Mutational hotspot in Exon 20 of PIK3CA in breast cancer among Singapore Chinese

The recent identification of somatic mutations in the catalytic region of PIK3 (PIK3CA) in breast cancer and demonstration of their oncogenic function has implicated PIK3CA in mammary carcinogenesis. To investigate possible ethnic differences in patterns of PIK3CA mutations in Singaporean Chinese breast cancer and to characterize these in a panel of cell lines, we sequenced exons 9 and 20 in 80 primary tumors, 19 breast cancer cell lines and 7 normal human mammary epithelial cells (HMECs). Searching for novel hotspots of mutation, we sequenced additional exons ( 1, 2, 6, 7, 14 and 18) in 20 primary tumors and 6 breast cancer cell lines. We detected 33 point mutations in 31 of 80 (39%) breast cancers, and 11 mutations in 10 of 19 (53%) breast cancer cell lines. No mutations were detected in normal breast tissue adjacent to the tumor, or in the 6 normal HMECs. The exon 20 A3140G (H1047R) substitution was identified most frequently (22/31, 71%) and showed a significant association with patient age ( p = 0.043) and stage of the disease ( p = 0.025), but not with ER/PR status or histological grade of the tumor. The incidence of point mutations in PIK3CA, the A3140G substitution in particular, in Singapore breast cancers are among the most frequent reported to date for any gene in breast cancer. The results suggest that mutation of PIK3CA might contribute to development of early stage breast cancer and could provide a potent target for early diagnosis and therapy.

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.

Modelling distributional trends to inform conservation strategies for endangered species

Aim: Species loss has increased significantly over the last 1000 years and is ultimately attributed to the direct and indirect consequences of increased human population growth across the planet. A growing number of species are becoming endangered and require human intervention to prevent their local extirpation or complete extinction. Management strategies aimed at mitigating a species loss can benefit greatly from empirical approaches that indicate the rate of decline of a species providing objective information on the need for immediate conservation actions, e.g. captive breeding; however, this is rarely employed. The current study used a novel method to examine the distributional trends of a model endangered species, the freshwater pearl mussel, Margaritifera margaritifera (L.).
Location: United Kingdom and Republic of Ireland.
Methods: Using species presence data within 10-km grid squares since records began three-parameter logistic regression curves were fitted to extrapolate an estimated date of regional extinction.
Results: This study has shown that freshwater pearl mussel distribution has contracted since known historical records and outlier populations were lost first. Within the United Kingdom and Republic of Ireland, distribution loss has been greatest in Scotland, Northern Ireland, Wales and England, respectively, with the Republic of Ireland containing the highest relative proportion of M. margaritifera distribution, in 1998.
Main conclusions: This study provides empirical evidence that this species could become extinct throughout countries within the United Kingdom within 170 years under the current trends and emphasizes that regionally specific management strategies need to be implemented to prevent extirpation of this species.

Assessing the conservation status of the freshwater pearl mussel in the North of Ireland - Relevance of growth and age characteristics

In order to conserve the freshwater pearl mussel in Ireland, populations that have a high risk of extinction must he identified and given priority for conservation. Growth of freshwater pearl mussels has been found to vary among populations on a wide geographic scale as well as on a local scale. Populations having a high growth constant (k), because of the small size of individuals and their shorter life-span and thus lower reproductive output, may be more likely to become extinct than those which have a low k and hence larger size and greater reproductive output. This study attempts to estimate the growth constant (k) in rivers in Donegal and Northern Ireland based on measuring lire largest shell in each population. Large differences in values of k were found among rivers and these are discussed in relation to catchment bedrock types and the identification of conservation priorities. Appropriate conservation strategies are recommended for Margaritifera margaritifera populations in the north of Ireland.

Towards a strategy for the conservation of the freshwater pearl mussel Margaritifera margaritifera in County Donegal, Ireland

This study attempts to identify the habitat requirements of the pearl mussel Margaritifea margaritifera in County Donegal, in north west Ireland, an area with little urban, industrial or intensive agricultural development. No mussels occur in rivers where calcium and conductivity levels are high or where the substratum is predominantly bedrock or fine sediment but it was not possible to distinguish clearly between mussel and non-mussel sites on the basis of ordination analysis. However, rivers which still support mussels and rivers with historical records of mussels are loosely grouped. Rivers which formerly supported mussels but lack living M. margaritifera appear to have suitable habitat for mussels; pearl fishing is the most likely reason for the extinction of these mussel populations. Where population densities are high, for example in locations on the rivers Eske, Clady and Owenea, conservation may necessitate the establishment of reserves. The prospect for the successful reintroduction of mussels into former mussel rivers such as the Finn and Eany Water, where suitable habitat exists and water quality is high, is very good.

