Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants

Targeted capture combined with massively parallel exome sequencing is a promising approach to identify genetic variants implicated in human traits. We report exome sequencing of 200 individuals from Denmark with targeted capture of 18,654 coding genes and sequence coverage of each individual exome at an average depth of 12-fold. On average, about 95% of the target regions were covered by at least one read. We identified 121,870 SNPs in the sample population, including 53,081 coding SNPs (cSNPs). Using a statistical method for SNP calling and an estimation of allelic frequencies based on our population data, we derived the allele frequency spectrum of cSNPs with a minor allele frequency greater than 0.02. We identified a 1.8-fold excess of deleterious, non-syonomyous cSNPs over synonymous cSNPs in the low-frequency range (minor allele frequencies between 2% and 5%). This excess was more pronounced for X-linked SNPs, suggesting that deleterious substitutions are primarily recessive.     

Evidence for complete denitrification in a benthic foraminifer

Benthic foraminifera are unicellular eukaryotes found abundantly in many types of marine sediments. Many species survive and possibly reproduce in anoxic habitats, but sustainable anaerobic metabolism has not been previously described. Here we demonstrate that the foraminifer Globobulimina pseudospinescens accumulates intracellular nitrate stores and that these can be respired to dinitrogen gas. The amounts of nitrate detected are estimated to be sufficient to support respiration for over a month. In a Swedish fjord sediment where G. pseudospinescens is the dominant foraminifer, the intracellular nitrate pool in this species accounted for 20% of the large, cell-bound, nitrate pool present in an oxygen-free zone. Similarly high nitrate concentrations were also detected in foraminifera Nonionella cf. stella and a Stainforthia species, the two dominant benthic taxa occurring within the oxygen minimum zone of the continental shelf off Chile. Given the high abundance of foraminifera in anoxic marine environments, these new findings suggest that foraminifera may play an important role in global nitrogen cycling and indicate that our understanding of the complexity of the marine nitrogen cycle is far from complete.     

Clinal variation and selection of MDH allozymes in honey bee populations

Latitudinal clines of malate dehydrogenase-1 (MDH-1) allozymes occur within honey bee populations on three continents: Europe, North America and South America. The North and South American populations are introduced and demonstrate that Mdh allelic clines were established within the last 150 years. The frequency of the medium electrophoretic allele increases in frequency with increasing latitude while the fast allele decreases with latitude on all the three continents. The clines are best explained by the average daily high temperature for July on all continents. These parallel clines provide evidence for selection on Mdh alleles in honey bees.     

Muramyl dipeptide responsive pathways in Crohn’s disease: from NOD2 and beyond

Crohn’s disease (CD) is one of main disease entities under the umbrella term chronic inflammatory bowel disease. The etiology of CD involves alterations in genetic, microbiological, and immunological factors. This review is devoted to the role of the bacterial wall compound muramyl dipeptide (MDP) for the activation of inflammatory pathways involved in the pathogenesis of CD. The importance of this molecule is underscored by the fact that (1) MDP, which is found in most Gram-negative and -positive bacteria, is able to trigger several immunological responses in the intestinal system, and (2) that alterations in several mediators of the MDP response including—but not restricted to—nucleotide oligomerization domain 2 (NOD2) are associated with CD. The normalization of MDP signaling is one of several important factors that influence the intestinal inflammatory response, a fact which emphasizes the pathogenic importance of MDP signaling for the pathogenesis of CD. The important aspects of NOD2 and non-NOD2 mediated effects of MDP for the development of CD are highlighted, as well as how alterations in these pathways might translate into the development of new therapeutic strategies.     

CCDC39 is required for assembly of inner dynein arms and the dynein regulatory complex and for normal ciliary motility in humans and dogs

Primary ciliary dyskinesia (PCD) is an inherited disorder characterized by recurrent infections of the upper and lower respiratory tract, reduced fertility in males and situs inversus in about 50% of affected individuals (Kartagener syndrome). It is caused by motility defects in the respiratory cilia that are responsible for airway clearance, the flagella that propel sperm cells and the nodal monocilia that determine left-right asymmetry. Recessive mutations that cause PCD have been identified in genes encoding components of the outer dynein arms, radial spokes and cytoplasmic pre-assembly factors of axonemal dyneins, but these mutations account for only about 50% of cases of PCD. We exploited the unique properties of dog populations to positionally clone a new PCD gene, CCDC39. We found that loss-of-function mutations in the human ortholog underlie a substantial fraction of PCD cases with axonemal disorganization and abnormal ciliary beating. Functional analyses indicated that CCDC39 localizes to ciliary axonemes and is essential for assembly of inner dynein arms and the dynein regulatory complex.     

Activation of complement by trypanosomes.

Factors exhibiting anti-complementary activity released from trypanosomes after incubation at 20 degrees C were described. The active material was shown to consume the first component of bovine complement. While the anti-complementary factor(s) from T. lewisi could activate bovine, human and guinea pig complement, the factor(s) from T. congolense was observed to activate bovine complement, but not guinea pig and only slightly human complement. The roles of complement activating factor(s) of trypanosomes in the pathology of the disease are discussed.     

Prevention of enteral radiocesium absorption by hexacyanoferrates(II) in piglets

Summary The efficacy of different hexacyanoferrates(II) in preventing the enteral absorption of¹³⁴Cs was studied in piglets. As compared to the controls, oral application of¹³⁴Cs together with KFe[Fe(CN)₆], NH₄Fe[Fe(CN)₆], or Fe₄[Fe(CN)₆]₃ resulted in a strong reduction of the¹³⁴Cs-uptake by more than 97%. The decrease in enteral absorption depends on the dose of administered hexacyanoferrate(II), whereas differences between the compounds under study were small. The biological half-life of¹³⁴Cs in non-hexacyanoferrate(II) treated piglets was 21.6±3.3 days (mean±SD).     

On the elimination of chlorprothixene in rat and man

Zusammenfassung Die Ausscheidung des neuen Neuroleptikums, Chlorprothixen, bei Menschen und Ratten wurde in Urin, Galle und Faeces untersucht und als einziges Abbauprodukt Chlorprothixen-Sulfoxyd gefunden. Ausscheidungsprodukte in % der verabreichten Dosis: Beim Menschen (orale Verabreichung) im Urin: 5–29% Sulfoxyd, Faeces: 0–41% unveränderter Stoff + Sulfoxyd. Bei der Ratte (orale oder parenterale Verabreichung) im Urin: bis zu 5% Sulfoxyd, Faeces: 1–7% Sulfoxyd, keine unveränderte Substanz, Galle: bis zu 24% Sulfoxyd.