Phospho.ELM:a database of experimentally verified phosphorylation sites in eukaryotic proteins

BACKGROUND: Post-translational phosphorylation is one of the most common protein modifications. Phosphoserine, threonine and tyrosine residues play critical roles in the regulation of many cellular processes. The fast growing number of research reports on protein phosphorylation points to a general need for an accurate database dedicated to phosphorylation to provide easily retrievable information on phosphoproteins.DESCRIPTION: Phospho.ELM http://phospho.elm.eu.org is a new resource containing experimentally verified phosphorylation sites manually curated from the literature and is developed as part of the ELM (Eukaryotic Linear Motif) resource. Phospho.ELM constitutes the largest searchable collection of phosphorylation sites available to the research community. The Phospho.ELM entries store information about substrate proteins with the exact positions of residues known to be phosphorylated by cellular kinases. Additional annotation includes literature references, subcellular compartment, tissue distribution, and information about the signaling pathways involved as well as links to the molecular interaction database MINT. Phospho.ELM version 2.0 contains 1703 phosphorylation site instances for 556 phosphorylated proteins.CONCLUSION: Phospho.ELM will be a valuable tool both for molecular biologists working on protein phosphorylation sites and for bioinformaticians developing computational predictions on the specificity of phosphorylation reactions.</p

Cystathionine beta synthase deficiency and brain edema associated with methionine excess under betaine supplementation: Four new cases and a review of the evidence.

CBS deficient individuals undergoing betaine supplementation without sufficient dietary methionine restriction can develop severe hypermethioninemia and brain edema. Brain edema has also been observed in individuals with severe hypermethioninemia without concomitant betaine supplementation. We systematically evaluated reports from 11 published and 4 unpublished patients with CBS deficiency and from additional four cases of encephalopathy in association with elevated methionine. We conclude that, while betaine supplementation does greatly exacerbate methionine accumulation, the primary agent causing brain edema is methionine rather than betaine. Clinical signs of increased intracranial pressure have not been seen in patients with plasma methionine levels below 559 μmol/L but occurred in one patient whose levels did not knowingly exceed 972 μmol/L at the time of manifestation. While levels below 500 μmol/L can be deemed safe it appears that brain edema can develop with plasma methionine levels close to 1000 μmol/L. Patients with CBS deficiency on betaine supplementation need to be regularly monitored for concordance with their dietary plan and for plasma methionine concentrations. Recurrent methionine levels above 500 μmol/L should alert clinicians to check for clinical signs and symptoms of brain edema and review dietary methionine intake. Levels approaching 1000 μmol/L do increase the risk of complications and levels exceeding 1000 μmol/L, despite best dietetic efforts, should be acutely addressed by reducing the prescribed betaine dose

A moving grid finite element method applied to a model biological pattern generator

Many problems in biology involve growth. In numerical simulations it can therefore be very convenient to employ a moving computational grid on a continuously deforming domain. In this paper we present a novel application of the moving grid finite element method to compute solutions of reaction–diffusion systems in two-dimensional continuously deforming Euclidean domains. A numerical software package has been developed as a result of this research that is capable of solving generalised Turing models for morphogenesis

Organic complementary-like inverters employing methanofullerene-based ambipolar field-effect transistors

Published versio

The SLUGGS Survey: Calcium Triplet-based Spectroscopic Metallicities for Over 900 Globular Clusters

Although the colour distribution of globular clusters in massive galaxies is well known to be bimodal, the spectroscopic metallicity distribution has been measured in only a few galaxies. After redefining the calcium triplet index-metallicity relation, we use our relation to derive the metallicity of 903 globular clusters in 11 early-type galaxies. This is the largest sample of spectroscopic globular cluster metallicities yet assembled. We compare these metallicities with those derived from Lick indices finding good agreement. In 6 of the 8 galaxies with sufficient numbers of high quality spectra we find bimodality in the spectroscopic metallicity distribution. Our results imply that most massive early-type galaxies have bimodal metallicity, as well as colour, distributions. This bimodality suggests that most massive galaxies early-type galaxies experienced two periods of star formation.Comment: 23 pages, 13 figures. Accepted for publication in MNRAS. For more information about the SLUGGS Survey please see http://sluggs.swin.edu.a

Cystathionine beta synthase deficiency and brain edema associated with methionine excess under betaine supplementation: Four new cases and a review of the evidence

CBS deficient individuals undergoing betaine supplementation without sufficient dietary methionine restriction can develop severe hypermethioninemia and brain edema. Brain edema has also been observed in individuals with severe hypermethioninemia without concomitant betaine supplementation. We systematically evaluated reports from 11 published and 4 unpublished patients with CBS deficiency and from additional four cases of encephalopathy in association with elevated methionine. We conclude that, while betaine supplementation does greatly exacerbate methionine accumulation, the primary agent causing brain edema is methionine rather than betain

Multibaryons with heavy flavors in the Skyrme model

We investigate the possible existence of multibaryons with heavy flavor quantum numbers using the bound state approach to the topological soliton model and the recently proposed approximation for multiskyrmion fields based on rational maps. We use an effective interaction lagrangian which consistently incorporates both chiral symmetry and the heavy quark symmetry including the corrections up to order 1/m_Q. The model predicts some narrow heavy flavored multibaryon states with baryon number four and seven.Comment: 8 pages, no figures, RevTe

Multibaryons as Symmetric Multiskyrmions

We study non-adiabatic corrections to multibaryon systems within the bound state approach to the SU(3) Skyrme model. We use approximate ansatze for the static background fields based on rational maps which have the same symmetries of the exact solutions. To determine the explicit form of the collective Hamiltonians and wave functions we only make use of these symmetries. Thus, the expressions obtained are also valid in the exact case. On the other hand, the inertia parameters and hyperfine splitting constants we calculate do depend on the detailed form of the ansatze and are, therefore, approximate. Using these values we compute the low lying spectra of multibaryons with B <= 9 and strangeness 0, -1 and -B. Finally, we show that the non-adiabatic corrections do not affect the stability of the tetralambda and heptalambda found in a previous work.Comment: 17 pages, RevTeX, no figure