A general method to eliminate laboratory induced recombinants during massive, parallel sequencing of cDNA library.

Massive, parallel sequencing is a potent tool for dissecting the regulation of biological processes by revealing the dynamics of the cellular RNA profile under different conditions. Similarly, massive, parallel sequencing can be used to reveal the complexity of viral quasispecies that are often found in the RNA virus infected host. However, the production of cDNA libraries for next-generation sequencing (NGS) necessitates the reverse transcription of RNA into cDNA and the amplification of the cDNA template using PCR, which may introduce artefact in the form of phantom nucleic acids species that can bias the composition and interpretation of original RNA profiles

Alanine scanning mutagenesis of a high-affinity nitrate transporter highlights the requirement for glycine and asparagine residues in the two nitrate signature motifs

Common to all of the nitrate nitrite porter family are two conserved motifs in transmembrane helices 5 and 11 termed NS (nitrate signature) 1 and NS2. Although perfectly conserved substrate-interacting arginine residues have been described in transmembrane helices 2 and 8, the role of NSs has not been investigated. In the present study, a combination of structural modelling of NrtA (nitrate transporter from Aspergillus nidulans) with alanine scanning mutagenesis of residues within and around the NSs has been used to shed light on the probable role of conserved residues in the NSs. Models show that Asn 168 in NS1 and Asn 459 in NS2 are positioned approximately midway within the protein at the central pivot point in close proximity to the substrate-binding residues Arg 368 and Arg 87 respectively, which lie offset from the pivot point towards the cytoplasmic face. The Asn 168 /Arg 368 and Asn 459 /Arg 87 residue pairs are relatively widely separated on opposite sides of the probable substrate translocation pore. The results of the present study demonstrate the critical structural contribution of several glycine residues in each NS at sites of close helix packing. Given the relative locations of Asn 168 /Arg 368 and Asn 459 /Arg 87 pairs, the validity of the models and possible role of the NSs together with the substrate-binding arginine residues are discusse

Application of relativistic scattering theory of x rays to diffraction anomalous fine structure in Cu

We apply our recent first-principles formalism of magnetic scattering of circularly polarized x rays to a single Cu crystal. We demonstrate the ability of our formalism to interpret the crystalline environment related near-edge fine structure features in the resonant x-ray scattering spectra at the Cu K absorption edge. We find good agreement between the computed and measured diffraction anomalous fine structure features of the x-ray scattering spectra

Design, synthesis, and subtype selectivity of 3,6-disubstituted b-carbolines at Bz/GABA(A)ergic receptors. SAR and studies directed toward agents for treatment of alcohol abuse

A series of 3,6-disubstituted ß-carbolines was synthesized and evaluated for their in vitro affinities at axß3V2 GABAA/benzodiazepine receptor subtypes by radioligand binding assays in search of a1 subtype selective ligands to treat alcohol abuse. Analogues of ß-carboline-3-carboxylate-t-butyl ester (ßCCt, 1) were synthesized via a CDI-mediated process and the related 6-substituted ß-carboline-3-carboxylates 6 including WYS8 (7) were synthesized via a Sonogashira or Stille coupling processes from 6-iodo-ßCCt (5). The bivalent ligands of ßCCt (32 and 33) were also designed and prepared via a palladium-catalyzed homocoupling process to expand the structure-activity relationships (SAR) to larger ligands

911 Calls in homicide cases: What does the verbal behavior of the caller reveal?

Each year, numerous 911 calls reporting a death or a serious injury that leads to death are received by emergency communications centers; many of these turn out to be related to a homicide. Interestingly, a small percentage of these calls are made by the perpetrator. These calls constitute the first available evidence in most homicide cases. They are recorded at times of great stress and are the first versions of what the callers purport to know. The ability to develop hypotheses about a caller’s truthfulness enhances the police response by objectively informing the process of formulating early investigative strategies. For example, knowing whether the caller uttered any words or phrases considered to be red flags that indicate deception would give an investigator an idea about whether the caller should be interviewed in greater depth. The present study examined 14 linguistic variables and an additional 4 “mitigating” variables in an effort to determine whether any of those variables, individually or in combination, were predictive of guilt or innocence. A sample of 50 calls to 911 centers was selected, including 36 innocent and 14 guilty callers. Five of the variables (Extraneous Information, Conflicting Facts, Incorrect Order, Proximity, and Weapon Touch) were significantly correlated (

