991 research outputs found

    Clustering of resting state networks

    Get PDF
    BACKGROUND: The goal of the study was to demonstrate a hierarchical structure of resting state activity in the healthy brain using a data-driven clustering algorithm. METHODOLOGY/PRINCIPAL FINDINGS: The fuzzy-c-means clustering algorithm was applied to resting state fMRI data in cortical and subcortical gray matter from two groups acquired separately, one of 17 healthy individuals and the second of 21 healthy individuals. Different numbers of clusters and different starting conditions were used. A cluster dispersion measure determined the optimal numbers of clusters. An inner product metric provided a measure of similarity between different clusters. The two cluster result found the task-negative and task-positive systems. The cluster dispersion measure was minimized with seven and eleven clusters. Each of the clusters in the seven and eleven cluster result was associated with either the task-negative or task-positive system. Applying the algorithm to find seven clusters recovered previously described resting state networks, including the default mode network, frontoparietal control network, ventral and dorsal attention networks, somatomotor, visual, and language networks. The language and ventral attention networks had significant subcortical involvement. This parcellation was consistently found in a large majority of algorithm runs under different conditions and was robust to different methods of initialization. CONCLUSIONS/SIGNIFICANCE: The clustering of resting state activity using different optimal numbers of clusters identified resting state networks comparable to previously obtained results. This work reinforces the observation that resting state networks are hierarchically organized

    Three-dimensional structure of the weakly associated protein homodimer SeR13 using RDCs and paramagnetic surface mapping

    Get PDF
    The traditional NMR-based method for determining oligomeric protein structure usually involves distinguishing and assigning intra- and intersubunit NOEs. This task becomes challenging when determining symmetric homo-dimer structures because NOE cross-peaks from a given pair of protons occur at the same position whether intra- or intersubunit in origin. While there are isotope-filtering strategies for distinguishing intra from intermolecular NOE interactions in these cases, they are laborious and often prove ineffectual in cases of weak dimers, where observation of intermolecular NOEs is rare. Here, we present an efficient procedure for weak dimer structure determination based on residual dipolar couplings (RDCs), chemical shift changes upon dilution, and paramagnetic surface perturbations. This procedure is applied to the Northeast Structural Genomics Consortium protein target, SeR13, a negatively charged Staphylococcus epidermidis dimeric protein (Kd 3.4 ± 1.4 mM) composed of 86 amino acids. A structure determination for the monomeric form using traditional NMR methods is presented, followed by a dimer structure determination using docking under orientation constraints from RDCs data, and scoring under residue pair potentials and shape-based predictions of RDCs. Validation using paramagnetic surface perturbation and chemical shift perturbation data acquired on sample dilution is also presented. The general utility of the dimer structure determination procedure and the possible relevance of SeR13 dimer formation are discussed. Published by Wiley-Blackwell. © 2010 The Protein Society

    Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics.

    Get PDF
    Novel metabolites distinct from canonical pathways can be identified through the integration of three cheminformatics tools: BinVestigate, which queries the BinBase gas chromatography-mass spectrometry (GC-MS) metabolome database to match unknowns with biological metadata across over 110,000 samples; MS-DIAL 2.0, a software tool for chromatographic deconvolution of high-resolution GC-MS or liquid chromatography-mass spectrometry (LC-MS); and MS-FINDER 2.0, a structure-elucidation program that uses a combination of 14 metabolome databases in addition to an enzyme promiscuity library. We showcase our workflow by annotating N-methyl-uridine monophosphate (UMP), lysomonogalactosyl-monopalmitin, N-methylalanine, and two propofol derivatives

    Star formation rates in Lyman break galaxies: radio stacking of LBGs in the COSMOS field and the sub-μ\muJy radio source population

    Get PDF
    We present an analysis of the radio properties of large samples of Lyman Break Galaxies (LBGs) at z3z \sim 3, 4, and 5 from the COSMOS field. The median stacking analysis yields a statistical detection of the z3z \sim 3 LBGs (U-band drop-outs), with a 1.4 GHz flux density of 0.90±0.21μ0.90 \pm 0.21 \muJy. The stacked emission is unresolved, with a size <1"< 1", or a physical size <8< 8kpc. The total star formation rate implied by this radio luminosity is 31±731\pm 7 MM_\odot year1^{-1}, based on the radio-FIR correlation in low redshift star forming galaxies. The star formation rate derived from a similar analysis of the UV luminosities is 17 MM_\odot year1^{-1}, without any correction for UV dust attenuation. The simplest conclusion is that the dust attenuation factor is 1.8 at UV wavelengths. However, this factor is considerably smaller than the standard attenuation factor 5\sim 5, normally assumed for LBGs. We discuss potential reasons for this discrepancy, including the possibility that the dust attenuation factor at z3z \ge 3 is smaller than at lower redshifts. Conversely, the radio luminosity for a given star formation rate may be systematically lower at very high redshift. Two possible causes for a suppressed radio luminosity are: (i) increased inverse Compton cooling of the relativistic electron population due to scattering off the increasing CMB at high redshift, or (ii) cosmic ray diffusion from systematically smaller galaxies. The radio detections of individual sources are consistent with a radio-loud AGN fraction of 0.3%. One source is identified as a very dusty, extreme starburst galaxy (a 'submm galaxy').Comment: 15 pages, 2 figures AASTEX, to appear in Ap

    Engineering Thermostability in Artificial Metalloenzymes to Increase Catalytic Activity

    Get PDF
    Protein engineering has shown widespread use in improving the industrial application of enzymes and broadening the conditions they are able to operate under by increasing their thermostability and solvent tolerance. Here, we show that protein engineering can be used to increase the thermostability of an artificial metalloenzyme. Thermostable variants of the human steroid carrier protein 2L, modified to bind a metal catalyst, were created by rational design using structural data and a 3DM database. These variants were tested to identify mutations that enhanced the stability of the protein scaffold, and a significant increase in melting temperature was observed with a number of modified metalloenzymes. The ability to withstand higher reaction temperatures resulted in an increased activity in the hydroformylation of 1-octene, with more than fivefold improvement in turnover number, whereas the selectivity for linear aldehyde remained high up to 80%
    corecore