IPD - the Immuno Polymorphism Database

The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors; IPD-MHC, a database of sequences of the Major Histocompatibility Complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC share the same database structure. The sharing of a common database structure makes it easier to implement common tools for data submission and retrieval. The data are currently available online from the website and ftp directory; files will also be made available in different formats to download from the website and ftp server. The data will also be included in SRS, BLAST and FASTA search engines at the European Bioinformatics Institute

Fluorescence of laser created electron-hole plasma in graphene

We present an experimental observation of non-linear up- and down-converted optical luminescence of graphene and thin graphite subject to picosecond infrared laser pulses. We show that the excitation yields to a high density electron-hole plasma in graphene. It is further shown that the excited charge carries can efficiently exchange energy due to scattering in momentum space. The recombination of the resulting non-equilibrium electron-hole pairs yields to the observed white light luminescence. Due to the scattering mechanism the power dependence of the luminescence is quadratic until it saturates for higher laser power. Studying the luminescence intensity as a function of layer thickness gives further insight into its nature and provides a new tool for substrate independent thickness determination of multilayer flakes

Lost and found dark matter in elliptical galaxies

The kinematical properties of elliptical galaxies formed during the mergers of equal mass, stars+gas+dark matter spiral galaxies are compared to the observed low velocity dispersions found for planetary nebulae on the outskirts of ellipticals, which have been interpreted as pointing to a lack of dark matter in ellipticals (which poses a problem for the standard model of galaxy formation). We find that the velocity dispersion profiles of the stars in the simulated ellipticals match well the observed ones. The low outer stellar velocity dispersions are mainly caused by the radial orbits of the outermost stars, which, for a given binding energy must have low angular momentum to reach their large radial distances, usually driven out along tidal tails.Comment: Talk presented at 21st IAP meeting, Mass Profiles andShapes of Cosmological Structures. Ed. G. A. Mamon, F. Combes, C. Deffayet & B. Fort (Paris: EDP), 4 pages, 3 figures (4 plots

The Hubble Legacy Archive NICMOS Grism Data

The Hubble Legacy Archive (HLA) aims to create calibrated science data from the Hubble Space Telescope archive and make them accessible via user-friendly and Virtual Observatory (VO) compatible interfaces. It is a collaboration between the Space Telescope Science Institute (STScI), the Canadian Astronomy Data Centre (CADC) and the Space Telescope - European Coordinating Facility (ST-ECF). Data produced by the Hubble Space Telescope (HST) instruments with slitless spectroscopy modes are among the most difficult to extract and exploit. As part of the HLA project, the ST-ECF aims to provide calibrated spectra for objects observed with these HST slitless modes. In this paper, we present the HLA NICMOS G141 grism spectra. We describe in detail the calibration, data reduction and spectrum extraction methods used to produce the extracted spectra. The quality of the extracted spectra and associated direct images is demonstrated through comparison with near-IR imaging catalogues and existing near-IR spectroscopy. The output data products and their associated metadata are publicly available through a web form at http://hla.stecf.org and via VO interfaces. In total, 2470 spectra of 1923 unique targets are included in the current release.Comment: 18 pages, 21 figures, accepted for publication in Astronomy & Astrophysic

A SILAC-based Approach Identifies Substrates of Caspase-dependent Cleavage upon TRAIL-induced Apoptosis

The extracellular ligand-induced extrinsic pathway of apoptosis is executed via caspase protease cascades that activate downstream effectors by means of site-directed proteolysis. Here we identify proteome changes upon the induction of apoptosis by the cytokine tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) in a Jurkat T cell line. We detected caspase-dependent cleavage substrates by quantifying protein intensities before and after TRAIL induction in SDS gel slices. Apoptotic protein cleavage events are identified by a characteristic stable isotope labeling with amino acids in cell culture (SILAC) ratio pattern across gel slices that results from differential migration of the cleaved and uncleaved proteins. We applied a statistical test to define apoptotic substrates in the proteome. Our approach identified more than 650 of these cleaved proteins in response to TRAIL-induced apoptosis, including many previously unknown substrates and cleavage sites. Inhibitor treatment combined with triple SILAC demonstrated that the detected cleavage events were caspase dependent. Proteins located in the lumina of organelles such as mitochondria and endoplasmic reticulum were significantly underrepresented in the substrate population. Interestingly, caspase cleavage is generally observed in not only one but several members of stable complexes, but often with lower stoichiometry. For instance, all five proteins of the condensin I complex were cleaved upon TRAIL treatment. The apoptotic substrate proteome data can be accessed and visualized in the MaxQB database and might prove useful for basic and clinical research into TRAIL-induced apoptosis. The technology described here is extensible to a wide range of other proteolytic cleavage events

Cyclic AMP Inhibits Secretion From Electroporated Human Neutrophils

It has long been known that Intracellular cAMP inhibits and cGMP enhances intact neutrophil function. However, these effects are modest and require relatively high concentrations of the cyclic nucleotides. We decided to re‐examine the effects of cyclic nucleotides on Ca2+‐induced secretion by electroporated cells. This system allowed us to bypass normal cell surface receptor‐ligand interactions as well as to directly expose the intracellular space to native cyclic nucleotides. We found that concentrations of cAMP as low as 3 μM inhibited Ca2+‐induced secretion; 30–300 μM cAMP was maximally inhibitory. cAMP was actually slightly more potent than dibutyryl cAMP, a membrane‐permeant derivative. In contrast, cGMP was only slightly stimulatory at 3 μM and modestly inhibitory at 300 μM; dibutyryl cGMP was ineffective. A more detailed investigation of the effects of cAMP showed that inhibition was only obtained in the presence of Mg2+. Half‐maximal inhibition by cAMP occurred at 10–30 μM. Inhibition by cAMP was achieved by shifting the Ca2+ dose‐response curve for secretion to the right; this was observed for the release of both specific granules (vitamin B12 binding protein) and azurophil granules (B‐glucuronidase). We previously showed that ATP could enhance Ca2+‐induced secretion in the presence of Mg2+, apparently by interacting with a cell surface purine receptor. However, increasing concentrations of ATP could not overcome inhibition by cAMP; this suggested that cAMP acted at some site other than the purine receptor. Inhibition by cAMP was also less apparent in the presence of the protein kinase C agonist phorbol myristate acetate (PMA), suggesting that the cyclic nucleotide did not produce systemic desensitization of the neutrophils. In summary, these results demonstrate that low, physiologically relevant concentrations of cAMP can modulate neutrophil responsiveness.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141578/1/jlb0172.pd

IPD—the Immuno Polymorphism Database

The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors; IPD-MHC, a database of sequences of the Major Histocompatibility Complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC share the same database structure. The sharing of a common database structure makes it easier to implement common tools for data submission and retrieval. The data are currently available online from the website and ftp directory; files will also be made available in different formats to download from the website and ftp server. The data will also be included in SRS, BLAST and FASTA search engines at the European Bioinformatics Institute