Data and Activity Representation for Grid Computing

Computational grids are becoming increasingly popular as an infrastructure for computa- tional science research. The demand for high-level tools and problem solving environments has prompted active research in Grid Computing Environments (GCEs). Many GCEs have been one-o development eorts. More recently, there have been many eorts to dene component ar- chitectures for constructing important pieces of a GCE. This paper examines another approach, based on a `data-centric' framework for building powerful, context-aware GCEs spanning mul- tiple layers of abstraction. We describe a scheme for representing data and activities in a GCE and outline various tools under development which use this representation

The Virginia Tech Computational Grid: A Research Agenda

An important goal of grid computing is to apply the rapidly expanding power of distributed computing resources to large-scale multidisciplinary scientic problem solving. Developing a usable computational grid for Virginia Tech is desirable from many perspectives. It leverages distinctive strengths of the university, can help meet the research computing needs of users with the highest demands, and will generate many challenging computer science research questions. By deploying a campus-wide grid and demonstrating its effectiveness for real applications, the Grid Computing Research Group hopes to gain valuable experience and contribute to the grid computing community. This report describes the needs and advantages which characterize the Virginia Tech context with respect to grid computing, and summarizes several current research projects which will meet those needs

Interaction of G-Protein beta gamma Complex with Chromatin Modulates GPCR-Dependent Gene Regulation

Heterotrimeric G-protein signal transduction initiated by G-protein-coupled receptors (GPCRs) in the plasma membrane is thought to propagate through protein-protein interactions of subunits, G alpha and G beta gamma in the cytosol. In this study, we show novel nuclear functions of G beta gamma through demonstrating interaction of G beta(2) with integral components of chromatin and effects of G beta(2) depletion on global gene expression. Agonist activation of several GPCRs including the angiotensin II type 1 receptor specifically augmented G beta(2) levels in the nucleus and G beta(2) interacted with specific nucleosome core histones and transcriptional modulators. Depletion of G beta(2) repressed the basal and angiotensin II-dependent transcriptional activities of myocyte enhancer factor 2. G beta(2) interacted with a sequence motif that was present in several transcription factors, whose genome-wide binding accounted for the G beta(2)-dependent regulation of approximately 2% genes. These findings suggest a wide-ranging mechanism by which direct interaction of G beta gamma with specific chromatin bound transcription factors regulates functional gene networks in response to GPCR activation in cells

Correction: Interaction of G-Protein βγ Complex with Chromatin Modulates GPCR-Dependent Gene Regulation

<p>Correction: Interaction of G-Protein βγ Complex with Chromatin Modulates GPCR-Dependent Gene Regulation</p

3-D model of the proposed Gβ₂ interaction with MEF2A and histone H4.

<p>(a) Multiple sequence alignment using the CLUSTAL W program revealed that the phosphopeptide motif (–LLpTPPG–) was conserved in the TFs that associated with Gβ₂ (MEF2A, STAT1, STAT3 and NFAT), but not in NFκB and GATA4. (b) Surface model of Gβ₂γ₁₂ based on Gβ₁γ₂ crystal coordinates. Gβ₂γ₁₂ is shown in gray, and the common site of interaction with cytoplasmic effectors (Gα and PLCβ) is shown in teal. The –LLpTPPG– peptide (shown as red ball and stick) anchors to the central core of the β-propeller structure and makes contact with the amino acid residues shown in green and purple. The purple side chains contacting the peptide are conserved charge interactions. The histone H4 tail peptide, shown in brown, may interact on the surface of the WD7 repeat. (c) Co-immunoprecipitation of Gβ₂ with the AngII-responsive TFs, NFAT, STAT1, and STAT3, but not with GATA4 and p65 NFκB. The nuclear fractions (100 µg) prepared from HEK-AT₁R cells treated with AngII (1 µM for 30 min) were subjected to pull-down with only ProtG (−) or with a Gβ₂ antibody and ProtG (+). The immunoblot on the right shows the abundance of the respective proteins in the immunoprecipitates (− and +) and input lysates for the − and + samples. (d) Gβ₂ interaction with selective AngII-responsive TFs, suggesting a role for Gβ₂ in genome wide transcription that eventually leads to changes in cellular functions.</p

Abundance of the G-protein β₂ subunit in the nucleus.

