Mobster: accurate detection of mobile element insertions in next generation sequencing data

Mobile elements are major drivers in changing genomic architecture and can cause disease. The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. Mobster has a low false discovery rate and high recall rate for both L1 and Alu elements. Mobster is available at http://sourceforge.net/projects/mobster.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0488-x) contains supplementary material, which is available to authorized users.     

'Return to home cage' as a reward for maze learning in young and old genetically heterogeneous mice

Recent studies have shown that 'return to home cage' can serve as a reward for maze learning in adult male mice. The present study examined whether the same reward is an effective motivator of learning in young and old mice and included females in the study design. We tested 25- and 65-d-old HS mice and 85- and 800-d-old B6D2F2 mice in a Lashley III maze. Return to home cage motivated maze acquisition in all groups. Compared with 65-d-old HS mice, 25-d-olds acquired the maze more slowly, took longer to achieve the test criterion, and showed increased latency to reach the goal box. There was no difference between 85- and 800-d-old B6D2F2 mice in rate of acquisition. This reward procedure may reduce the potentially confounding effects of deprivation or aversive stimuli on maze performance and may be suitable as a motivational procedure for a wide range of subject groups.     

Isolation and structure of a cytotoxic epoxy sterol from the marine mollusc Planaxis sulcatus

A novel epoxy sterol isolated from the marine mollusc Planaxis sulcatus has been identified as 9 alpha,11 alpha-epoxycholest-7-ene-3 beta,5 alpha,6 beta-triol by spectrometric methods.     

Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates

Linking variation in quantitative traits to variation in the genome is an important, but challenging task in the study of life-history evolution. Linkage maps provide a valuable tool for the unravelling of such trait−gene associations. Moreover, they give insight into recombination landscapes and between-species karyotype evolution. Here we used genotype data, generated from a 10k single-nucleotide polymorphism (SNP) chip, of over 2000 individuals to produce high-density linkage maps of the great tit (Parus major), a passerine bird that serves as a model species for ecological and evolutionary questions. We created independent maps from two distinct populations: a captive F2-cross from The Netherlands (NL) and a wild population from the United Kingdom (UK). The two maps contained 6554 SNPs in 32 linkage groups, spanning 2010 cM and 1917 cM for the NL and UK populations, respectively, and were similar in size and marker order. Subtle levels of heterochiasmy within and between chromosomes were remarkably consistent between the populations, suggesting that the local departures from sex-equal recombination rates have evolved. This key and surprising result would have been impossible to detect if only one population was mapped. A comparison with zebra finch Taeniopygia guttata, chicken Gallus gallus and the green anole lizard Anolis carolinensis genomes provided further insight into the evolution of avian karyotypes.     

Induced Bactericidal Response in the Hagfish

Hagfish were shown to be capable of synthesizing bactericidins after injection of gram-negative bacteria. The bactericidins could be detected as early as 2 days after injection. The degree of specificity was not as impressive as in mammalian systems.     

Der metabolismus von 3H-α-ecdyson bei larven von Tenebrio molitor

The metabolism of ³H-α-ecdysone has been investigated in larvae of Tenebrio molitor within a moulting cycle. The metabolization occurs by hydroxylation, dehydration, and conjugation. A total of 8 metabolites including α- and β-ecdysone were found. Peak I was cleaved enzymatically up to 56%. The hydrolized part consists of esters of sulfuric- and glucuronic acid with compounds II and III, also with α-ecdysone and 3-dehydroecdysterone to a lesser degree.The hydroxylation of α-ecdysone to β-ecdysone is a very rapid one. Velocity and intensity depends on the physiological stage of the larvae. On days with a large endogenous hormone titer they are maximal and on days with a low endogenous titer they are lower. The rate of conversion of α- to β-ecdysone shows a correlation with the endogenous titer and vice versa.At a low endogenous titer the rate of excretion is very strong, in larvae aged to 2 to 5 days and also 7 to 8 days, 8 h after injection 50 to 80% of injected activity was recovered in the faeces. At the beginning of the moulting cycle 3% and at the 6th day 30% (hormone titer maximum) of activity is excreted. The unexpected high rate of excretion at the first day is compensated by increasing metabolism and storage.The faeces mainly consist of conjugates and α- and β-ecdysone. A correlation between the appearance of these compounds and the physiological stage of the larvae could be found. On those days with low endogenous titer the quota of ecdysone (α and β) is higher.