Probing the role of the cation–π interaction in the binding sites of GPCRs using unnatural amino acids

We describe a general application of the nonsense suppression methodology for unnatural amino acid incorporation to probe drug–receptor interactions in functional G protein-coupled receptors (GPCRs), evaluating the binding sites of both the M2 muscarinic acetylcholine receptor and the D2 dopamine receptor. Receptors were expressed in Xenopus oocytes, and activation of a G protein-coupled, inward-rectifying K^+ channel (GIRK) provided, after optimization of conditions, a quantitative readout of receptor function. A number of aromatic amino acids thought to be near the agonist-binding site were evaluated. Incorporation of a series of fluorinated tryptophan derivatives at W6.48 of the D2 receptor establishes a cation–π interaction between the agonist dopamine and W6.48, suggesting a reorientation of W6.48 on agonist binding, consistent with proposed “rotamer switch” models. Interestingly, no comparable cation–π interaction was found at the aligning residue in the M2 receptor

Quasiperpendicular high Mach number Shocks

Shock waves exist throughout the universe and are fundamental to understanding the nature of collisionless plasmas. Reformation is a process, driven by microphysics, which typically occurs at high Mach number supercritical shocks. While ongoing studies have investigated this process extensively both theoretically and via simulations, their observations remain few and far between. In this letter we present a study of very high Mach number shocks in a parameter space that has been poorly explored and we identify reformation using in situ magnetic field observations from the Cassini spacecraft at 10 AU. This has given us an insight into quasi-perpendicular shocks across two orders of magnitude in Alfven Mach number (MA) which could potentially bridge the gap between modest terrestrial shocks and more exotic astrophysical shocks. For the first time, we show evidence for cyclic reformation controlled by specular ion reflection occurring at the predicted timescale of ~0.3 {\tau}c, where {\tau}c is the ion gyroperiod. In addition, we experimentally reveal the relationship between reformation and MA and focus on the magnetic structure of such shocks to further show that for the same MA, a reforming shock exhibits stronger magnetic field amplification than a shock that is not reforming.Comment: Accepted and Published in Physical Review Letters (2015

The exp-log normal form of types

Lambda calculi with algebraic data types lie at the core of functional programming languages and proof assistants, but conceal at least two fundamental theoretical problems already in the presence of the simplest non-trivial data type, the sum type. First, we do not know of an explicit and implemented algorithm for deciding the beta-eta-equality of terms---and this in spite of the first decidability results proven two decades ago. Second, it is not clear how to decide when two types are essentially the same, i.e. isomorphic, in spite of the meta-theoretic results on decidability of the isomorphism. In this paper, we present the exp-log normal form of types---derived from the representation of exponential polynomials via the unary exponential and logarithmic functions---that any type built from arrows, products, and sums, can be isomorphically mapped to. The type normal form can be used as a simple heuristic for deciding type isomorphism, thanks to the fact that it is a systematic application of the high-school identities. We then show that the type normal form allows to reduce the standard beta-eta equational theory of the lambda calculus to a specialized version of itself, while preserving the completeness of equality on terms. We end by describing an alternative representation of normal terms of the lambda calculus with sums, together with a Coq-implemented converter into/from our new term calculus. The difference with the only other previously implemented heuristic for deciding interesting instances of eta-equality by Balat, Di Cosmo, and Fiore, is that we exploit the type information of terms substantially and this often allows us to obtain a canonical representation of terms without performing sophisticated term analyses

Analysis of within subjects variability in mouse ultrasonic vocalization: Pups exhibit inconsistent, state-like patterns of call production

Mice produce ultrasonic vocalizations (USV) in multiple communicative contexts, including adult social interaction (e.g., male to female courtship), as well as pup calls when separated from the dam. Assessment of pup USV has been widely applied in models of social and communicative disorders, dozens of which have shown alterations to this conserved behavior. However, features such as call production rate can vary substantially even within experimental groups and it is unclear to what extent aspects of USV represent stable trait-like influences or are vulnerable to an animal's state. To address this question, we have employed a mixed modeling approach to describe consistency in USV features across time, leveraging multiple large cohorts recorded from two strains, and across ages/times. We find that most features of pup USV show consistent patterns within a recording session, but inconsistent patterns across postnatal development. This supports the conclusion that pup USV is most strongly influenced by state-like variables. In contrast, adult USV call rate and call duration show higher consistency across sessions and may reflect a stable trait. However, spectral features of adult song such as the presence of pitch jumps do not show this level of consistency, suggesting that pitch modulation is more susceptible to factors affecting the animal's state at the time of recording. Overall, the utility of this work is threefold. First, as variability necessarily affects the sensitivity of the assay to detect experimental perturbation, we hope the information provided here will be used to help researchers plan sufficiently powered experiments, as well as prioritize specific ages to study USV behavior and to decide which features to consider most strongly in analysis. Second, via the mouseTube platform, we have provided these hundreds of recordings and associated data to serve as a shared resource for other researchers interested in either benchmark data for these strains or in developing algorithms for studying features of mouse song. Finally, we hope that this work informs both interpretation of USV studies in models of developmental disorder, and helps to further research into understanding the neural processes that contribute to the production and predictability of USV behavior

