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https://www.readbyqxmd.com/read/29041965/enrichment-allows-identification-of-diverse-rare-elements-in-metagenomic-resistome-virulome-sequencing
#1
Noelle R Noyes, Maggie E Weinroth, Jennifer K Parker, Chris J Dean, Steven M Lakin, Robert A Raymond, Pablo Rovira, Enrique Doster, Zaid Abdo, Jennifer N Martin, Kenneth L Jones, Jaime Ruiz, Christina A Boucher, Keith E Belk, Paul S Morley
BACKGROUND: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/29040687/mortality-risk-in-patients-on-hemodiafiltration-versus-hemodialysis-a-real-world-comparison-from-the-dopps
#2
Francesco Locatelli, Angelo Karaboyas, Ronald L Pisoni, Bruce M Robinson, Joan Fort, Raymond Vanholder, Hugh C Rayner, Werner Kleophas, Stefan H Jacobson, Christian Combe, Friedrich K Port, Francesca Tentori
Background: With its convective component, hemodiafiltration (HDF) provides better middle molecule clearance compared with hemodialysis (HD) and is postulated to improve survival. A previous analysis of Dialysis Outcomes and Practice Patterns Study (DOPPS) data in 1998-2001 found lower mortality rates for high replacement fluid volume HDF versus HD. Randomized controlled trials have not shown uniform survival advantage for HDF; in secondary (non-randomized) analyses, better outcomes were observed in patients receiving the highest convection volumes...
October 11, 2017: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/29038993/the-ups-and-downs-of-repeated-cleavage-and-internal-fragment-production-in-top-down-proteomics
#3
Yana A Lyon, Dylan Riggs, Luca Fornelli, Philip D Compton, Ryan R Julian
Analysis of whole proteins by mass spectrometry, or top-down proteomics, has several advantages over methods relying on proteolysis. For example, proteoforms can be unambiguously identified and examined. However, from a gas-phase ion-chemistry perspective, proteins are enormous molecules that present novel challenges relative to peptide analysis. Herein, the statistics of cleaving the peptide backbone multiple times are examined to evaluate the inherent propensity for generating internal versus terminal ions...
October 16, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29038036/overexpression-of-notch-ligand-delta-like-1-by-dendritic-cells-enhances-their-immunoregulatory-capacity-and-exerts-antiallergic-effects-on-th2-mediated-allergic-asthma-in-mice
#4
Chen-Chen Lee, Chu-Lun Lin, Sy-Jye Leu, Yueh-Lun Lee
Dendritic cells (DCs) are professional antigen-presenting cells, and Notch ligand Delta-like-1 (DLL1) on DCs was implicated in type 1T helper (Th1) differentiation. In this study, we produced genetically engineered bone marrow-derived DCs that expressed DLL1 (DLL1-DCs) by adenoviral transduction. DLL1-DCs exerted a fully mature phenotype, and had positive effects on expression levels of interleukin (IL)-12 and costimulatory molecules. Coculture of allogeneic T cells with ovalbumin (OVA)-pulsed DLL1-DCs enhanced T cell proliferative responses and promoted Th1 cell differentiation...
October 13, 2017: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/29036425/motif-independent-identification-of-potential-rna-g-quadruplexes-by-g4rna-screener
#5
Jean-Michel Garant, Jean-Pierre Perreault, Michelle S Scott
Motivation: G-quadruplex structures in RNA molecules are known to have regulatory impacts in cells but are difficult to locate in the genome. The minimal requirements for G-quadruplex folding in RNA (G ≥3 N 1-7  G ≥3 N 1-7  G ≥3 N 1-7  G ≥3 ) is being challenged by observations made on specific examples in recent years. The definition of potential G-quadruplex sequences has major repercussions on the observation of the structure since it introduces a bias. The canonical motif only describes a sub-population of the reported G-quadruplexes...