<p>(a) Mass spectrometry evidence for the differential nuclear translocation of Gβ₂. The Gβ₂-specific tryptic peptide (LLVSASQDGK) was monitored in control and AngII treated samples. The right hand corner in each panel gives identity of peptide by m/z ratio and the 100% abundance value of the peptide in that chromatogram. In the chromatogram shown, m/z ratio 509.5–511.5 identified the Gβ₂ peptide and the 100% abundance value of 1.3E6 after AngII treatment is 2.47-fold higher when compared to the 100% abundance value 5.5E5 of the control. Applying the same calculation, change in abundance of spiked-in control trypsin peptide, m/z 421.0–423 was 0.79. The actual fold change of Gβ₂ peptide was calculated, 2.47/0.79 = 3.13 in this chromatogram. (b) An increase in Gβ₂ in the nuclear fraction upon exposure of HASM cells to various prohypertrophic agonists (1 µM AngII for AT₁R, 1 µM 5-HT for 5-HT2AR; 10 µM isoproterenol for βAR and 1 µM dobutamine for β1AR). Nuclear fractions were immunoblotted for Gβ₂ and histone H1 as loading controls. See schematic for the relative levels of Gβ₂ in the nuclei of samples treated with various agonists compared with the untreated (UT) control.</p

Gβ₂-dependent global gene expression patterns.

<p>Altered gene expression patterns and gene networks that engage common biological processes are shown. Of the >47,000 transcripts monitored, 705 unique and annotated transcripts (2% of the transcriptome) were differentially affected by AngII stimulation in the Gβ₂i cells (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052689#pone.0052689.s016" target="_blank">Table S5</a>). Out of these, 299 transcripts were identical to the transcripts in the Gβ₂Sc control, indicating that these transcripts were regulated by Gβ₂-independent signals from AT₁R, and the remaining ≈400 transcripts were specifically regulated by Gβ₂. The false discovery rate was <3%. (a) Venn diagram: a total of 800 genes were modulated in Gβ₂Sc cells, and 705 genes were modulated upon Gβ₂ knockdown (Gβ₂i) in AT₁R-expressing cells treated with AngII (1 µM for 30 min). (b) The altered cell functions upon Gβ₂ knockdown. (c) The hierarchy of gene functions, Δ<i>p</i>-value, number of molecules involved and genes regulated by the Gβ₂-interacting TFs, MEF2A, NFAT, and STAT1/STAT3 (derived from the ‘Build Networks – Expand by one group interaction’ algorithm in MetaCore™). Shown in green are down regulated genes, in red are up regulated genes in an independent experiment. Additional promoter information is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052689#pone.0052689.s013" target="_blank">Table S2</a>.</p

Agonist-activated nuclear translocation of Gβ₂ in intact cells.

<p>(a) The HEK-AT₁R, HASM and NRVM cells were treated with vehicle or 1 µM AngII for 30 min and fixed. Gβ₂ is shown in green. The nucleus (blue, stained with DAPI) shows green staining that corresponds to Gβ₂ in the nuclei. (b) Post-isolation viability and AngII response as assessed by calcium signals in AMVMs. The AMVMs that were paced at a frequency of 0.5 Hz displayed steady-state [Ca²⁺]_i transient signals. When AMVM pacing was stopped, the [Ca²⁺]_i signals ceased, and upon treatment with 1 µM AngII, the [Ca²⁺]_i signal resumed. (c) Beating AMVMs were treated with vehicle or 1 µM AngII for 30 min and fixed. α-Actinin-1 was labeled red and Gβ was labeled green. The far right-hand inset shows a magnified image (1000×) of a single nucleus. The nucleus displays green staining that corresponds to Gβ. Note: α-actinin-1 is a sarcomeric marker and does not translocate to the nucleus. (d) 3-D reconstruction of a mouse cardiac myocyte nucleus (confocal microscopy image). Green fluorescence represents Gβ₂, and blue represents DAPI staining. The top panel shows the localization of Gβ₂ (in Z-plane) from the top to the bottom of the myocyte nucleus. The lower panel shows an intact AMVM nucleus and a slice through the nuclear image that depicts a significant accumulation of Gβ₂ inside the nucleus of the AMVM cell upon AngII/AT₁R activation. Note: all images were acquired using a 63× objective (1.4 N.A.) at 0.232 µM/pixel in the plane resolution and 0.041 µM/pixel in the Z-axis resolution. The confocal image is a representative image of N = 3, and in each experiment, >50 cells were scored. Scale bars = 50 µm.</p