3D simulation of the image formation in soft x ray microscopes

In water window soft x ray microscopy the studied object is typically larger than the depth of focus and the sample illumination is often partially coherent. This blurs out of focus features and may introduce considerable fringing. Understanding the influence of these phenomena on the image formation is therefore important when interpreting experimental data. Here we present a wave propagation model operating in 3D for simulating the image formation of thick objects in partially coherent soft xray microscopes. The model is compared with present simulation methods as well as with experiments. The results show that our model predicts the image formation of transmission soft x ray microscopes more accurately than previous model

Cross-species amplification of 41 microsatellites in European cyprinids: A tool for evolutionary, population genetics and hybridization studies

<p>Abstract</p> <p>Background</p> <p>Cyprinids display the most abundant and widespread species among the European freshwater Teleostei and are known to hybridize quite commonly. Nevertheless, a limited number of markers for conducting comparative differentiation, evolutionary and hybridization dynamics studies are available to date.</p> <p>Findings</p> <p>Five multiplex PCR sets were optimized in order to assay 41 cyprinid-specific polymorphic microsatellite loci (including 10 novel loci isolated from <it>Chondrostoma nasus nasus, Chondrostoma toxostoma toxostoma </it>and <it>Leuciscus leuciscus</it>) for 503 individuals (440 purebred specimens and 63 hybrids) from 15 European cyprinid species. The level of genetic diversity was assessed in <it>Alburnus alburnus, Alburnoides bipunctatus, C. genei, C. n. nasus, C. soetta, C. t. toxostoma, L. idus, L. leuciscus, Pachychilon pictum, Rutilus rutilus, Squalius cephalus </it>and <it>Telestes souffia</it>. The applicability of the markers was also tested on <it>Abramis brama, Blicca bjoerkna </it>and <it>Scardinius erythrophtalmus </it>specimens. Overall, between 24 and 37 of these markers revealed polymorphic for the investigated species and 23 markers amplified for all the 15 European cyprinid species.</p> <p>Conclusions</p> <p>The developed set of markers demonstrated its performance in discriminating European cyprinid species. Furthermore, it allowed detecting and characterizing hybrid individuals. These microsatellites will therefore be useful to perform comparative evolutionary and population genetics studies dealing with European cyprinids, what is of particular interest in conservation issues and constitutes a tool of choice to conduct hybridization studies.</p

Iron Biogeochemistry in the High Latitude North Atlantic Ocean

Iron (Fe) is an essential micronutrient for marine microbial organisms, and low supply controls productivity in large parts of the world’s ocean. The high latitude North Atlantic is seasonally Fe limited, but Fe distributions and source strengths are poorly constrained. Surface ocean dissolved Fe (DFe) concentrations were low in the study region (<0.1 nM) in summer 2010, with significant perturbations during spring 2010 in the Iceland Basin as a result of an eruption of the Eyjafjallajökull volcano (up to 2.5 nM DFe near Iceland) with biogeochemical consequences. Deep water concentrations in the vicinity of the Reykjanes Ridge system were influenced by pronounced sediment resuspension, with indications for additional inputs by hydrothermal vents, with subsequent lateral transport of Fe and manganese plumes of up to 250–300 km. Particulate Fe formed the dominant pool, as evidenced by 4–17 fold higher total dissolvable Fe compared with DFe concentrations, and a dynamic exchange between the fractions appeared to buffer deep water DFe. Here we show that Fe supply associated with deep winter mixing (up to 103 nmol m−2 d−1) was at least ca. 4–10 times higher than atmospheric deposition, diffusive fluxes at the base of the summer mixed layer, and horizontal surface ocean fluxes

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.Peer reviewe

Reduction of volatile halocarbons in anoxic seawater, results from a study in the Black Sea

The Black Sea is characterised by an oxic surface water layer and anoxic deep water rich in both hydrogen sulphide and methane, and in between a suboxic zone with very low concentrations of both oxygen and hydrogen sulphide. This makes the Black Sea a useful site for the study of oxidation-reduction reactions in seawater. In this study, the distributions of tetrachloromethane, trichloromethane, 1,1,1,-trichloroethane, dibromomethane, dibromochloromethane and bromodichloromethane across the oxic-anoxic interlace were related to the oxygen/hydrogen sulphide concentrations and thereby the redox potential gradient. All of the investigated halocarbons decrease rapidly in concentration as the oxygen decreases, most likely due to reduction. The results show that the higher the redox potential of a halocarbon, the higher up in the water column, i.e. at a higher oxygen level, reduction occurs. Most of the tetrachloromethane is transformed to trichloromethane as an intermediate product

Tomographic reconstruction in soft x ray microscopy using focus stack back projection

Tomographic reconstruction in soft x ray microscopy is a powerful technique for obtaining high resolution 3D images of biological samples. However, the depth of focus of such zone plate based microscopes is typically shorter than the thickness of many relevant biological objects, challenging the validity of the projection assumption used in conventional reconstruction algorithms. In order to make full use of the soft x ray microscopes high resolution, the tomographic reconstruction needs to take the depth of focus into account. Here we present a method to achieve high resolution in the full sample when the depth of focus is short compared to the sample thickness. The method relies on the back projection of focus stacked image data from x ray microscopy. We demonstrate the method on theoretical and experimental dat

The distribution of man-made and naturally produced halocarbons in a double layer flow strait system

The Bosphorus Strait, which connects the Black Sea and Mediterranean Sea via the Marmara Sea, is characterised by two distinct water masses. The upper layer consists of low density Black Sea water (sigma-t 10-11) flowing southward, and it is underlain by high density water (sigma-t > 28) of Mediterranean origin flowing northward. The sharp density gradient between the two layers is due to the difference in salinities. Here we report measurements on a suite of low molecular weight halocarbons together with basic hydrographic parameters in the strait