84 research outputs found
New and continuing developments at PROSITE
PROSITE (http://prosite.expasy.org/) consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule a collection of rules, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE signatures, together with ProRule, are used for the annotation of domains and features of UniProtKB/Swiss-Prot entries. Here, we describe recent developments that allow users to perform whole-proteome annotation as well as a number of filtering options that can be combined to perform powerful targeted searches for biological discovery. The latest version of PROSITE (release 20.85, of 30 August 2012) contains 1308 patterns, 1039 profiles and 1041 ProRule
Electrospun gelatin-based scaffolds as a novel 3D platform to study the function of contractile smooth muscle cells in vitro
Contractile dysfunction of smooth muscle (SM) is a feature of chronic cardiovascular, respiratory and gastro-intestinal diseases. Owing to the low availability of human ex vivo tissue for the assessment of SM contractile function, the aim of this study was to develop a novel in vitro SM model that possesses the ability to contract, and a method to measure its contractility. A range of electrospun scaffolds were produced from crosslinked gelatin and methacrylated gelatin (GelMA), generating highly aligned scaffolds with average fibre diameters ranging from 200 nm to several micrometres. Young's moduli of the scaffolds ranged from 1x105 to 1x107 Pa. Primary aortic smooth muscle cells (AoSMCs; rat) cells readily adhered to and proliferated on the fibrous scaffolds for up to 10 days. They formed highly aligned populations following the topographical cues of the aligned scaffolds and stained positive for SM markers, indicating a contractile phenotype. Cell-seeded GelMA scaffolds were able, upon stimulation with uridine 5'-triphosphate (UTP), to contract and their attachment to a force transducer allowed the force of contraction to be measured. Hence, these electrospun GelMA fibres can be used as biomimetic scaffolds for SM cell culture and in vitro model development, and enables the contractile forces generated by the aligned three-dimensional sheet of cells to be directly measured. This will supplement in vitro drug screening tools and facilitate discovery of disease mechanisms
Galaxy Pairs in the Sloan Digital Sky Survey - II: The Effect of Environment on Interactions
We use a sample of close galaxy pairs selected from the Sloan Digital Sky
Survey Data Release 4 (SDSS DR4) to investigate in what environments galaxy
mergers occur and how the results of these mergers depend on differences in
local galaxy density. The galaxies are quantified morphologically using
two-dimensional bulge-plus-disk decompositions and compared to a control sample
matched in stellar mass, redshift and local projected density. Lower density
environments have fractionally more galaxy pairs with small projected
separations (r_p) and relative velocities (Delta v), but even high density
environments contain significant populations of pairs with parameters that
should be conducive to interactions. Metrics of asymmetry and colour are used
to identify merger activity and triggered star formation. The location of star
formation is inferred by distinguishing bulge and disk colours and calculating
bulge fractions from the SDSS images. Galaxies in the lowest density
environments show the largest changes in star formation rate, asymmetry and
bulge-total fractions at small separations, accompanied by bluer bulge colours.
