Development of a Genotyping Microarray for Studying the Role of Gene-Environment Interactions in Risk for Lung Cancer

A microarray (LungCaGxE), based on Illumina BeadChip technology, was developed for high-resolution genotyping of genes that are candidates for involvement in environmentally driven aspects of lung cancer oncogenesis and/or tumor growth. The iterative array design process illustrates techniques for managing large panels of candidate genes and optimizing marker selection, aided by a new bioinformatics pipeline component, Tagger Batch Assistant. The LungCaGxE platform targets 298 genes and the proximal genetic regions in which they are located, using ∼13,000 DNA single nucleotide polymorphisms (SNPs), which include haplotype linkage markers with a minimum allele frequency of 1% and additional specifically targeted SNPs, for which published reports have indicated functional consequences or associations with lung cancer or other smoking-related diseases. The overall assay conversion rate was 98.9%; 99.0% of markers with a minimum Illumina design score of 0.6 successfully generated allele calls using genomic DNA from a study population of 1873 lung-cancer patients and controls.     

When to estimate sex ratio in natural populations of insects? A study on sex ratio variations of gall midges within a generation

Precise estimation of arthropods' sex ratio is an important issue in a wide range of ecological studies and biological control programs. Although, in many cases changes in arthropods' sex ratio may be under the control of parents or some symbiotic microorganisms, biased sex ratios in some other species are caused by some extrinsic factors, neglect of which may lead to under/overestimation of true sex ratio. In this paper, we pursued those factors that cause false estimation of sex ratio in insects' species. We studied the predatory gall midge, Aphidoletes aphidimyza Rondani (Diptera: Cecidomyiidae), an important biological control agent of aphids, that shows protandry (i.e. early male emergence), differential lifespan of sexes, and differential distribution of sexes across habitat. Ten populations of A. aphidimyza were released separately in transparent cages and their sex ratio variations were recorded every 12 hours. The primary sex ratio in this species seems to be slightly male‐biased (52.41% males), however early emergence of males biases the sex ratio up to 72% males in a few hours after emergence. Shortly after the emergence of females, the sex ratio reaches its primary situation, but as a result of male‐biased mortality after mating, the proportion of females increases gradually to 97% by the fourth and fifth days after emergence. These results explicitly suggest that direct estimation of sex ratio in natural populations may be affected by some secondary factors such as differential mortality of sexes, protandry, and differential distribution of males and females over time and/or across habitat.     

Development of an expert system for the integration of biomarker responses in mussels into an animal health index

Biomarkers on sentinel organisms are utilised worldwide in biomonitoring programs. However, the lack of effective interpretational capacity has hampered their uptake for use for assessment of risk in environmental management. The aim of the present study was to develop and test an objective decision-support or expert system capable of integrating biomarker results into a five-level health-status index. The expert system is based on a set of rules derived from available data on responses to natural and contaminant-induced stress of marine mussels. Integration of parameters includes: level of biological organization; biological significance; mutual inter-relationship; and qualitative trends in a stress gradient. The system was tested on a set of biomarker data obtained from the field and subsequently validated with data from previous studies. The results demonstrate that the expert system can effectively quantify the biological effects of different levels of pollution. The system represents a simple tool for risk assessment of the harmful impact of contaminants by providing a clear indication of the degree of stress syndrome induced by pollutants in mussels.     

Evaluating the effectiveness of conservation site networks under climate change: accounting for uncertainty

We forecasted potential impacts of climate change on the ability of a network of key sites for bird conservation (Important Bird Areas; IBAs) to provide suitable climate for 370 bird species of current conservation concern in two Asian biodiversity hotspots: the Eastern Himalaya and Lower Mekong. Comparable studies have largely not accounted for uncertainty, which may lead to inappropriate conclusions. We quantified the contribution of four sources of variation (choice of general circulation models, emission scenarios and species distribution modelling methods and variation in species distribution data) to uncertainty in forecasts and tested if our projections were robust to these uncertainties. Declines in the availability of suitable climate within the IBA network by 2100 were forecast as ‘extremely likely’ for 45% of species, whereas increases were projected for only 2%. Thus, we predict almost 24 times as many ‘losers’ as ‘winners’. However, for no species was suitable climate ‘extremely likely’ to be completely lost from the network. Considerable turnover (median = 43%, 95% CI = 35–69%) in species compositions of most IBAs were projected by 2100. Climatic conditions in 47% of IBAs were projected as ‘extremely likely’ to become suitable for fewer priority species. However, no IBA was forecast to become suitable for more species. Variation among General Circulation Models and Species Distribution Models contributed most to uncertainty among forecasts. This uncertainty precluded firm conclusions for 53% of species and IBAs because 95% confidence intervals included projections of no change. Considering this uncertainty, however, allows robust recommendations concerning the remaining species and IBAs. Overall, while the IBA network will continue to sustain bird conservation, climate change will modify which species each site will be suitable for. Thus, adaptive management of the network, including modified site conservation strategies and facilitating species' movement among sites, is critical to ensure effective future conservation.