Simulations of the Alternating Access Mechanism of the Sodium Symporter Mhp1

AbstractSodium coupled cotransporters of the five-helix inverted repeat (5HIR) superfamily use an alternating access mechanism to transport a myriad of small molecules across the cell membrane. One of the primary steps in this mechanism is the conformational transition from a state poised to bind extracellular substrates to a state that is competent to deliver substrate to the cytoplasm. Here, we construct a coarse-grained model of the 5HIR benzylhydantoin transporter Mhp1 that incorporates experimental structures of the outward- and inward-open states to investigate the mechanism of this conformational change. Using the weighted ensemble path-sampling method, we rigorously sample the outward- to inward-facing transition path ensemble. The transition path ensemble reveals a heterogeneous set of pathways connecting the two states and identifies two modes of transport: one consistent with a strict alternating access mechanism and another where decoupling of the inner and outer gates causes the transient formation of a continuous permeation pathway through the transporter. We also show that the conformational switch between the outward- and inward-open states results from rigid body motions of the hash motif relative to the substrate bundle, supporting the rocking bundle hypothesis. Finally, our methodology provides the groundwork for more chemically detailed investigations of the alternating mechanism

The nature of red dwarf galaxies

Using dark matter halos traced by galaxy groups selected from the Sloan Digital Sky Survey Data Release 4, we find that about 1/4 of the faint galaxies (\rmag >-17.05, hereafter dwarfs) that are the central galaxies in their own halo are not blue and star forming, as expected in standard models of galaxy formation, but are red. In contrast, this fraction is about 1/2 for dwarf satellite galaxies. Many red dwarf galaxies are physically associated with more massive halos. In total, about $\sim 45$% of red dwarf galaxies reside in massive halos as satellites, while another $\sim 25$% have a spatial distribution that is much more concentrated towards their nearest massive haloes than other dwarf galaxies. We use mock catalogs to show that the reddest population of non-satellite dwarf galaxies are distributed within about 3 times the virial radii of their nearest massive halos. We suggest that this population of dwarf galaxies are hosted by low-mass halos that have passed through their massive neighbors, and that the same environmental effects that cause satellite galaxies to become red are also responsible for the red colors of this population of galaxies. We do not find any significant radial dependence of the population of dwarf galaxies with the highest concentrations, suggesting that the mechanisms operating on these galaxies affect color more than structure. However, over 30% of dwarf galaxies are red and isolated and their origin remains unknown.Comment: 9 pages, 8 figures, Accepted for publication in Ap

Sloan Digital Sky Survey Multicolor Observations of GRB010222

The discovery of an optical counterpart to GRB010222 (detected by BeppoSAX; Piro 2001) was announced 4.4 hrs after the burst by Henden (2001a). The Sloan Digital Sky Survey's 0.5m photometric telescope (PT) and 2.5m survey telescope were used to observe the afterglow of GRB010222 starting 4.8 hours after the GRB. The 0.5m PT observed the afterglow in five, 300 sec g' band exposures over the course of half an hour, measuring a temporal decay rate in this short period of F_nu \propto t^{-1.0+/-0.5}. The 2.5m camera imaged the counterpart nearly simultaneously in five filters (u' g' r' i' z'), with r' = 18.74+/-0.02 at 12:10 UT. These multicolor observations, corrected for reddening and the afterglow's temporal decay, are well fit by the power-law F_nu \propto nu^{-0.90+/-0.03} with the exception of the u' band UV flux which is 20% below this slope. We examine possible interpretations of this spectral shape, including source extinction in a star forming region.Comment: 8 pages, 4 figures, accepted for publication in ApJ. Two figures added, minor changes to text in this draft. Related material can be found at: http://sdss.fnal.gov:8000/grb

Galaxy Zoo 1 : Data Release of Morphological Classifications for nearly 900,000 galaxies

Morphology is a powerful indicator of a galaxy's dynamical and merger history. It is strongly correlated with many physical parameters, including mass, star formation history and the distribution of mass. The Galaxy Zoo project collected simple morphological classifications of nearly 900,000 galaxies drawn from the Sloan Digital Sky Survey, contributed by hundreds of thousands of volunteers. This large number of classifications allows us to exclude classifier error, and measure the influence of subtle biases inherent in morphological classification. This paper presents the data collected by the project, alongside measures of classification accuracy and bias. The data are now publicly available and full catalogues can be downloaded in electronic format from http://data.galaxyzoo.org.Comment: Accepted by MNRAS, 14 pages. Updated to match final version; problem with table 7 header fixed. Full tables available at http://data.galaxyzoo.or