At the highest local densities, the only galaxy property to show an enhancement
in the closest pairs is asymmetry. We interpret these results as evidence that
whilst interactions (leading to tidal distortions) occur at all densities,
triggered star formation is seen only in low-to-intermediate density
environments. We suggest that this is likely due to the typically higher gas
fractions of galaxies in low density environments. Finally, by
cross-correlating our sample of galaxy pairs with a cluster catalogue, we
investigate the dependence of interactions on clustercentric distance. It is
found that for close pairs the fraction of asymmetric galaxies is highest in
the cluster centres.Comment: Accepted by MNRAS, 15 page
LSST Science Book, Version 2.0
A survey that can cover the sky in optical bands over wide fields to faint
magnitudes with a fast cadence will enable many of the exciting science
opportunities of the next decade. The Large Synoptic Survey Telescope (LSST)
will have an effective aperture of 6.7 meters and an imaging camera with field
of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over
20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with
fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a
total point-source depth of r~27.5. The LSST Science Book describes the basic
parameters of the LSST hardware, software, and observing plans. The book
discusses educational and outreach opportunities, then goes on to describe a
broad range of science that LSST will revolutionize: mapping the inner and
outer Solar System, stellar populations in the Milky Way and nearby galaxies,
the structure of the Milky Way disk and halo and other objects in the Local
Volume, transient and variable objects both at low and high redshift, and the
properties of normal and active galaxies at low and high redshift. It then
turns to far-field cosmological topics, exploring properties of supernovae to
z~1, strong and weak lensing, the large-scale distribution of galaxies and
baryon oscillations, and how these different probes may be combined to
constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at
http://www.lsst.org/lsst/sciboo
Challenges and perspectives for naming lipids in the context of lipidomics
Introduction: Lipids are key compounds in the study of metabolism and are increasingly studied in biology projects. It is a very broad family that encompasses many compounds, and the name of the same compound may vary depending on the community where they are studied. Objectives: In addition, their structures are varied and complex, which complicates their analysis. Indeed, the structural resolution does not always allow a complete level of annotation so the actual compound analysed will vary from study to study and should be clearly stated. For all these reasons the identification and naming of lipids is complicated and very variable from one study to another, it needs to be harmonized. Methods & Results: In this position paper we will present and discuss the different way to name lipids (with chemoinformatic and semantic identifiers) and their importance to share lipidomic results. Conclusion: Homogenising this identification and adopting the same rules is essential to be able to share data within the community and to map data on functional networks
The Astropy Problem
The Astropy Project (http://astropy.org) is, in its own words, "a community
effort to develop a single core package for Astronomy in Python and foster
interoperability between Python astronomy packages." For five years this
project has been managed, written, and operated as a grassroots,
self-organized, almost entirely volunteer effort while the software is used by
the majority of the astronomical community. Despite this, the project has
always been and remains to this day effectively unfunded. Further, contributors
receive little or no formal recognition for creating and supporting what is now
critical software. This paper explores the problem in detail, outlines possible
solutions to correct this, and presents a few suggestions on how to address the
sustainability of general purpose astronomical software
A gain-of-function variant in <i>DIAPH1 </i>causes dominant macrothrombocytopenia and hearing loss
Macrothrombocytopenia (MTP) is a heterogeneous group of disorders characterized by enlarged and reduced numbers of circulating platelets, sometimes resulting in abnormal bleeding. In most MTP, this phenotype arises because of altered regulation of platelet formation from megakaryocytes (MK). We report the identification of DIAPH1, which encodes the Rho-effector diaphanous-related formin 1 (DIAPH1), as a candidate gene for MTP using exome sequencing, ontological phenotyping and similarity regression. We describe two unrelated pedigrees with MTP and sensorineural hearing loss that segregate with a DIAPH1 p.R1213* variant predicting partial truncation of the DIAPH1 diaphanous autoregulatory domain. The R1213* variant was associated with reduced proplatelet formation from cultured MKs, cell clustering and abnormal cortical filamentous actin. Similarly, in platelets there was increased filamentous actin and stable microtubules, indicating constitutive activation of DIAPH1. Over-expression of DIAPH1 R1213* in cells reproduced the cytoskeletal alterations found in platelets. Our description of a novel disorder of platelet formation and hearing loss extends the repertoire of DIAPH1-related disease and provides new insights into the autoregulation of DIAPH1 activity
Toward community standards in the quest for orthologs
The identification of orthologs—genes pairs descended from a common ancestor through speciation, rather than duplication—has emerged as an essential component of many bioinformatics applications, ranging from the annotation of new genomes to experimental target prioritization. Yet, the development and application of orthology inference methods is hampered by the lack of consensus on source proteomes, file formats and benchmarks. The second ‘Quest for Orthologs' meeting brought together stakeholders from various communities to address these challenges. We report on achievements and outcomes of this meeting, focusing on topics of particular relevance to the research community at large. The Quest for Orthologs consortium is an open community that welcomes contributions from all researchers interested in orthology research and applications. Contact: [email protected]
An intrinsically disordered proteins community for ELIXIR.
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled "An intrinsically disordered protein user community proposal for ELIXIR" held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders
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InterPro in 2019: improving coverage, classification and access to protein sequence annotations
The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we report recent developments with InterPro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new InterPro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new programmatic interface and website. These developments extend and enrich the information provided by InterPro, and provide greater flexibility in terms of data access. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB, and discuss how our evaluation of residue coverage may help guide future curation activities
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