August 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29025896/high-throughput-single-molecule-telomere-characterization
#6
Jennifer McCaffrey, Eleanor Young, Katy Lassahn, Justin Sibert, Steven Pastor, Harold Riethman, Ming Xiao
We have developed a novel method that enables global subtelomere and haplotype-resolved analysis of telomere lengths at the single-molecule level. An in vitro CRISPR/Cas9 RNA-directed nickase system directs the specific labeling of human (TTAGGG)n DNA tracts in genomes that have also been barcoded using a separate nickase enzyme that recognizes a 7-bp motif genome-wide. High-throughput imaging and analysis of large DNA single molecules from genomes labeled in this fashion using a nanochannel array system permits mapping through subtelomere repeat element (SRE) regions to unique chromosomal DNA while simultaneously measuring the (TTAGGG)n tract length at the end of each large telomere-terminal DNA segment...
October 12, 2017: Genome Research
https://www.readbyqxmd.com/read/29021958/complete-mitochondrial-genome-sequence-of-fruit-piercing-moth-eudocima-phalonia-linnaeus-1763-lepidoptera-noctuoidea
#7
Kuppusamy Sivasankaran, Pratheesh Mathew, Sekar Anand, Stanislaus Antony Ceasar, Soosaimanikam Mariapackiam, Savarimuthu Ignacimuthu
The complete mitochondrial genome of the fruit piercing moth Eudocima phalonia (Linnaeus, 1763) (Lepidoptera: Noctuoidea) was sequenced and characterized (Genbank Accession No: KY196412). The complete mitogenome is a circular molecule of 15,575 bp length, consisting of 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS and rrnL), 22 transfer RNA (tRNA) genes and an A + T-rich region (D-loop). The nucleotide composition of the genome is highly A + T biased, accounting for 80.67% of nucleotides...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28993669/cell-cell-communication-enhances-bacterial-chemotaxis-toward-external-attractants
#8
Zhicheng Long, Bryan Quaife, Hanna Salman, Zoltán N Oltvai
Bacteria are able to coordinate their movement, growth and biochemical activities through cell-cell communication. While the biophysical mechanism of bacterial chemotaxis has been well understood in individual cells, the role of communication in the chemotaxis of bacterial populations is not clear. Here we report experimental evidence for cell-cell communication that significantly enhances the chemotactic migration of bacterial populations, a finding that we further substantiate using numerical simulations...
October 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28986444/metabolomic-analysis-reveals-that-the-drosophila-gene-lysine%C3%A2-influences-diverse-aspects-of-metabolism
#9
Samantha L St Clair, Hongde Li, Usman Ashraf, Jonathan A Karty, Jason M Tennessen
The fruit fly Drosophila melanogaster has emerged as a powerful model for investigating the molecular mechanisms that regulate animal metabolism. A major limitation of these studies, however, is that many metabolic assays are tedious, dedicated to analyzing a single molecule, and rely on indirect measurements. As a result, Drosophila geneticists commonly use candidate gene approaches, which, while important, bias studies towards known metabolic regulators. In an effort to expand the scope of Drosophila metabolic studies, we used the classic mutant lysine (lys) to demonstrate how a modern metabolomics approach can be used to conduct forward genetic studies...
October 6, 2017: Genetics
https://www.readbyqxmd.com/read/28985083/single-molecule-photocurrent-at-a-metal-molecule-semiconductor-junction
#10
Andrea Vezzoli, Richard James Brooke, Simon J Higgins, Walther Schwarzacher, Richard J Nichols
We demonstrate here a new concept for a metal-molecule-semiconductor nanodevice employing Au and GaAs contacts that acts as a photodiode. Current-voltage traces for such junctions are recorded using a STM and the "blinking" or "I(t)" method is used to record electrical behaviour at the single-molecule level in the dark and under illumination, with both low and highly doped GaAs samples and with two different types of molecular bridge: non-conjugated pentanedithiol and the more conjugated 1,4-phenylene(dimethanethiol)...
