A genome-wide genetic signature of Jewish ancestry perfectly separates individuals with and without full Jewish ancestry in a large random sample of European Americans

Background  

It was recently shown that the genetic distinction between self-identified Ashkenazi Jewish and non-Jewish individuals is a prominent component of genome-wide patterns of genetic variation in European Americans. No study however has yet assessed how accurately self-identified (Ashkenazi) Jewish ancestry can be inferred from genomic information, nor whether the degree of Jewish ancestry can be inferred among individuals with fewer than four Jewish grandparents.     

On the after‐use and restoration of abandoned extracted peatlands in the Baltic countries

In the Baltic countries (Estonia, Latvia, and Lithuania), mires directly affected by peat extraction cover almost 90,000 ha. Of these, over 26,200 ha have already been extracted and are abandoned. The main aim of this article is to give an overview of the extent of extracted peatlands in the Baltics, the legislative background around the land‐use options, and the directions of after‐use of peatlands since the middle of the 20th century. We also critically review results from restoration of abandoned extracted peatlands and assess whether they are on a trajectory toward reinitiation of paludification and functioning mire ecosystems. Almost all currently existing abandoned extracted peatlands in the Baltics were abandoned during and shortly after the Soviet period (1940–1991) without any restoration measures. The rest of the extracted areas were mostly afforested, converted into agricultural lands, berry plantations, or water bodies. The after‐use was mostly experimental, lacking systematic, proper assessment of outcome, cost and benefits, and side effects. The data are scarce but it could be estimated that only <10% (Estonia and Lithuania) and <20% (Latvia) of the total area of abandoned extracted peatlands were used for some purposes after peat extraction. Recently, several trials aimed at restoring the mire vegetation and ecosystem functions have been started in abandoned extracted peatlands in all three countries. In the coming years, the restoration of extracted peatlands in the Baltics will start on much bigger areas within different projects and initiatives cofinanced by the European Union.     

Wolf population genetics in Europe: a systematic review,meta‐analysis and suggestions for conservation and management

The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long represented a primary source of human–carnivore conflict, which has led to long‐term persecution of wolves, resulting in a significant decrease in their numbers, genetic diversity and gene flow between populations. For more effective protection and management of wolf populations in Europe, robust scientific evidence is crucial. This review serves as an analytical summary of the main findings from wolf population genetic studies in Europe, covering major studies from the ‘pre‐genomic era’ and the first insights of the ‘genomics era’. We analyse, summarize and discuss findings derived from analyses of three compartments of the mammalian genome with different inheritance modes: maternal (mitochondrial DNA), paternal (Y chromosome) and biparental [autosomal microsatellites and single nucleotide polymorphisms (SNPs)]. To describe large‐scale trends and patterns of genetic variation in European wolf populations, we conducted a meta‐analysis based on the results of previous microsatellite studies and also included new data, covering all 19 European countries for which wolf genetic information is available: Norway, Sweden, Finland, Estonia, Latvia, Lithuania, Poland, Czech Republic, Slovakia, Germany, Belarus, Russia, Italy, Croatia, Bulgaria, Bosnia and Herzegovina, Greece, Spain and Portugal. We compared different indices of genetic diversity in wolf populations and found a significant spatial trend in heterozygosity across Europe from south‐west (lowest genetic diversity) to north‐east (highest). The range of spatial autocorrelation calculated on the basis of three characteristics of genetic diversity was 650?850 km, suggesting that the genetic diversity of a given wolf population can be influenced by populations up to 850 km away. As an important outcome of this synthesis, we discuss the most pressing issues threatening wolf populations in Europe, highlight important gaps in current knowledge, suggest solutions to overcome these limitations, and provide recommendations for science‐based wolf conservation and management at regional and Europe‐wide scales.     

