will act like an oscillating current ring, whose induced magnetic flux can be measured by an external pickup loop inductively coupled to a SQUID magnetometer. We consider both resonant and broadband readout circuits and show that a broadband approach has advantages at small axion masses...
September 30, 2016: Physical Review Letters
Gergely N Nagy, Reynier Suardiaz, Anna Lopata, Olivér Ozohanics, Károly Vékey, Bernard R Brooks, Ibolya Leveles, Judit Toth, Beata G Vertessy, Edina Rosta
Arginine finger is a highly conserved and essential residue in many GTPase and AAA+ ATPase enzymes that completes the active site from a distinct protomer, forming contacts with the γ-phosphate of the nucleotide. To date, no pyrophosphatase has been identified that employs an arginine finger fulfilling all the above properties, all essential arginine fingers are used to catalyze the cleavage of the γ-phosphate. Here, we identify and unveil the role of a conserved arginine residue in trimeric dUTPases that meets all the criteria established for arginine fingers...
October 14, 2016: Journal of the American Chemical Society
Mona A Alqazzaz, Kerry L Price, Sarah C R Lummis
Cys-loop receptors play important roles in signal transduction in multicellular organisms, but similar proteins exist in prokaryotes, the best studied of which is the Gloeobacter ligand-gated ion channel (GLIC). GLIC is activated by protons with 50% activation (pH50) at pH 5.5, and while a histidine residue in its pore-forming α-helix (M2) is known to be involved in gating, there is also evidence of a proton-sensitive region in the extracellular domain. However, this proton-sensitive region does not appear to be located in the region of GLIC equivalent to the agonist binding site in related proteins...
October 14, 2016: Biochemistry
Nooshin Atashfeshan, Hamideh Razavi
OBJECTIVE: Analysis of the effect of mental fatigue on a cognitive task and determination of the right start time for rest breaks in work environments. BACKGROUND: Mental fatigue has been recognized as one of the most important factors influencing individual performance. Subjective and physiological measures are popular methods for analyzing fatigue, but they are restricted to physical experiments. Computational cognitive models are useful for predicting operator performance and can be used for analyzing fatigue in the design phase, particularly in industrial operations and inspections where cognitive tasks are frequent and the effects of mental fatigue are crucial...
October 13, 2016: Human Factors
Alexander R Siegel, David E Wemmer
Bacterial sigma factors are subunits of RNA polymerase that direct the holoenzyme to specific sets of promoters in the genome, and are a central element of regulating transcription. Most polymerase holoenzymes open the promoter and initiate transcription rapidly after binding. However, polymerase containing members of the σ(54) family must be acted on by a transcriptional activator before DNA opening and initiation occur. A key domain in these transcriptional activators forms a hexameric AAA+ ATPase that acts through conformational changes brought on by ATP hydrolysis...
October 9, 2016: Journal of Molecular Biology
Daniel Ian McSkimming, Shima Dastgheib, Timothy R Baffi, Dominic P Byrne, Samantha Ferries, Steven Thomas Scott, Alexandra C Newton, Claire E Eyers, Krzysztof J Kochut, Patrick A Eyers, Natarajan Kannan
Multiple sequence alignments (MSAs) are a fundamental analysis tool used throughout biology to investigate relationships between protein sequence, structure, function, evolutionary history, and patterns of disease-associated variants. However, their widespread application in systems biology research is currently hindered by the lack of user-friendly tools to simultaneously visualize, manipulate and query the information conceptualized in large sequence alignments, and the challenges in integrating MSAs with multiple orthogonal data such as cancer variants and post-translational modifications, which are often stored in heterogeneous data sources and formats...
October 12, 2016: Molecular BioSystems
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