An X-Ray Jet from a White Dwarf - Detection of the Collimated Outflow from CH Cygni with Chandra

Most symbiotic stars consist of a white dwarf accreting material from the wind of a red giant. An increasing number of these objects have been found to produce jets. Analysis of archival Chandra data of the symbiotic system CH Cygni reveals faint extended emission to the south, aligned with the optical and radio jets seen in earlier HST and VLA observations. CH Cygni thus contains only the second known white dwarf with an X-ray jet, after R Aquarii. The X-rays from symbiotic-star jets appear to be produced when jet material is shock-heated following collision with surrounding gas, as with the outflows from some protostellar objects and bipolar planetary nebulae.Comment: 4 & a bit pages, 4 figures, accepted by ApJL; uses emulateapj.cls and revtex4. Minor changes following referees report, & shortened to meet page limi

Ketamine Inside Neurons?

Clinically used antidepressants, such as selective serotonin reuptake inhibitors (SSRIs), aid only a fraction of patients. Furthermore, even successful use of SSRIs takes 2 to 6 weeks of maintained medication. Depressed patients need faster help. Since 2000, several clinical studies report that depressed patients given subanesthetic doses of ketamine showed improvement within 2 hours. Trials continue for various dosing regimens, formulations, and populations. It is not understood what causes the therapeutic action of the SSRIs, and it is also not clear how ketamine exerts its effects. The best-known behavioral effect of ketamine is dissociative anesthesia. The drug retains Food and Drug Administration (FDA) approval for anesthesia in special populations as well as for veterinary use. The dissociative effects presumably arise from ketamine’s action to block N-methyl-D-aspartate (NMDA) receptor channels that have been opened by glutamate. The kinetics, equilibrium, and voltage sensitivity of open-channel blockers is a well-studied topic, and recent work shows how ketamine becomes trapped within the channel pore of NMDA receptors at local concentrations of ∼1 µM, which are expected to occur at the clinically effective antidepressant human doses. How might blockade of NMDA receptors lead to the antidepressant effects? Most studies emphasize signal transduction pathways that could be modulated by the locally decreased Ca^(2+) flux through NMDA receptors, especially extrasynaptic GluN2B subunit-containing NMDA receptors. In one series of experiments, the decreased Ca^(2+) flux led to decreased activity of eukaryotic elongation factor 2 kinase, which in turn desuppressed eukaryotic elongation factor 2. This ribosome-binding protein then increased translation of brain-derived neurotrophic factor (BDNF). Many other experiments show that BDNF is released during antidepressant action

The Liquidus Temperature for Methanol-Water Mixtures at High Pressure and Low Temperature, with Application to Titan

Methanol is a potentially important impurity in subsurface oceans on Titan and Enceladus. We report measurements of the freezing of methanol-water samples at pressures up to 350~MPa using a volumetric cell with sapphire windows. For low concentrations of methanol, the liquidus temperature is typically a few degrees below the corresponding ice freezing point, while at high concentrations it follows the pure methanol trend. In the Ice-III regime, we observe several long-lived metastable states. The results suggest that methanol is a more effective antifreeze than previously estimated, and might have played an important role in the development of Titan's subsurface ocean

High resolution radio observations of the colliding-wind binary WR140

Milli-arcsecond resolution Very Long Baseline Array (VLBA) observations of the archetype WR+O star colliding-wind binary (CWB) system WR140 are presented for 23 epochs between orbital phases 0.74 and 0.97. At 8.4 GHz, the emission in the wind-collision region (WCR) is clearly resolved as a bow-shaped arc that rotates as the orbit progresses. We interpret this rotation as due to the O star moving from SE to approximately E of the WR star, which leads to solutions for the orbit inclination of 122+/-5 deg, the longitude of the ascending node of 353+/-3 deg, and an orbit semi-major axis of 9.0+/-0.5 mas. The distance to WR140 is determined to be 1.85+/-0.16 kpc, which requires the O star to be a supergiant. The inclination implies the mass of the WR and O star to be 20+/-4 and 54+/-10 solar masses respectively. We determine a wind-momentum ratio of 0.22, with an expected half-opening angle for the WCR of 63 deg, consistent with 65+/-10 deg derived from the VLBA observations. Total flux measurements from Very Large Array (VLA) observations show the radio emission from WR140 is very closely the same from one orbit to the next, pointing strongly toward emission, absorption and cooling mechanism(s) that are controlled largely by the orbital motion. The synchrotron spectra evolve dramatically through the orbital phases observed, exhibiting both optically thin and optically thick emission. We discuss a number of absorption and cooling mechanisms that may determine the evolution of the synchrotron spectrum with orbital phase.Comment: Accepted by ApJ, to appear in v623, April 20, 2005. 14 pages, 13 figs, requires emulateapj.cls. A version with full resolution figs can be obtained from http://www.drao.nrc.ca/~smd/preprint/wr140_data.pd