91 research outputs found

    A System for Performing High Throughput Assays of Synaptic Function

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    Unbiased, high-throughput screening has proven invaluable for dissecting complex biological processes. Application of this general approach to synaptic function would have a major impact on neuroscience research and drug discovery. However, existing techniques for studying synaptic physiology are labor intensive and low-throughput. Here, we describe a new high-throughput technology for performing assays of synaptic function in primary neurons cultured in microtiter plates. We show that this system can perform 96 synaptic vesicle cycling assays in parallel with high sensitivity, precision, uniformity, and reproducibility and can detect modulators of presynaptic function. By screening libraries of pharmacologically defined compounds on rat forebrain cultures, we have used this system to identify novel effects of compounds on specific aspects of presynaptic function. As a system for unbiased compound as well as genomic screening, this technology has significant applications for basic neuroscience research and for the discovery of novel, mechanism-based treatments for central nervous system disorders

    MISCAST : MIssense variant to protein StruCture Analysis web SuiTe

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    Human genome sequencing efforts have greatly expanded, and a plethora of missense variants identified both in patients and in the general population is now publicly accessible. Interpretation of the molecular-level effect of missense variants, however, remains challenging and requires a particular investigation of amino acid substitutions in the context of protein structure and function. Answers to questions like 'Is a variant perturbing a site involved in key macromolecular interactions and/or cellular signaling?', or 'Is a variant changing an amino acid located at the protein core or part of a cluster of known pathogenic mutations in 3D?' are crucial. Motivated by these needs, we developed MISCAST (missense variant to protein structure analysis web suite; http://miscast.broadinstitute.org/). MISCAST is an interactive and user-friendly web server to visualize and analyze missense variants in protein sequence and structure space. Additionally, a comprehensive set of protein structural and functional features have been aggregated in MISCAST from multiple databases, and displayed on structures alongside the variants to provide users with the biological context of the variant location in an integrated platform. We further made the annotated data and protein structures readily downloadable from MISCAST to foster advanced offline analysis of missense variants by a wide biological community.Peer reviewe

    Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants

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    Interpretation of the colossal number of genetic variants identified from sequencing applications is one of the major bottlenecks in clinical genetics, with the inference of the effect of amino acid-substituting missense variations on protein structure and function being especially challenging. Here we characterize the three-dimensional (3D) amino acid positions affected in pathogenic and population variants from 1,330 disease-associated genes using over 14,000 experimentally solved human protein structures. By measuring the statistical burden of variations (i.e., point mutations) from all genes on 40 3D protein features, accounting for the structural, chemical, and functional context of the variations' positions, we identify features that are generally associated with pathogenic and population missense variants. We then perform the same amino acid-level analysis individually for 24 protein functional classes, which reveals unique characteristics of the positions of the altered amino acids: We observe up to 46% divergence of the class-specific features from the general characteristics obtained by the analysis on all genes, which is consistent with the structural diversity of essential regions across different protein classes. We demonstrate that the function-specific 3D features of the variants match the readouts of mutagenesis experiments for BRCA1 and PTEN, and positively correlate with an independent set of clinically interpreted pathogenic and benign missense variants. Finally, we make our results available through a web server to foster accessibility and downstream research. Our findings represent a crucial step toward translational genetics, from highlighting the impact of mutations on protein structure to rationalizing the variants' pathogenicity in terms of the perturbed molecular mechanisms.Peer reviewe

    Spatial Patterns of Aflatoxin Levels in Relation to Ear-Feeding Insect Damage in Pre-Harvest Corn

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    Key impediments to increased corn yield and quality in the southeastern US coastal plain region are damage by ear-feeding insects and aflatoxin contamination caused by infection of Aspergillus flavus. Key ear-feeding insects are corn earworm, Helicoverpa zea, fall armyworm, Spodoptera frugiperda, maize weevil, Sitophilus zeamais, and brown stink bug, Euschistus servus. In 2006 and 2007, aflatoxin contamination and insect damage were sampled before harvest in three 0.4-hectare corn fields using a grid sampling method. The feeding damage by each of ear/kernel-feeding insects (i.e., corn earworm/fall armyworm damage on the silk/cob, and discoloration of corn kernels by stink bugs), and maize weevil population were assessed at each grid point with five ears. The spatial distribution pattern of aflatoxin contamination was also assessed using the corn samples collected at each sampling point. Aflatoxin level was correlated to the number of maize weevils and stink bug-discolored kernels, but not closely correlated to either husk coverage or corn earworm damage. Contour maps of the maize weevil populations, stink bug-damaged kernels, and aflatoxin levels exhibited an aggregated distribution pattern with a strong edge effect on all three parameters. The separation of silk- and cob-feeding insects from kernel-feeding insects, as well as chewing (i.e., the corn earworm and maize weevil) and piercing-sucking insects (i.e., the stink bugs) and their damage in relation to aflatoxin accumulation is economically important. Both theoretic and applied ramifications of this study were discussed by proposing a hypothesis on the underlying mechanisms of the aggregated distribution patterns and strong edge effect of insect damage and aflatoxin contamination, and by discussing possible management tactics for aflatoxin reduction by proper management of kernel-feeding insects. Future directions on basic and applied research related to aflatoxin contamination are also discussed

