Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.).

Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size ('size shifts'), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.

Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease

We performed a meta-analysis of 14 genome-wide association studies of coronary artery disease (CAD) comprising 22,233 individuals with CAD (cases) and 64,762 controls of European descent followed by genotyping of top association signals in 56,682 additional individuals. This analysis identified 13 loci newly associated with CAD at P < 5 x 10(-8) and confirmed the association of 10 of 12 previously reported CAD loci. The 13 new loci showed risk allele frequencies ranging from 0.13 to 0.91 and were associated with a 6% to 17% increase in the risk of CAD per allele. Notably, only three of the new loci showed significant association with traditional CAD risk factors and the majority lie in gene regions not previously implicated in the pathogenesis of CAD. Finally, five of the new CAD risk loci appear to have pleiotropic effects, showing strong association with various other human diseases or traits.

Two-dimensional particle-in-cell simulation of the expansion of a plasma into a rarefied medium

The expansion of a dense plasma through a more rarefied ionized medium has been studied by means of two-dimensional particle-in-cell simulations. The initial conditions involve a density jump by a factor of 100, located in the middle of an otherwise equally dense electron-proton plasma with uniform proton and electron temperatures of 10 eV and 1 keV, respectively. Simulations show the creation of a purely electrostatic collisionless shock together with an ion-acoustic soliton tied to its downstream region. The shock front is seen to evolve in filamentary structures consistently with the onset of the ion-ion instability. Meanwhile, an un-magnetized drift instability is triggered in the core part of the dense plasma. Such results explain recent experimental laser-plasma experiments, carried out in similar conditions, and are of intrinsic relevance to non-relativistic shock scenarios in the solar and astrophysical systems.

Skills, Conflict and Spatial Planning in Northern Ireland

The skills to manage sustainable and cohesive communities have placed a particular emphasis on collaborative and consensual methods of working. This paper suggests that in ethnically divided places, the notion of collaboration is largely conceptual and that more agonistic strategies provide a sounder basis for marginal communities to advance their claims and rights. Specifically, it draws on research conducted in Northern Ireland to suggest that situated approaches to territorial competition can place learning, the sharing of knowledge, and the transformation of conflict at the heart of the skills debate.

Identification of a methylation hotspot in the death receptor Fas/CD95 in bladder cancer

We characterized Fas immunoreactivity, functionality and its role in the response to mitomycin-C (MMC) chemotherapy in vitro in cell lines and in vivo in bladder washings from 23 transitional cell carcinoma of the bladder (TCCB) patients, harvested prior to and during MMC intravesical treatment. Having established the importance of functional Fas, we investigated the methylation and exon 9 mutation as mechanisms of Fas silencing in TCCB. For the first time, we report p53 up-regulation in 9/14 and Fas up-regulation in 7/9 TCCB patients during intravesical MMC treatment. Fas immunoreactivity was strong in the TCCB cell line T24 and in 17/20 (85%) tumor samples from patients with advanced TCCB. T24 and HT1376 cells were resistant to MMC and recombinant Fas ligand, whilst RT4 cells were responsive to Fas ligand and MMC. Using RT4 cells as a model, siRNA targeting p53 significantly reduced MMC-induced p53 and Fas up-regulation and stable DN-FADD transfection decreased MMC-induced apoptosis, suggesting that functional Fas enhances chemotherapy responses in a p53-dependent manner. In HT1376 cells, 5-aza-2-deoxycytidine (12 µM) induced Fas immunoreactivity and reversed methylation at CpG site -548 within the Fas promoter. This site was methylated in 13/24 (54%) TCCB patient samples assessed using Methylation-Specific Polymerase Chain Reaction. There was no methylation at either the p53 enhancer region within the first intron or at the SP-1 binding region in the promoter and no mutation within exon 9 in tumor DNA extracted from 38 patients. Methylation at CpG site -548 is a potential target for demethylating drugs.

The impact of biomarkers in multivariate algorithms for bladder cancer diagnosis in patients with hematuria

BACKGROUND: We appraised 23 biomarkers previously associated with urothelial cancer in a case-control study. Our aim was to determine whether single biomarkers and/or multivariate algorithms significantly improved on the predictive power of an algorithm based on demographics for prediction of urothelial cancer in patients presenting with hematuria. METHODS: Twenty-two biomarkers in urine and carcinoembryonic antigen (CEA) in serum were evaluated using enzyme-linked immunosorbent assays (ELISAs) and biochip array technology in 2 patient cohorts: 80 patients with urothelial cancer, and 77 controls with confounding pathologies. We used Forward Wald binary logistic regression analyses to create algorithms based on demographic variables designated prior predicted probability (PPP) and multivariate algorithms, which included PPP as a single variable. Areas under the curve (AUC) were determined after receiver-operator characteristic (ROC) analysis for single biomarkers and algorithms. RESULTS: After univariate analysis, 9 biomarkers were differentially expressed (t test; P

Apoptosis and chemotherapy in bladder cancer in bladder cancer

Purpose: To discuss the role of apoptosis, gene directed self-destruction of a cell, in the response of transitional cell carcinoma of the bladder cells to chemotherapy. Methods: A directed MEDLINE literature search of apoptosis, bladder cancer and chemotherapy was performed to extract the relevant information, which was reviewed. The characteristics of apoptotic cells were defined and the methods in common use to detect these traits were described. The role of the key mediators of the apoptotic process in bladder cancer is discussed in the context of chemosensitivity and stage of disease. The importance of induction of apoptosis post chemotherapy is highlighted. Results: On stimulus by appropriate external or internal signals, a cell may alter the expression of genes coding for proteins associated with the apoptotic process. The development of apoptosis depends on the balance between pro- and anti- apoptotic proteins. Key alterations in genes and proteins related to apoptosis within bladder cancer result in a shift away from an ability to undergo apoptosis towards a cell with increased survival properties that is chemoresistant. Conclusions: Much current research in bladder cancer is aimed at restoring chemosensitivity by shifting the balance in a cell towards a pro-apoptotic phenotype. Successful translation of this work into clinical practice may improve survival in patients in whom prognosis is currently poor.