Identification of genes in the liver of Psammomys obesus associated with Type II diabetes

Type II diabetes is characterised by hyperglycemia and disturbances of fat, carbohydrate and protein metabolism. It occurs mainly in adults, with obesity being the most modifiable risk factor. This project utilised the Israeli Sand Rat (Psammomys obesus) and some of the latest molecular biology technology including differential display, membrane microarray and real-time PCR to detect genes in the liver that may be associated with the development of Type II diabetes and/or obesity. This study showed calpain, a proteolytic inhibitor and calpastatin, its natural inhibitor to be disregulated in the liver during the diabetic state.

Influence of age on expression of DNA repair genes in Arabidopsis

Numerous studies suggest that ageing in mammals may be associated with a reduction in DNA repair, whereas little is known about the DNA repair capacity of plants as they age. In this study we examined the effects of ageing on the expression of genes thought to be involved in nucleotide excision repair (AtERCC1, AtGTF2H2, AtGTF2H5, AtXPB1, AtXPD, AtXPF) or translesion replication (AtPOLH, AtREV1, AtREV3, AtUBC2) of UV photoproducts in Arabidopsis (Arabidopsis thaliana). Two- or four-week old plants were unirradiated or treated with 254 nm ultraviolet (UV) radiation (0.75 or 1.5 kJm^-2), incubated for 3 or 9 hr, and gene expression was analysed via quantitative PCR. With the exception of AtPOLH, transcript levels for all genes investigated were at least four-fold greater in unirradiated four-week old plants than unirradiated two-week old plants. Compared to unirradiated age-matched plants, two-week old plants generally showed no consistent change in transcript levels for either UV dose or post-irradiation incubation period. On the other hand, transcript levels in four-week old plants were increased over those in two-week old plants for the majority of genes by 9 hr post-irradiation with 0.75 or 1.5 kJm^-2 UV. No other consistent responses were observed for UV treatment. Collectively, our results are consistent with the possibility that ageing may be associated with increased DNA repair capacity in plants.

Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies

Background
Automated candidate gene prediction systems allow geneticists to hone in on disease genes more rapidly by identifying the most probable candidate genes linked to the disease phenotypes under investigation. Here we assessed the ability of eight different candidate gene prediction systems to predict disease genes in intervals previously associated with type 2 diabetes by benchmarking their performance against genes implicated by recent genome-wide association studies.

Results
Using a search space of 9556 genes, all but one of the systems pruned the genome in favour of genes associated with moderate to highly significant SNPs. Of the 11 genes associated with highly significant SNPs identified by the genome-wide association studies, eight were flagged as likely candidates by at least one of the prediction systems. A list of candidates produced by a previous consensus approach did not match any of the genes implicated by 706 moderate to highly significant SNPs flagged by the genome-wide association studies. We prioritized genes associated with medium significance SNPs.

Conclusion
The study appraises the relative success of several candidate gene prediction systems against independent genetic data. Even when confronted with challengingly large intervals, the candidate gene prediction systems can successfully select likely disease genes. Furthermore, they can be used to filter statistically less-well-supported genetic data to select more likely candidates. We suggest consensus approaches fail because they penalize novel predictions made from independent underlying databases. To realize their full potential further work needs to be done on prioritization and annotation of genes.