October 6, 2017: Nano Letters
https://www.readbyqxmd.com/read/28981266/a-computational-scheme-to-evaluate-hamaker-constants-of-molecules-with-practical-size-and-anisotropy
#11
Kenta Hongo, Ryo Maezono
We propose a computational scheme to evaluate Hamaker constants, A, of molecules with practical sizes and anisotropies. Upon the increasing feasibility of diffusion Monte Carlo (DMC) methods to evaluate binding curves for such molecules to extract the constants, we discussed how to treat the averaging over anisotropy and how to correct the bias due to the non-additivity. We have developed a computational procedure for dealing with the anisotropy and reducing statistical errors and biases in DMC evaluations, based on possible validations on predicted A...
October 5, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28980819/high-mobility-ultrathin-organic-semiconducting-films-realized-by-surface-mediated-crystallization
#12
I Vladimirov, M Kellermeier, T Geßner, Zarah Molla, S Grigorian, U Pietsch, L S Schaffroth, M Kühn, F May, R T Weitz
The functionality of common organic semiconductor materials is determined by their chemical structure and crystal modification. While the former can be fine-tuned via synthesis, a priori control over the crystal structure has remained elusive. We show that the surface tension is the main driver for the plate-like crystallization of a novel small organic molecule n-type semiconductor at the liquid-air interface. This interface provides an ideal environment for the growth of millimeter-sized semiconductor platelets that are only few nanometers thick and thus highly attractive for application in transistors...
October 10, 2017: Nano Letters
https://www.readbyqxmd.com/read/28975932/the-stm-bias-voltage-dependent-polymorphism-of-a-binary-supramolecular-network
#13
F Cometto, K Frank, B Stel, N Arisnabarreta, K Kern, M Lingenfelder
A Scanning Tunneling Microscope (STM) is used to induce a reversible transition between different polymorphs in a binary supramolecular network at the liquid/solid interface. The transition is driven externally by switching the polarity of the sample by positive or negative sample bias potentials. We demonstrate that by mixing bias-sensitive and non-sensitive molecules, we gain access to a variety of binary porous structures that can be prepared and reliably actuated for each relative concentration.
October 4, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28973888/a-protean-clamp-guides-membrane-targeting-of-tail-anchored-proteins
#14
Un Seng Chio, SangYoon Chung, Shimon Weiss, Shu-Ou Shan
Proper localization of proteins to target membranes is a fundamental cellular process. How the nature and dynamics of the targeting complex help guide substrate proteins to the target membrane is not understood for most pathways. Here, we address this question for the conserved ATPase guided entry of tail-anchored protein 3 (Get3), which targets the essential class of tail-anchored proteins (TAs) to the endoplasmic reticulum (ER). Single-molecule fluorescence spectroscopy showed that, contrary to previous models of a static closed Get3•TA complex, Get3 samples open conformations on the submillisecond timescale upon TA binding, generating a fluctuating "protean clamp" that stably traps the substrate...
September 26, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28972783/multiple-myeloma-cell-drug-responses-differ-in-thermoplastic-vs-pdms-microfluidic-devices
#15
Thomas A Moore, Peter Brodersen, Edmond W K Young
Poly(dimethylsiloxane) (PDMS) is a commonly used elastomer for fabricating microfluidic devices, but it has previously been shown to absorb hydrophobic molecules. Although this has been demonstrated for molecules such as estrogen and Nile Red, the absorption of small hydrophobic molecules in PDMS specifically used to treat cancer and its subsequent impact on cytotoxicity measurements and assays have not been investigated. This is critical for the development of microfluidic chemosensitivity and resistance assay (CSRA) platforms that have shown potential to help guide clinical therapy selection and which rely on the accuracy of the readout involving interactions between patient-derived cells and cancer drugs...
October 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28972148/time-course-negative-stain-electron-microscopy-based-analysis-for-investigating-protein-protein-interactions-at-the-single-molecule-level
#16
Bartek Nogal, Charles A Bowman, Andrew B Ward
Several biophysical approaches are available to study protein-protein interactions. Most approaches are conducted in bulk solution, and are therefore limited to an average measurement of the ensemble of molecular interactions. Here, we show how single-particle EM can enrich our understanding of protein-protein interactions at the single-molecule level and potentially capture states that are unobservable with ensemble methods because they are below the limit of detection or not conducted on an appropriate timescale...