Linear and Nonlinear Absorption Properties of Diamond-Like Carbon Doped With Cu Nanoparticles

Ultrafast relaxation processes in diamond-like carbon (DLC) thin films with embedded Cu nanoparticles (DLC:Cu nanocomposites) were investigated by means of transient absorption spectroscopy focusing on localized surface plasmon resonance (LSPR) of photoexcited Cu nanoparticles. Absorption spectra of the composite films correspond to the sum of absorption spectra of DLC matrix and Cu nanoparticles; however, Cu nanoparticles strongly dominate in the transient differential absorption. Excitations of DLC matrix and of Cu nanoparticles relax independently revealing no strong interaction. High sensitivity measurements enabled to obtain the hot electron relaxation dynamics in Cu nanoparticles in the low excitation intensity conditions. The relaxation time was found to be independent of the excitation intensity up to tens of microjoule per square centimeter per pulse and to increase at higher intensities. The relaxation time obtained at low excitation intensity was also found to increase by about 30 % in the samples with high Cu concentration, where larger nanoparticles were formed.     

Whole-genome QTL analysis for MAGIC

Key message

An efficient whole genome method of QTL analysis is presented for Multi-parent advanced generation integrated crosses.

Abstract

Multi-parent advanced generation inter-cross (MAGIC) populations have been developed for mice and several plant species and are useful for the genetic dissection of complex traits. The analysis of quantitative trait loci (QTL) in these populations presents some additional challenges compared with traditional mapping approaches. In particular, pedigree and marker information need to be integrated and founder genetic data needs to be incorporated into the analysis. Here, we present a method for QTL analysis that utilizes the probability of inheriting founder alleles across the whole genome simultaneously, either for intervals or markers. The probabilities can be found using three-point or Hidden Markov Model (HMM) methods. This whole-genome approach is evaluated in a simulation study and it is shown to be a powerful method of analysis. The HMM probabilities lead to low rates of false positives and low bias of estimated QTL effect sizes. An implementation of the approach is available as an R package. In addition, we illustrate the approach using a bread wheat MAGIC population.     

Plasmodium relictum (lineage SGS1) and Plasmodium ashfordi (lineage GRW2): the effects of the co-infection on experimentally infected passerine birds

The effects of avian malaria parasites of the genus Plasmodium on their hosts are insufficiently understood. This is particularly true for malarial co-infections, which predominant in many bird populations. We investigated effects of primary co-infection of Plasmodium relictum (lineage SGS1) and Plasmodium ashfordi (GRW2) on experimentally infected naive juveniles of siskin Spinus spinus, crossbill Loxia curvirostra and starling Sturnus vulgaris. All siskins and crossbills were susceptible but starlings resistant to both these infections. A general pattern of the co-infections was that heavy parasitemia (over 35% during peaks) of both parasites developed in both susceptible host species. There were no significant effects of the co-infections on mean body mass of the majority of infected birds. Mean haematocrit value decreased approximately 1.5 and 3 times in siskins and crossbills at the peak of parasitemia, respectively. Mortality was recorded among infected crossbills. We conclude that co-infections of P. relictum and P. ashfordi are highly virulent and act synergetically during primary infections in some but not all passerine birds.     

Ontogenetic dietary shifts in European common frog (Rana temporaria) revealed by stable isotopes

During migrations and ontogeny amphibians change their habitat and feeding, and thus are important in linking terrestrial and aquatic ecosystems. We measured δ ¹³C and δ ¹⁵N values of early stages (egg, embryo, tadpole) and toes of adult frogs Rana temporaria, collected from a small wetland in Lithuania. We compared the isotopic composition of these tissues with potential food sources, excrements of tadpoles, and filled intestinal tracts. We found that δ ¹³C values in R. temporaria tadpoles were markedly depleted in comparison to adults, eggs or embryos, demonstrating a terrestrial to aquatic shift in energy sources. After the onset of feeding, tadpoles approached isotopic equilibrium with available food (algae and litter). Tadpoles had higher δ ¹⁵N than both algae and litter, differing by 3.6 and 2.4‰, respectively, and similar δ ¹³C to these sources. However, tadpole excrements and body tissue diverged, with mean δ ¹³C values of excrements (−30.3 ± 1.6‰ SD) more similar to litter (−31.7 ± 1.2‰ SD) and body tissue δ ¹³C (−34.8 ± 0.7‰ SD) more similar to algae (−34.2 ± 4.1‰ SD). This suggests that algal resources are critical in early life stages of this anuran, particularly at stages characterized by high growth and low development (stages: 25–35).     

