Quark-gluon vertex in general kinematics

The original publication can be found at www.springerlink.com Submitted to Cornell University’s online archive www.arXiv.org in 2007 by Jon-Ivar Skullerud. Post-print sourced from www.arxiv.org.We compute the quark–gluon vertex in quenched lattice QCD in the Landau gauge, using an off-shell mean-field O(a)-improved fermion action. The Dirac-vector part of the vertex is computed for arbitrary kinematics. We find a substantial infrared enhancement of the interaction strength regardless of the kinematics.Ayse Kizilersu, Derek B. Leinweber, Jon-Ivar Skullerud and Anthony G. William

<i>MYC</i> and <i>PVT1</i> synergize to regulate RSPO1 levels in breast cancer

<p>Copy number gain of the 8q24 region including the v-myc avian myelocytomatosis viral oncogene homolog (<i>MYC)</i> oncogene has been observed in many different cancers and is associated with poor outcomes. While the role of <i>MYC</i> in tumor formation has been clearly delineated, we have recently shown that co-operation between adjacent long non-coding RNA plasmacytoma variant transcription 1 (<i>PVT1)</i> and <i>MYC</i> is necessary for tumor promotion. Chromosome engineered mice containing an increased copy of <i>Myc-Pvt1</i> (Gain <i>Myc-Pvt1</i>) accelerates mammary tumors in <i>MMTV-Neu</i> mice, while single copy increase of each is not sufficient. In addition, mammary epithelium from the Gain <i>Myc-Pvt1</i> mouse show precancerous phenotypes, notably increased DNA replication, elevated -<i>H2AX</i> phosphorylation and increased ductal branching. In an attempt to capture the molecular signatures in pre-cancerous cells we utilized RNA sequencing to identify potential targets of supernumerary <i>Myc-Pvt1</i> cooperation in mammary epithelial cells. In this extra view we show that an extra copy of both <i>Myc</i> and <i>Pvt1</i> leads to increased levels of <i>Rspo1</i>, a crucial regulator of canonical β-catenin signaling required for female development. Human breast cancer tumors with high levels of <i>MYC</i> transcript have significantly more <i>PVT1</i> transcript and <i>RSPO1</i> transcript than tumors with low levels of MYC showing that the murine results are relevant to a subset of human tumors. Thus, this work identifies a key mechanism in precancerous and cancerous tissue by which a main player in female differentiation is transcriptionally activated by supernumerary <i>MYC</i> and <i>PVT1</i>, leading to increased premalignant features, and ultimately to tumor formation.</p

List of differentially expressed genes in 5-AzadC and 4-PBA treated Saos2 cells.

<p>List of differentially expressed genes in 5-AzadC and 4-PBA treated Saos2 cells.</p

Combinatorial Treatment of DNA and Chromatin-Modifying Drugs Cause Cell Death in Human and Canine Osteosarcoma Cell Lines

<div><p>Downregulation of microRNAs (miRNAs) at the 14q32 locus stabilizes the expression of cMYC, thus significantly contributing to osteosarcoma (OS) pathobiology. Here, we show that downregulation of 14q32 miRNAs is epigenetically regulated. The predicted promoter regions of miRNA clusters at 14q32 locus showed no recurrent patterns of differential methylation, but Saos2 cells showed elevated histone deacetylase (HDAC) activity. Treatment with 4-phenylbutyrate increased acetylation of histones associated with 14q32 miRNAs, but interestingly, robust restoration of 14q32 miRNA expression, attenuation of cMYC expression, and induction of apoptosis required concomitant treatment with 5-Azacytidine, an inhibitor of DNA methylation. These events were associated with genome-wide gene expression changes including induction of pro-apoptotic genes and downregulation of cell cycle genes. Comparable effects were achieved in human and canine OS cells using the HDAC inhibitor suberoylanilide hydroxamic acid (SAHA/Vorinostat) and the DNA methylation inhibitor Zebularine (Zeb), with significantly more pronounced cytotoxicity in cells whose molecular phenotypes were indicative of aggressive biological behavior. These results suggested that the combination of these chromatin-modifying drugs may be a useful adjuvant in the treatment of rapidly progressive OS.</p> </div

Genome-wide gene expression changes induced by treatment of 5-AzadC and 4-PBA in Saos2 cells.

