FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease

Background  

Candidate single nucleotide polymorphisms (SNPs) from genome-wide association studies (GWASs) were often selected for validation based on their functional annotation, which was inadequate and biased. We propose to use the more than 200,000 microarray studies in the Gene Expression Omnibus to systematically prioritize candidate SNPs from GWASs.     

Climate change impacts on potential recruitment in an ecosystem engineer

Climate variability and the rapid warming of seas undoubtedly have huge ramifications for biological processes such as reproduction. As such, gametogenesis and spawning were investigated at two sites over 200 km apart on the south coast of Ireland in an ecosystem engineer, the common cockle, Cerastoderma edule. Both sites are classed as Special Areas of Conservation (SACs), but are of different water quality. Cerastoderma edule plays a significant biological role by recycling nutrients and affecting sediment structure, with impacts upon assemblage biomass and functional diversity. It plays a key role in food webs, being a common foodstuff for a number of marine birds including the oystercatcher. Both before and during the study (early 2010–mid 2011), Ireland experienced its two coldest winters for 50 years. As the research demonstrated only slight variation in the spawning period between sites, despite site differences in water and environmental quality, temperature and variable climatic conditions were the dominant factor controlling gametogenesis. The most significant finding was that the spawning period in the cockle extended over a greater number of months compared with previous studies and that gametogenesis commenced over winter rather than in spring. Extremely cold winters may impact on the cockle by accelerating and extending the onset and development of gametogenesis. Whether this impact is positive or negative would depend on the associated events occurring on which the cockle depends, that is, presence of primary producers and spring blooms, which would facilitate conversion of this extended gametogenesis into successful recruitment.     

Quantitative assays for uracil-DNA glycosylase of high sensitivity

We have developed a sensitive fluorometric assay using bisulfite deaminated (C----U), covalently-closed circular PM2 DNA as the substrate. We describe a reliable way to prepare this substrate without nicking the PM2 DNA. Methods, which depend on toluenization of the cells, are described for reproducibly and quantitatively assaying uracil-DNA glycosylase. The sensitivity is such that only 200 EL4 mouse thymoma cells or 30,000 Escherichia coli cells are needed for each point in a kinetic assay.     

Uracil-DNA glycosylase in insects. Drosophila and the locust

It has been reported that Drosophila lacks a uracil-DNA glycosylase but that a direct incising activity on uracil-containing DNA appeared developmentally only in third instar larvae. In contrast we have found by two independent assays, that uracil-DNA glycosylase exists in both Drosophila eggs as well as in third instar larvae. The first assay shows the liberation of [3H] uracil from a d(AT)n polymer randomly substituted with [3H]uracil by its synthesis in the presence of [3H] dUTP. The second fluorometric assay for uracil-DNA glycosylase depends on the unique topological properties of circular DNAs and has the advantage of detecting apyrimidinic/apurinic (AP) endonuclease activity as well. To test one other insect, locust eggs were also assayed for uracil-DNA glycosylase. The amount of uracil-DNA glycosylase correlated well with the amount of DNA in actively replicating cells.     

The elemental composition of the chloragosomes of two earthworm species (Lumbricus terrestris and Allolobophora longa) determined by electron probe X-ray microanalysis of freeze-dired cryosections

Summary The elemental composition of the chloragosomes of the two earthworm species, one with complex highly active Ca-secreting calciferous glands (L. terrestris) and the other with non-secretory glands (A. longa), was determined by the electron probe X-ray microanalysis of unfixed freeze-dried cryosections. The predominant constituents of the chloragosomes of both species were P, Ca, Zn and S, with lesser quantities of K, Cl and Fe. The most striking species differences in chloragosomal chemistry were the higher concentrations (expressed as relative mass fractions) of P(×2.1), Ca(×1.5), and Zn(×2.3) in L. terrestris, and the much higher S(×19.6) in A. longa. These differences were discussed in relation to the general ecophysiology of the two species, and more specifically in relation to heavy metal uptake and binding.