Altered intracellular calcium fluxes in pancreatic cancer induced diabetes mellitus: Relevance of the S100A8 N‐terminal peptide (NT‐S100A8)

After isolating NT‐S100A8 from pancreatic cancer (PC) tissue of diabetic patients, we verified whether this peptide alters PC cell growth and invasion and/or insulin release and [Ca²⁺]_i oscillations of insulin secreting cells and/or insulin signaling. BxPC3, Capan1, MiaPaCa2, Panc1 (PC cell lines) cell growth, and invasion were assessed in the absence or presence of 50, 200, and 500 nM NT‐S100A8. In NT‐S100A8 stimulated β‐TC6 (insulinoma cell line) culture medium, insulin and [Ca²⁺] were measured at 2, 3, 5, 10, 15, 30, and 60 min, and [Ca²⁺]_i oscillations were monitored (epifluorescence) for 3 min. Five hundred nanomolars NT‐S100A8 stimulated BxPC3 cell growth only and dose dependently reduced MiaPaCa2 and Panc1 invasion. Five hundred nanomolars NT‐S100A8 induced a rapid insulin release and enhanced β‐TC6 [Ca²⁺]_i oscillations after both one (F = 6.05, P < 0.01) and 2 min (F = 7.42, P < 0.01). In the presence of NT‐S100A8, [Ca²⁺] in β‐TC6 culture medium significantly decreased with respect to control cells (F = 6.3, P < 0.01). NT‐S100A8 did not counteract insulin induced phosphorylation of the insulin receptor, Akt and IκB‐α, but it independently activated Akt and NF‐κB signaling in PC cells. In conclusion, NT‐S100A8 exerts a mild effect on PC cell growth, while it reduces PC cell invasion, possibly by Akt and NF‐κB signaling, NT‐S100A8 enhances [Ca²⁺]_i oscillations and insulin release, probably by inducing Ca²⁺ influx from the extracellular space, but it does not interfere with insulin signaling. J. Cell. Physiol. 226: 456–468, 2011. © 2010 Wiley‐Liss, Inc.     

DRG Axon Elongation and Growth Cone Collapse Rate Induced by Sema3A are Differently Dependent on NGF Concentration

Regeneration of embryonic and adult dorsal root ganglion (DRG) sensory axons is highly impeded when they encounter neuronal growth cone-collapsing factor semaphorin3A (Sema3A). On the other hand, increasing evidence shows that DRG axon’s regeneration can be stimulated by nerve growth factor (NGF). In this study, we aimed to evaluate whether increased NGF concentrations can counterweight Sema3A-induced inhibitory responses in 15-day-old mouse embryo (E15) DRG axons. The DRG explants were grown in Neurobasal-based medium with different NGF concentrations ranging from 0 to 100 ng/mL and then treated with Sema3A at constant 10 ng/mL concentration. To evaluate interplay between NGF and Sema3A number of DRG axons, axon outgrowth distance and collapse rate were measured. We found that the increased NGF concentrations abolish Sema3A-induced inhibitory effect on axon outgrowth, while they have no effect on Sema3A-induced collapse rate.     

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories have extensively sampled the conformational space accessible to B-DNA at room temperature. We confirm that base sequence effects depend strongly not only on the specific base pair step, but also on the specific base pairs that flank each step. Beyond sequence effects on average helical parameters and conformational fluctuations, we also identify tetranucleotide sequences that oscillate between several distinct conformational substates. By analyzing the conformation of the phosphodiester backbones, it is possible to understand for which sequences these substates will arise, and what impact they will have on specific helical parameters.