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.     

Effects of Management on Economic Profitability of Forest Biomass Production and Carbon Neutrality of Bioenergy Use in Norway Spruce Stands Under the Changing Climate

We analyzed the effects of management on the economic profitability of forest biomass production and carbon neutrality of bioenergy use in Norway spruce (Picea abies L. Karst) stands under the changing climate. We employed a forest ecosystem model and life cycle assessment tool. In particular, we studied the effects of thinning, nitrogen fertilization, and rotation length on: (1) the production of timber and energy biomass, and its economic profitability (net present value), (2) carbon stock in the forest ecosystem and carbon balance in forestry, and (3) carbon dioxide (CO₂) emissions from the use of biomass in energy production. Results showed that the current Finnish baseline management with and without nitrogen fertilization resulted in the highest mean annual timber production and net present value (NPV) for long rotations (60 to 80 years), regardless of climate scenario. Mean annual production of energy biomass was enhanced by increasing stocking by 20–30 % compared to the baseline management, and/or use of nitrogen fertilization. Such management gave lower CO₂ emissions per unit of energy compared to the baseline management, as the carbon stock in the forest ecosystem and the carbon balance in forestry increased. Overall, the carbon neutrality and net present value were, on average, the highest in the baseline management or with a 20 % increase in stocking, with nitrogen fertilization and 60- to 80-year rotation lengths, regardless of the climate applied. However, it was not possible to simultaneously maximize the NPV of forest biomass production and the carbon neutrality of bioenergy use.     

Visceral obesity is associated with high levels of serum squalene

Objective: To investigate the impact of visceral obesity on cholesterol metabolism in normoglycemic offspring of patients with type 2 diabetes. Research Methods and Procedures: The proportion of intra‐abdominal fat (IAF) was measured by abdominal computer tomography, and serum cholesterol synthesis and absorption markers were determined by gas‐liquid chromatography in 109 normoglycemic offspring of patients with type 2 diabetes. Insulin action was measured with the hyperinsulinemic euglycemic clamp. The gene encoding squalene synthase (farnesyl‐diphosphate farnesyltransferase 1) was screened with the single‐strand conformation polymorphism analysis and direct sequencing. Results: Cholesterol synthesis markers correlated positively with IAF (r = 0.213 to 0.309, p ≤ 0.027) and negatively with the rates of insulin‐stimulated whole‐body glucose uptake (r = ?0.372 to ?0.248, p ≤ 0.010). However, serum squalene, the first measured precursor of cholesterol synthesis, showed a positive correlation with IAF (r = 0.309, p = 0.001) without any association with subcutaneous fat or insulin sensitivity. Variation in the farnesyl‐diphosphate farnesyltransferase 1 gene did not explain elevated serum squalene levels in viscerally obese subjects. From the cholesterol absorption markers, cholestanol was associated negatively with IAF and positively with whole‐body glucose uptake (p < 0.05). Discussion: High serum squalene levels are associated with visceral obesity but not with subcutaneous obesity. Whether this finding is causally connected to visceral obesity remains to be established.     

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.     

Costs of two alternative <Emphasis Type="Italic">Salmonella</Emphasis> control policies in Finnish broiler production

Background  

Costs and benefits of two Salmonella control policies for broiler production were described and compared. The control options were the Zoonosis Directive 92/117/EC and the more intense strategy, the Finnish Salmonella Control Programme (FSCP).     

Dynamics of daily height growth in Scots pine trees at elevated temperature and CO2

The aim of this study was to analyse and model the effects of elevated temperature and carbon dioxide concentration on daily height growth of 20-year-old Scots pines (Pinus sylvestris L.). The trees were grown with a low nitrogen supply in closed chambers with a factorial combination of two temperature regimes (ambient and elevated) and two carbon dioxide concentrations (ambient and twice ambient). The temperature elevation corresponded to the predicted increase at the site after a doubling in atmospheric CO₂. The height growth of Scots pines was first empirically studied in terms of its onset, cessation and duration, and the allocation of daily height growth within the growing period in 2000 and 2001, and then a model predicting daily height growth as a function of daily temperature and temperature sum was developed. The empirical results showed elevated temperature to be the dominant variable explaining variation in daily height growth. Elevated temperature also hastened both the onset and cessation of height growth, and the temperature sums for both of them were higher in the elevated than in the ambient temperature treatments. The daily variation in height growth could also be explained by the daily mean temperature in the model. Elevated CO₂ concentration had no effect on the onset, cessation or duration of height growth. The amount of height growth was not affected by any of the treatments.