Power tests of a string of magnets comprising a full cell of the Superconducting Super Collider

In this paper we describe the operation and testing of a string of magnets comprising a full cell of the Superconducting Super Collider (SSC). The full cell configuration composed of ten dipoles, two quadrupoles, and three spool pieces is the longest SSC magnet string ever tested. Although the tests of the full cell were undertaken after the SSC project was marked for termination, their completion was deemed necessary and useful to future efforts at other accelerator laboratories utilizing Superconducting magnets. The focus of this work is on the electrical and cryogenic performance of the string components and the quench protection system with an emphasis on solving some of the questions concerning electrical performance raised during the previous two experimental runs involving a half cell configuration

Interaction of photons with plasmas and liquid metals: photoabsorption and scattering

Formulas to describe the photoabsorption and the photon scattering by a plasma or a liquid metal are derived in a unified manner with each other. It is shown how the nuclear motion, the free-electron motion and the core-electron behaviour in each ion in the system determine the structure of photoabsorption and scattering in an electron-ion mixture. The absorption cross section in the dipole approximation consists of three terms which represent the absorption caused by the nuclear motion, the absorption owing to the free-electron motion producing optical conductivity or inverse Bremsstrahlung, and the absorption ascribed to the core-electron behaviour in each ion with the Doppler correction. Also, the photon scattering formula provides an analysis method for experiments observing the ion-ion dynamical structure factor (DSF), the electron-electron DSF giving plasma oscillations, and the core-electron DSF yielding the X-ray Raman (Compton) scattering with a clear definition of the background scattering for each experiment, in a unified manner. A formula for anomalous X-ray scattering is also derived for a liquid metal. At the same time, Thomson scattering in plasma physics is discussed from this general point of view.Comment: LaTeX file: 18 pages without figur

Structure of the Janus Protein Human CLIC2

Chloride intracellular channel (CLIC) proteins possess the remarkable property of being able to convert from a water-soluble state to a membrane channel state. We determined the three-dimensional structure of human CLIC2 in its water-soluble form by X-ray crystallography at 1.8-Å resolution from two crystal forms. In contrast to the previously characterized CLIC1 protein, which forms a possibly functionally important disulfide-induced dimer under oxidizing conditions, we show that CLIC2 possesses an intramolecular disulfide and that the protein remains monomeric irrespective of redox conditions. Site-directed mutagenesis studies show that removal of the intramolecular disulfide or introduction of cysteine residues in CLIC2, equivalent to those that form the intramolecular disulfide in CLIC1, does not cause dimer formation under oxidizing conditions.We also show that CLIC2 forms pH-dependent chloride channels in vitro with higher channel activity at low pH levels and that the channels are subject to redox regulation. In both crystal forms, we observed an extended loop region from the C-terminal domain, called the foot loop, inserting itself into an interdomain crevice of a neighboring molecule. The equivalent region in the structurally related glutathione transferase superfamily corresponds to the active site. This so-called foot-in-mouth interaction suggests that CLIC2 might recognize other proteins such as the ryanodine receptor through a similar interaction

Poly-strengths Skill Building for Urban Teens at High-risk for Violence Exposure: Leveraging Community After-school Programs to Promote Youth

Violence exposure increases teens’ risk for emotion dysregulation, anxiety, depression, and aggression towards peers. Urban teens are disproportionately more likely to be exposed to violence and less likely to receive mental health services. Community after-school programs can help to reduce these disparities by offering opportunities for skills development and mental health promotion to mitigate risk associated with violence exposure. The current study examined the implementation and promise of brief meditation and sleep health journaling activities infused within a pre-existing parks-based after-school program for black and Latinx teens. Data include pre-/post-measures of violent and non-violent adversity, emotion regulation, anxiety, depression, and self-efficacy to manage peer conflict. Teens also completed anonymous feedback forms after each activity. Teens with more violence exposure at time 1 reported reductions in anxiety at time 2. Teens with more overall adversity reported reductions in anxiety and improvements in self-efficacy to resolve peer conflict. Strong evidence for fidelity and teen enthusiasm (adherence, utility, and generalizability) were found. Overall, findings indicate poly-strengths training may be infused within community after-school programs to promote resilience among urban teens at high-risk for violence exposure