Structural Properties of Central Galaxies in Groups and Clusters

Using a representative sample of 911 central galaxies (CENs) from the SDSS DR4 group catalogue, we study how the structure of the most massive members in groups and clusters depend on (1) galaxy stellar mass (Mstar), (2) dark matter halo mass of the host group (Mhalo), and (3) their halo-centric position. We establish and thoroughly test a GALFIT-based pipeline to fit 2D Sersic models to SDSS data. We find that the fitting results are most sensitive to the background sky level determination and strongly recommend using the SDSS global value. We find that uncertainties in the background translate into a strong covariance between the total magnitude, half-light size (r50), and Sersic index (n), especially for bright/massive galaxies. We find that n depends strongly on Mstar for CENs, but only weakly or not at all on Mhalo. Less (more) massive CENs tend to be disk (spheroid)-like over the full Mhalo range. Likewise, there is a clear r50-Mstar relation for CENs, with separate slopes for disks and spheroids. When comparing CENs with satellite galaxies (SATs), we find that low mass (<10e10.75 Msun/h^2) SATs have larger median n than CENs of similar Mstar. Low mass, late-type SATs have moderately smaller r50 than late-type CENs of the same Mstar. However, we find no size differences between spheroid-like CENs and SATs, and no structural differences between CENs and SATs matched in both mass and colour. The similarity of massive SATs and CENs shows that this distinction has no significant impact on the structure of spheroids. We conclude that Mstar is the most fundamental property determining the basic structure of a galaxy. The lack of a clear n-Mhalo relation rules out a distinct group mass for producing spheroids, and the responsible morphological transformation processes must occur at the centres of groups spanning a wide range of masses. (abridged)Comment: 22 pages, 14 figures, submitted to MNRA

Baryon Acoustic Oscillations in the Sloan Digital Sky Survey Data Release 7 Galaxy Sample

The spectroscopic Sloan Digital Sky Survey (SDSS) Data Release 7 (DR7) galaxy sample represents the final set of galaxies observed using the original SDSS target selection criteria. We analyse the clustering of galaxies within this sample, including both the Luminous Red Galaxy (LRG) and Main samples, and also include the 2-degree Field Galaxy Redshift Survey (2dFGRS) data. Baryon Acoustic Oscillations are observed in power spectra measured for different slices in redshift; this allows us to constrain the distance--redshift relation at multiple epochs. We achieve a distance measure at redshift z=0.275, of r_s(z_d)/D_V(0.275)=0.1390+/-0.0037 (2.7% accuracy), where r_s(z_d) is the comoving sound horizon at the baryon drag epoch, D_V(z)=[(1+z)^2D_A^2cz/H(z)]^(1/3), D_A(z) is the angular diameter distance and H(z) is the Hubble parameter. We find an almost independent constraint on the ratio of distances D_V(0.35)/D_V(0.2)=1.736+/-0.065, which is consistent at the 1.1sigma level with the best fit Lambda-CDM model obtained when combining our z=0.275 distance constraint with the WMAP 5-year data. The offset is similar to that found in previous analyses of the SDSS DR5 sample, but the discrepancy is now of lower significance, a change caused by a revised error analysis and a change in the methodology adopted, as well as the addition of more data. Using WMAP5 constraints on Omega_bh^2 and Omega_ch^2, and combining our BAO distance measurements with those from the Union Supernova sample, places a tight constraint on Omega_m=0.286+/-0.018 and H_0 = 68.2+/-2.2km/s/Mpc that is robust to allowing curvature and non-Lambda dark energy. This result is independent of the behaviour of dark energy at redshifts greater than those probed by the BAO and supernova measurements. (abridged)Comment: 22 pages, 16 figures, minor changes to match version published in MNRA

A Small Conductance Calcium-Activated K⁺ Channel in C. elegans, KCNL-2, Plays a Role in the Regulation of the Rate of Egg-Laying

In the nervous system of mice, small conductance calcium-activated potassium (SK) channels function to regulate neuronal excitability through the generation of a component of the medium afterhyperpolarization that follows action potentials. In humans, irregular action potential firing frequency underlies diseases such as ataxia, epilepsy, schizophrenia and Parkinson's disease. Due to the complexity of studying protein function in the mammalian nervous system, we sought to characterize an SK channel homologue, KCNL-2, in C. elegans, a genetically tractable system in which the lineage of individual neurons was mapped from their early developmental stages. Sequence analysis of the KCNL-2 protein reveals that the six transmembrane domains, the potassium-selective pore and the calmodulin binding domain are highly conserved with the mammalian homologues. We used widefield and confocal fluorescent imaging to show that a fusion construct of KCNL-2 with GFP in transgenic lines is expressed in the nervous system of C. elegans. We also show that a KCNL-2 null strain, kcnl-2(tm1885), demonstrates a mild egg-laying defective phenotype, a phenotype that is rescued in a KCNL-2-dependent manner. Conversely, we show that transgenic lines that overexpress KCNL-2 demonstrate a hyperactive egg-laying phenotype. In this study, we show that the vulva of transgenic hermaphrodites is highly innervated by neuronal processes and by the VC4 and VC5 neurons that express GFP-tagged KCNL-2. We propose that KCNL-2 functions in the nervous system of C. elegans to regulate the rate of egg-laying. © 2013 Chotoo et al

On the variability of quasars: a link between Eddington ratio and optical variability?

