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

Development and application of gene mapping approaches, towards an integrated physical, radiation-hybrid and comparative map of dog chromosome five

Efforts to generate a genome map for the domestic dog (Canis familiaris, CFA) have to date largely focussed on the isolation and characterisation of anonymous markers. This study was aimed at the development and application of techniques by which gene markers might be added to the map and integrated with data both from other approaches and from the genomes of other species. This is essential for the continuing use of the dog as a model system for the study of inherited traits. The generation of expressed sequence tags (partial cDNA sequences) was investigated as a route for achieving this aim. Seventeen of 76 cDNA clones analysed shared significant nucleotide similarity with previously annotated gene sequences from other species, forming a panel of resources for the extension of the existing dog gene map. Two gene markers were assigned to a specific dog chromosome by fluorescence in situ hybridisation. In a contrasting approach, reciprocal chromosome painting analysis was used to identify evolutionarily conserved chromosome segments (ECCS) between dog chromosome five (CFA 5) and human chromosomes 1, 11, 16 and 17. The boundaries between ECCS, and their relative orientation in the two genomes, were investigated by the assignment to CFA 5 of 12 genes selected from loci located at proximal and distal extremes of the corresponding human ECCS. Radiation hybrid mapping was performed for eleven gene markers and ten anonymous markers from CFA 5. One marker of each type was also analysed by meiotic linkage analysis. An integrated physical, radiation-hybrid and comparative map of CFA 5 is presented, and the relative merits of the mapping techniques investigated are discussed with reference to future prospects for the dog gene map

Structure-Based Design of a B Cell Antigen from <i>B. pseudomallei</i>

<i>Burkholderia pseudomallei</i> is the etiological agent of melioidosis, a severe endemic disease in South-East Asia, causing septicemia and organ failure with high mortality rates. Current treatments and diagnostic approaches are largely ineffective. The development of new diagnostic tools and vaccines toward effective therapeutic opportunities against <i>B. pseudomallei</i> is therefore an urgent priority. In the framework of a multidisciplinary project tackling melioidosis through reverse and structural vaccinology, BPSL1050 was identified as a candidate for immunodiagnostic and vaccine development based on its reactivity against the sera of melioidosis patients. We determined its NMR solution structure and dynamics, and by novel computational methods we predicted immunogenic epitopes that once synthesized were able to elicit the production of antibodies inducing the agglutination of the bacterium and recognizing both BPSL1050 and <i>B. pseudomallei</i> crude extracts. Overall, these results hold promise for novel chemical biology approaches in the discovery of new diagnostic and prophylactic tools against melioidosis

List of significantly associated haplotypes.

<p>List of significantly associated haplotypes.</p

Differentially expressed genes by the risk alleles at 29 Mb and 33 Mb play important role in T-cell immunity.

<p>A. The risk allele at the 29 Mb at homozygous state has a clear cis-regulation effect on the expression levels of <i>TRPC6</i>, <i>KIAA1377</i>, and <i>ANGPTL5</i>, three of the most proximal genes. <i>BIRC3</i>, which is also proximal to the 29 Mb risk locus, had a significant p-value, however the FDR value was slightly above the threshold of 0.05. The risk allele at 29 Mb was also associated with a regulatory effect on genes near the 33 Mb locus and a change in the expression of <i>PIK3R6</i> significantly. B. A large network of molecules that play a major role in activation of T-lymphocyte and other immune cells (IPA category: cell-to-cell signaling and interaction, hematological system development and function). This network includes 15 molecules of which expressions are significantly altered in individuals carrying at least one copy of the shared risk allele at the 33 Mb locus. The outcomes of such expression changes are significantly linked to decrease in T-cell activation.</p

Top 10 differentially expressed genes by the risk haplotype at each locus.

<p>Top 10 differentially expressed genes by the risk haplotype at each locus.</p

Two neighboring loci on chromosome 5 are independently associated with disease risk.

<p>A. The top SNP of the first peak (29 Mb) is in high LD with nearby variants and shows no evidence of linkage to the top SNPs in the second peak (33 Mb). B. The 29 Mb peak is comprised of two haplotype blocks, and C. the risk haplotypes for the 29 Mb peak are rather common in the population. Similarly, D. the second peak also shows no linkage with the first peak in the combined analysis, whereas E. analysis of only B-cell lymphoma shows SNPs in strong LD within the second peak and in moderate LD with SNPs in the first peak. The top SNPs in the combined analysis and B-cell-lymphoma-only analysis are independent, and F. make up separate haplotypes at the second locus. G. Both risk haplotypes at the second locus are rare. Color-coding of SNPs in A, D, E, reflects their r² value relative the top SNP of that region, ranging from grey (not in LD) to red (strong LD).</p