September 29, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28972140/a-conserved-energetic-footprint-underpins-recognition-of-human-leukocyte-antigen-e-by-two-distinct-%C3%AE-%C3%AE-t-cell-receptors
#17
Lucy C Sullivan, Nicholas G Walpole, Carine Farenc, Gabriella Pietra, Matthew J Wenhwa Sum, Craig S Clements, Eleanor J Lee, Travis Beddoe, Michela Falco, Maria Cristina Mingari, Lorenzo Moretta, Stephanie Gras, Jamie Rossjohn, Andrew G Brooks
αβ T cell receptors (TCRs) interact with peptides bound to the polymorphic Major Histocompatibility Complex class Ia (MHC-Ia) and class II (MHC-II) molecules, as well as the essentially monomorphic MHC class Ib (MHC-Ib) molecules. While there is a large amount of information on how TCRs engage with MHC-Ia and MHC-II, our understanding of TCR-MHC-Ib interactions is very limited. Infection with cytomegalovirus (CMV) can elicit a CD8+ T cell response restricted by the human MHC-Ib molecule, Human Leukocyte Antigen (HLA)-E, and specific for an epitope from UL40 (VMAPRTLIL), which is characterized by biased TRBV14 gene usage...
September 25, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28970920/heterospin-biradicals-provide-insight-into-molecular-conductance-and-rectification
#18
Martin L Kirk, David A Shultz, Jinyuan Zhang, Ranjana Dangi, Laura Ingersol, Jing Yang, Nathaniel S Finney, Roger D Sommer, Lukasz Wojtas
The correlation of electron transfer with molecular conductance (g: electron transport through single molecules) by Nitzan and others has contributed to a fundamental understanding of single-molecule electronic materials. When an unsymmetric, dipolar molecule spans two electrodes, the possibility exists for different conductance values at equal, but opposite electrode biases. In the device configuration, these molecules serve as rectifiers of the current and the efficiency of the device is given by the rectification ratio (RR = gforward/greverse)...
August 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28969574/day-night-and-summer-winter-changes-in-serum-total-antioxidant-capacity
#19
Armando L Morera-Fumero, Pedro Abreu-Gonzalez, Manuel Henry-Benitez, Lourdes Fernandez-Lopez, Estefania Diaz-Mesa, Maria Del Rosario Cejas-Mendez, Fernando Guillen-Pino
BACKGROUND: Seasonal and circadian changes are two factors described to affect blood levels of some biological molecules. The Total Antioxidant Capacity (TAC) is one global measure of the antioxidant capacity of a system. There is no agreement about the existence of day/night changes in TAC levels as well as there is no information about seasonal changes in TAC levels. OBJECTIVE: The aims of this research are studying if there are summer/winter changes in TAC concentrations or if TAC concentrations have day/night changes...
October 2, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28968085/quantum-point-contact-single-nucleotide-conductance-for-dna-and-rna-sequence-identification
#20
Sepideh Afsari, Lee Erik Korshoj, Gary R Abel, Sajida Khan, Anushree Chatterjee, Prashant Nagpal
Several nanoscale electronic methods have been proposed for high-throughput single-molecule nucleic acid sequence identification. While many studies display a large ensemble of measurements as "electronic fingerprints" with some promise for distinguishing the DNA and RNA nucleobases (adenine, guanine, cytosine, thymine, and uracil), important metrics like accuracy and confidence of base calling fall well below the current genomic methods. Issues such as unreliable metal-molecule junction formation, variation of nucleotide conformations, insufficient differences between the molecular orbitals responsible for single-nucleotide conduction, and lack of rigorous base-calling algorithms lead to overlapping nanoelectronic measurements and poor nucleotide discrimination, especially at low coverage on single molecules...
October 2, 2017: ACS Nano
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