Repeat scans by the Sloan Digital Sky Survey (SDSS) of a 278 square degree stripe along the Celestial equator have yielded an average of over 10 observations each for nearly 8,000 spectroscopically confirmed quasars. Over 2500 of these quasars are in the redshift range such that the CIV emission line is visible in the SDSS spectrum. Utilising the width of these CIV lines and the luminosity of the nearby continuum, we estimate black hole masses for these objects. In an effort to isolate the effects of black hole mass and luminosity on the photometric variability of our dataset, we create several subsamples by binning in these two physical parameters. By comparing the ensemble structure functions of the quasars in these bins, we are able to reproduce the well-known anticorrelation between luminosity and variability, now showing that this anticorrelation is independent of the black hole mass. In addition, we find a correlation between variability and the mass of the central black hole. By combining these two relations, we identify the Eddington ratio as a possible driver of quasar variability, most likely due to differences in accretion efficiency.Comment: 13 pages, 5 figures, Accepted for publication in MNRA

Nebular Attenuation in H\alpha-selected Star-forming Galaxies at z=0.8 from the NewH\alpha\ Survey

We present measurements of the dust attenuation of H\alpha-selected emission-line galaxies at z=0.8 from the NewH\alpha\ narrowband survey. The analysis is based on deep follow-up spectroscopy with Magellan/IMACS, which captures the strong rest-frame optical emission lines from [OII] \lambda 3727 to [OIII] \lambda 5007. The spectroscopic sample used in this analysis consists of 341 confirmed H\alpha\ emitters. We place constraints on the AGN fraction using diagnostics which can be applied at intermediate redshift. We find that at least 5% of the objects in our spectroscopic sample can be classified as AGN and 2% are composite, i.e. powered by a combination of star-formation and AGN activity. We measure the dust attenuation for individual objects from the ratios of the higher order Balmer lines. The H\beta\ and H\gamma\ pair of lines is detected with S/N>5 in 55 individual objects and the H\beta\ and H\delta\ pair is detected in 50 individual objects. We also create stacked spectra to probe the attenuation in objects without individual detections. The median attenuation at H\alpha\ based on the objects with individually detected lines is A(H\alpha)=0.9+-1.0 magnitudes, in good agreement with the attenuation found in local samples of star-forming galaxies. We find that the z=0.8 galaxies occupy a similar locus of attenuation as a function of magnitude, mass and SFR as a comparison sample drawn from the SDSS DR4. Both the results from the individual z=0.8 galaxies and from the stacked spectra show consistency with the mass -- attenuation and SFR -- attenuation relations found in the local Universe, indicating that these relations are also applicable at intermediate redshift.Comment: Submitted to AJ. Revised per referee's comment

Galaxy Zoo: Dust in Spirals

We investigate the effect of dust on spiral galaxies by measuring the inclination-dependence of optical colours for 24,276 well-resolved SDSS galaxies visually classified in Galaxy Zoo. We find clear trends of reddening with inclination which imply a total extinction from face-on to edge-on of 0.7, 0.6, 0.5 and 0.4 magnitudes for the ugri passbands. We split the sample into "bulgy" (early-type) and "disky" (late-type) spirals using the SDSS fracdeV (or f_DeV) parameter and show that the average face-on colour of "bulgy" spirals is redder than the average edge-on colour of "disky" spirals. This shows that the observed optical colour of a spiral galaxy is determined almost equally by the spiral type (via the bulge-disk ratio and stellar populations), and reddening due to dust. We find that both luminosity and spiral type affect the total amount of extinction, with "disky" spirals at M_r ~ -21.5 mags having the most reddening. This decrease of reddening for the most luminous spirals has not been observed before and may be related to their lower levels of recent star formation. We compare our results with the latest dust attenuation models of Tuffs et al. We find that the model reproduces the observed trends reasonably well but overpredicts the amount of u-band attenuation in edge-on galaxies. We end by discussing the effects of dust on large galaxy surveys and emphasize that these effects will become important as we push to higher precision measurements of galaxy properties and their clustering.Comment: MNRAS in press. 25 pages, 22 figures (including an abstract comparing GZ classifications with common automated methods for selecting disk/early type galaxies in SDSS data). v2 corrects typos found in proof