<p>mRNA expression patterns in Saos2 cells treated with 3.0 µM 5-AzadC and 3.0 mM 4-PBA relative to sham treated Saos2 cells. mRNA expression profiles in normal bone (n = 4) and OS patient samples (n = 13) were used for comparison and shown relative to normal bone. The heatmap with gene names are detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043720#pone.0043720.s002" target="_blank">Figure S2</a>.</p

COmbined Bisuifite Restriction Analysis (COBRA) for CpG regions upstream of miR-127, -411, -431 and -432 in OS and normal bone tissue samples.

<p>The following enzymes were used as indicated (B-<i>Bst</i> UI; H-<i>Hpy</i> CH4IV; T-<i>Taq</i> I; N- no enzyme). Bisulfite conversion of methylated CpGs created new restriction sites and the level of digestion of the bisulfite converted PCR product with listed enzymes was directly related to its intrinsic methylation, hence indicative of level of DNA methylation. As a reference for normal DNA methylation status, identical analysis for each region was performed with DNA from normal bone tissues. Relative difference in the digestion insensitivity of the PCR product (marked by arrow) in OS patients relative to normal bone tissue was indicative of similar or relative hypomethylation of these loci in OS patients.</p

5-AzadC and 4-PBA induce apoptosis in Saos2 cells.

<p><b>A</b>) Cells treated with 5-AzadC and 4-PBA alone or in combination along with sham and untreated cells were subjected to western blot analysis using anti-cMYC antibody. The blot was stripped and re-probed with anti-GAPDH antibody. Signal intensity was measured by densitometry analysis using image J software. cMYC/GAPDH ratio of sham treated cells was considered as unity and relative cMYC/GAPDH ratios were calculated (plotted on the top of the blot). The results show that treatment of Saos2 cells with 5-AzadC and 4-PBA decreased endogenous cMYC levels. <b>B</b>) Cells were treated with 5-AzadC and 4-PBA at concentrations of i) 0 µM & 0 mM; ii) 0 µM & 3 mM; iii) 1.5 µM & 1.5 mM; iv) 1.5 µM & 3 mM; v) 3 µM & 1.5 mM; vi) 3 µM & 0 mM; and vii) 3 µM & 3 mM, respectively. Green and red color staining represents live and dead cells, respectively. <b>C</b>) FACS analysis of cells treated with 5-AzadC and 4-PBA at various dose combinations led to apoptosis (% given in parenthesis). FACS analysis of cells treated with 5-AzadC and 4-PBA together with Z-VAD-fmk, which led to a significant reduction in the apoptosis of treated cells shown on the right panel. <b>D</b>) Cytotoxicty assay in 5-Aza and 4-PBA treated Saos2 cells with untreated (control) and sham treated (0/0) controls. Maximum LDH release from equal number of sham treated cells grown under identical condition is shown as positive control.</p

SAHA and Zeb show additive cytotoxicity in human and in canine OS cells with aggressive biological behavior.

<p><b>A</b>) Human Saos2 and U2OS cells were cultured in the presence of SAHA and Zeb at the indicated concentrations at 48 hr. Cell viability was measured at 48 hrs using the MTS assay. Data are normalized hence100% viability reflects the number of cells present in control cultures (treated with vehicle only). <b>B</b>) Canine OSCA-40, OSCA-78, and OSCA-32 cells were cultured in the presence of SAHA and Zeb at the indicated concentrations and cell viability was measured as in panel A. Data show means ± SD for three independent experiments, performed in triplicates. Data for each condition were normally distributed with <15% intra- and inter-experimental variation from the mean. Conditions that were significantly different from control by paired Student's t-test are denoted by asterisks (* p≤0.05; ** p≤0.01).</p

5-AzadC and 4-PBA activates 14q32 miRNAs expression and destabilize cMYC in Saos2 cells.

<p><b>A</b>) 5-AzadC and 4-PBA treated Saos2 cells were subjected to western blot analysis with Anti-acetylated histone-H3 antibody; and GAPDH is shown as control. Note an increase in the level of acetylated Histone-H3 in the treated cells. <b>B</b>) 5-AzadC and 4-PBA significantly increased the acetylation of histone-H3 of representative 14q32 miRNA upstream regions (−200 bp); *p values <0.005. <b>C</b>) Quantitative RT-PCR analysis of 14q32 miRNAs following the treatments with 3 µM 5-AzadC and 3 mM 4-PBA. Saos2 cells were treated with 3.0 µM 5-AzadC and 3.0 mM 4-PBA for 6 days, unless otherwise mentioned.</p

Kaplan Meier Survival Curve showing decreased survival in triple transgenic experimental animals compared to double transgenic controls.

<p>Significance determined using Logrank test.</p