    British signals intelligence and the 1916 Easter Rising in Ireland

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    Historians for decades have placed Room 40, the First World War British naval signals intelligence organization, at the centre of narratives about the British anticipation of and response to the Easter Rising in Ireland in 1916. A series of crucial decrypts of telegrams between the German embassy in Washington and Berlin, it has been believed, provided significant advance intelligence about the Rising before it took place. This article upends previous accounts by demonstrating that Room 40 possessed far less advance knowledge about the Rising than has been believed, with most of the supposedly key decrypts not being generated until months after the Rising had taken place

    The GALAH survey: Co-orbiting stars and chemical tagging

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    We present a study using the second data release of the GALAH survey of stellar parameters and elemental abundances of 15 pairs of stars identified by Oh et al 2017. They identified these pairs as potentially co-moving pairs using proper motions and parallaxes from Gaia DR1. We find that 11 very wide (>1.7 pc) pairs of stars do in fact have similar Galactic orbits, while a further four claimed co-moving pairs are not truly co-orbiting. Eight of the 11 co-orbiting pairs have reliable stellar parameters and abundances, and we find that three of those are quite similar in their abundance patterns, while five have significant [Fe/H] differences. For the latter, this indicates that they could be co-orbiting because of the general dynamical coldness of the thin disc, or perhaps resonances induced by the Galaxy, rather than a shared formation site. Stars such as these, wide binaries, debris of past star formation episodes, and coincidental co-orbiters, are crucial for exploring the limits of chemical tagging in the Milky Way.Comment: 14 pages, 9 figures, submitted to MNRAS. Updated for Gaia DR2 value

    The GALAH survey: Co-orbiting stars and chemical tagging

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    We present a study using the second data release of the GALAH survey of stellar parameters and elemental abundances of 15 pairs of stars identified by Oh et al 2017. They identified these pairs as potentially co-moving pairs using proper motions and parallaxes from Gaia DR1. We find that 11 very wide (>1.7 pc) pairs of stars do in fact have similar Galactic orbits, while a further four claimed co-moving pairs are not truly co-orbiting. Eight of the 11 co-orbiting pairs have reliable stellar parameters and abundances, and we find that three of those are quite similar in their abundance patterns, while five have significant [Fe/H] differences. For the latter, this indicates that they could be co-orbiting because of the general dynamical coldness of the thin disc, or perhaps resonances induced by the Galaxy, rather than a shared formation site. Stars such as these, wide binaries, debris of past star formation episodes, and coincidental co-orbiters, are crucial for exploring the limits of chemical tagging in the Milky Way.Comment: 14 pages, 9 figures, submitted to MNRAS. Updated for Gaia DR2 value

    Spectral matching for abundances and clustering analysis of stars on the giant branches of {\omega} Centauri

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    We have determined stellar parameters and abundances for 221 giant branch stars in the globular cluster {\omega} Centauri. A combination of photometry and lower-resolution spectroscopy was used to determine temperature, gravity, metallicity, [C/Fe], [N/Fe] and [Ba/Fe]. These abundances agree well with those found by previous researchers and expand the analysed sample of the cluster. k-means clustering analysis was used to group the stars into four homogeneous groups based upon these abundances. These stars show the expected anticorrelation in [C/Fe] to [N/Fe]. We investigated the distribution of CN-weak/strong stars on the colour-magnitude diagram. Asymptotic giant branch stars, which were selected from their position on the colour-magnitude diagram, were almost all CN-weak. This is in contrast to the red giant branch where a large minority were CN-strong. The results were also compared with cluster formation and evolution models. Overall, this study shows that statistically significant elemental and evolutionary conclusions can be obtained from lower resolution spectroscopy.Comment: The paper contains 13 figures and 7 tables. Tables 2 and 4 will be published in full online only. Accepted for publication by MNRA

    The GALAH survey: tracing the Galactic disk with Open Clusters

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    Open clusters are unique tracers of the history of our own Galaxy's disk. According to our membership analysis based on \textit{Gaia} astrometry, out of the 226 potential clusters falling in the footprint of GALAH or APOGEE, we find that 205 have secure members that were observed by at least one of the survey. Furthermore, members of 134 clusters have high-quality spectroscopic data that we use to determine their chemical composition. We leverage this information to study the chemical distribution throughout the Galactic disk of 21 elements, from C to Eu. The radial metallicity gradient obtained from our analysis is -0.076±\pm0.009 dex kpc1^{-1}, which is in agreement with previous works based on smaller samples. Furthermore, the gradient in the [Fe/H] - guiding radius (rguid_{\rm guid}) plane is -0.073±\pm0.008 dex kpc1^{-1}. We show consistently that open clusters trace the distribution of chemical elements throughout the Galactic disk differently than field stars. In particular, at given radius, open clusters show an age-metallicity relation that has less scatter than field stars. As such scatter is often interpreted as an effect of radial migration, we suggest that these differences are due to the physical selection effect imposed by our Galaxy: clusters that would have migrated significantly also had higher chances to get destroyed. Finally, our results reveal trends in the [X/Fe]-rguid_{\rm guid}-age space, which are important to understand production rates of different elements as a function of space and time.Comment: 18 pages, 10 figures, accepted for publication MNRA
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