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.     

Pathways and mechanisms of avian trunk neural crest cell migration and localization

Crest cells individualized at the dorsal border of the neural tube, while they became surrounded by a fibronectin-rich matrix. Crest cells initiated their migration between the basement membranes of the neural tube and the ectoderm. In the vagal region, crest cells migrated in a fibronectin-rich environment between the ectoderm and the dermomyotome, very rapidly reaching the apex of the pharynx. In the trunk region, crest cells opposite the bulk of the somite accumulated at the junction between the somite, the neural tube, and the ectoderm; they resumed their migration at the onset of the dissociation of the somite into dermomyotome and sclerotome. Migration occurred more ventrally along the neural tube; nevertheless, the formation of the rapidly expanding sclerotome prevented crest cells from reaching the paranotochordal region. Thereafter, crest cells accumulated between the neural tube, the dermomyotome, and the sclerotome, where ultimately they formed the dorsal root ganglia. In contrast, cells opposite the intersomitic space did not encounter these obstacles and utilized a narrow pathway formed between the basement membranes of the two adjacent somites. This pathway allowed crest cells to reach the most ventral regions of the embryo very rapidly; they accumulated along the aorta to form the aortic plexuses, the adrenal medulla, and the sympathetic ganglia. The basic features of the migration pathways are (1) a strict delimitation by the fibronectin-rich basement membranes of the surrounding tissues, (2) a formation of space concomitant with the migration of crest cells, (3) a transient existence: continued migration is correlated with the presence of fibronectin, whereas cessation is correlated with its focal disappearance. The crest cells are characterized by their inability to traverse basement membranes and penetrate within tissues. We propose that the combination of active proliferation, unique motility properties, and the presence of narrow pathways are the major mechanisms ensuring correct directionality. Morphologically defined transient routes of migration along with developmentally regulated changes in the extracellular matrix and in the adhesive properties of crest cells are most probably involved in their stabilization in defined territories and their aggregation into ganglia.     

S100 alpha, CAPL, and CACY: molecular cloning and expression analysis of three calcium-binding proteins from human heart.

Elevated levels of intracellular calcium are a major cause of myocardial dysfunction. To find possible mediators of the deregulated calcium we searched for EF-hand calcium-binding proteins of the S100 family. By PCR technology we identified three members of the S100 protein family (S100 alpha, CACY, and CAPL) in the human heart. We cloned the corresponding cDNAs and examined their expression levels in various human tissues by Northern blot analysis. All three proteins are expressed at high levels in the human heart. Whereas CACY and CAPL mRNAs are expressed ubiquitously, S100 alpha mRNA is restricted to heart, skeletal muscle, and brain. Interestingly, the expression pattern of S100 alpha, CACY, and CAPL in human tissues differs significantly from that in rodent tissues.     

Plasma selenium levels in healthy blood bank donors in the central-eastern part of Belgium

Graphite furnace atomic absorption spectrometry, with Zeeman background correction and after improved matrix modification, was used to measure the plasma selenium content of healthy blood bank donors in the central part of Belgium.

The mean plasma selenium concentration of 80 men and 80 women was 79.7±4.4 ng/mL with a range of 55.0–117.4 ng/mL.

There was no gender difference observed. Plasma selenium level was significantly highest for the adult group, aged 45–64 years, compared to the others, except the young adults (18–24 years).

The mean plasma selenium concentration measured corresponded well with literature data for Belgium. The obtained values were found to be in the medium range, compared with recent literature values for the European countries.     

Deep-sea squat lobster biogeography (Munidopsidae: Leiogalathea) unveils Tethyan vicariance and evolutionary patterns shared by shallow-water relatives

The ecology, abundance and diversity of galatheoid squat lobsters make them an ideal group to study deep-sea diversification processes. Here, we reconstructed the evolutionary and biogeographic history of Leiogalathea, a genus of circum-tropical deep-sea squat lobsters, in order to compare patterns and processes that have affected shallow-water and deep-sea squat lobster species. We first built a multilocus phylogeny and a calibrated species tree with a relaxed clock using StarBEAST2 to reconstruct evolutionary relationships and divergence times among Leiogalathea species. We used BioGeoBEARS and a DEC model, implemented in RevBayes, to reconstruct ancestral distribution ranges and the biogeographic history of the genus. Our results showed that Leiogalathea is monophyletic and comprises four main lineages; morphological homogeneity is common within and between clades, except in one; the reconstructed ancestral range of the genus is in the Atlantic and Indian oceans (Tethys). They also revealed the divergence of the Atlantic species around 25 million years ago (Ma), intense cladogenesis 15–25 Ma and low levels of speciation over the last 5 million years (Myr). The four Leiogalathea lineages showed similar patterns of speciation: allopatric speciation followed by range expansion and subsequent stasis. Leiogalathea started diversifying during the Oligocene, likely in the Tethyan. The Atlantic lineage then split from its Indo-Pacific sister group due to vicariance driven by closure of the Tethys Seaway. The Atlantic lineage is less speciose compared with the Indo-Pacific lineages, with the Tropical Southwestern Pacific being the current centre of diversity. Leiogalathea diversification coincided with cladogenetic peaks in shallow-water genera, indicating that historical biogeographic events similarly shaped the diversification and distribution of both deep-sea and shallow-water squat lobsters.     

Interference at several temporal and spatial scales between two chestnut insects

Detection of interspecific competition between insects is often sensitive to scaling. We give an example of scale-dependent interference between the weevil Curculio elephas and the moth Cydia splendana, which both have larvae that develop in the fruits of chestnut Castanea sativa. Measures at three scales were considered: chestnut, husk (with one to three fertile fruits) and tree. Data come from observations in the field over 14 years, complemented by experiments done directly in trees. Data on individual chestnut fruits revealed a marked statistical interference between the two insects. Experiments demonstrated that presence of a moth larva in a fruit usually inhibits weevil egg-laying. Conversely, weevil presence does not strongly modify moth larval behavior. Cases of double infestation often correspond to fruits first attacked by the weevil. With measures on husks, interference between the two insects was observed only in some trees; its intensity was always weaker than in the chestnuts themselves. At the scale of entire trees, rates of infestation by each insect are not correlated. Interference in chestnut fruits is interpreted by assuming that the weevil female either is sensitive to a repellent molecule originating from a moth larva or its frass, or can detect moth larval sounds. Mechanisms governing infestation rates from data per tree are discussed in relation to those found at fruit scale and to plant-insect interactions. The need to estimate available resources both from quantitative and qualitative points of view is emphasized.