The conservation of bees: a global perspective

Bees are major pollinators of Angiosperms and therefore their apparent decline is of importance for humans and biodiversity. We synthesise results of 12 recent reviews to provide a global picture of the threats they face. Habitat loss is the major threat to bee diversity, whilst invasive species, emerging diseases, pesticide use, and climate change also have the potential to impact bee populations. We suggest that future conservation strategies need to prioritise (i) minimising habitat loss, (ii) making agricultural habitats bee-friendly, (iii) training scientists and the public in bee taxonomy and identification, (iv) basic autecological and population genetic studies to underpin conservation strategies, (v) assessing the value of DNA barcoding for bee conservation, (vi) determining the impact of invasive plants, animals, parasites and pathogens, and (vii) integrating this information to understand the potential impact of climate change on current bee diversity.

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 long-term impacts of fisheries on epifaunal assemblage function and structure, in a special area of conservation

Fisheries can have profound effects on epifaunal community function and structure. We analysed the results from five dive surveys (1975–1976, 1980, 1983, 2003 and 2007), taken in a Special Area of Conservation, Strangford Lough, Northern Ireland before and after a ten year period of increased trawling activity between 1985 and 1995. There were no detectable differences in the species richness or taxonomic distinctiveness before (1975–1983) and after (2003–2007) this period. However, there was a shift in the epifaunal assemblage between the surveys in 1975–1983 and 2003–2007. In general, the slow-moving, or sessile, erect, filterfeeders were replaced by highly mobile, swimming, scavengers and predators. There were declines in the frequency of the fished bivalve Aequipecten opercularis and the non-fished bivalves Modiolus modiolus and Chlamys varia and some erect sessile invertebrates between the surveys in 1975–1983 and 2003–2007. In contrast, there were increases in the frequency of the fished and reseeded bivalves Pecten maximus and Ostrea edulis, the fished crabs Cancer pagurus and Necora puber and the non-fished sea stars Asterias rubens, Crossaster papposus and Henricia oculata between the surveys in 1975–1983 and 2003–2007. We suggest that these shifts could be directly and indirectly attributed to the long-termimpacts of trawl fishing gear, although increases in the supply of discarded bait and influxes of sediment may also have contributed to changes in the frequency of some taxa. These results suggest that despite their limitations, historical surveys and repeat sampling over long periods can help to elucidate the inferred patterns in the epifaunal community. The use of commercial fishing gear was banned from two areas in Strangford Lough in 2011, making it a model ecosystem for assessing the long-term recovery of the epifaunal community from the impacts of mobile and pot fishing gear.

Conundrums in Conservation: Complexity in Control

The departure point for this investigation is to highlight the centrality of regulation theory as a praxis in planning enforcement. The value of the conceptual framework is demonstrated by application in the problematic arena of conservation regulatory compliance, where there is currently a dearth of investigation. It is evidenced that this thematic approach provides a lens to scrutinise problematic areas of control and provides a deeper understanding of the difficulties faced by planning enforcement operational practice generally and heritage regimes specifically. The utility of the proposed mechanism is that it remedies the current well documented pitfalls of disjointed, piecemeal strategies by providing a framework for robust, coherent decision making not only in planning but in the wider regulatory arena.

SNP in the genome-wide association study hotspot on chromosome 9p21 confers susceptibility to diabetic nephropathy in type 1 diabetes

AIMS/HYPOTHESIS: Parental type 2 diabetes mellitus increases the risk of diabetic nephropathy in offspring with type 1 diabetes mellitus. Several single nucleotide polymorphisms (SNPs) that predispose to type 2 diabetes mellitus have recently been identified. It is, however, not known whether such SNPs also confer susceptibility to diabetic nephropathy in patients with type 1 diabetes mellitus. METHODS: We genotyped nine SNPs associated with type 2 diabetes mellitus in genome-wide association studies in the Finnish population, and tested for their association with diabetic nephropathy as well as with severe retinopathy and cardiovascular disease in 2,963 patients with type 1 diabetes mellitus. Replication of significant SNPs was sought in 2,980 patients from three other cohorts. RESULTS: In the discovery cohort, rs10811661 near gene CDKN2A/B was associated with diabetic nephropathy. The association remained after robust Bonferroni correction for the total number of tests performed in this study (OR 1.33 [95% CI 1.14, 1.56], p?=?0.00045, p (36tests)?=?0.016). In the meta-analysis, the combined result for diabetic nephropathy was significant, with a fixed effects p value of 0.011 (OR 1.15 [95% CI 1.02, 1.29]). The association was particularly strong when patients with end-stage renal disease were compared with controls (OR 1.35 [95% CI 1.13, 1.60], p?=?0.00038). The same SNP was also associated with severe retinopathy (OR 1.37 [95% CI 1.10, 1.69] p?=?0.0040), but the association did not remain after Bonferroni correction (p (36tests)?=?0.14). None of the other selected SNPs was associated with nephropathy, severe retinopathy or cardiovascular disease. CONCLUSIONS/INTERPRETATION: A SNP predisposing to type 2 diabetes mellitus, rs10811661 near CDKN2A/B, is associated with diabetic nephropathy in patients with type 1 diabetes mellitus.