Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range

Background

Anadromous migratory fish species such as Atlantic salmon (Salmo salar) have significant economic, cultural and ecological importance, but present a complex case for management and conservation due to the range of their migration. Atlantic salmon exist in rivers across the North Atlantic, returning to their river of birth with a high degree of accuracy; however, despite continuing efforts and improvements in in-river conservation, they are in steep decline across their range. Salmon from rivers across Europe migrate along similar routes, where they have, historically, been subject to commercial netting. This mixed stock exploitation has the potential to devastate weak and declining populations where they are exploited indiscriminately. Despite various tagging and marking studies, the effect of marine exploitation and the marine element of the salmon lifecycle in general, remain the "black-box" of salmon management. In a number of Pacific salmonid species and in several regions within the range of the Atlantic salmon, genetic stock identification and mixed stock analysis have been used successfully to quantify exploitation rates and identify the natal origins of fish outside their home waters - to date this has not been attempted for Atlantic salmon in the south of their European range.

Results

To facilitate mixed stock analysis (MSA) of Atlantic salmon, we have produced a baseline of genetic data for salmon populations originating from the largest rivers from Spain to northern Scotland, a region in which declines have been particularly marked. Using 12 microsatellites, 3,730 individual fish from 57 river catchments have been genotyped. Detailed patterns of population genetic diversity of Atlantic salmon at a sub-continent-wide level have been evaluated, demonstrating the existence of regional genetic signatures. Critically, these appear to be independent of more commonly recognised terrestrial biogeographical and political boundaries, allowing reporting regions to be defined. The implications of these results on the accuracy of MSA are evaluated and indicate that the success of MSA is not uniform across the range studied; our findings indicate large differences in the relative accuracy of stock composition estimates and MSA apportioning across the geographical range of the study, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the area studied. This result probably reflects the more genetically distinct nature of populations in the database from Spain, northwest France and southern England. Genetic stock identification has been undertaken and validation of the baseline microsatellite dataset with rod-and-line and estuary net fisheries of known origin has produced realistic estimates of stock composition at a regional scale.

Conclusions

This southern European database and supporting phylogeographic and mixed-stock analyses of net samples provide a unique tool for Atlantic salmon research and management, in both their natal rivers and the marine environment. However, the success of MSA is not uniform across the area studied, with large differences in the relative accuracy of stock composition estimates and MSA apportioning, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the region. More broadly, this study provides a basis for long-term salmon management across the region and confirms the value of this genetic approach for fisheries management of anadromous species.     

New extracellular resistance mechanism for cisplatin

The HSQC NMR spectrum of ¹⁵N-cisplatin in cell growth media shows resonances corresponding to the monocarbonato complex, cis-[Pt(NH₃)₂(CO₃)Cl]⁻, 4, and the dicarbonato complex, cis-[Pt(NH₃)₂(CO₃)₂]⁻², 5, in addition to cisplatin itself, cis-[Pt(NH₃)₂Cl₂], 1. The presence of Jurkat cells reduces the amount of detectable carbonato species by (2.8 ± 0.7) fmol per cell and has little effect on species 1. Jurkat cells made resistant to cisplatin reduce the amount of detectable carbonato species by (7.9 ± 5.6) fmol per cell and also reduce the amount of 1 by (3.4 ± 0.9) fmol per cell. The amount of detectable carbonato species is also reduced by addition of the drug to medium that has previously been in contact with normal Jurkat cells (cells removed); the reduction is greater when drug is added to medium previously in contact with resistant Jurkat cells (cells removed). This shows that the platinum species are modified by a cell-produced substance that is released to the medium. Since the modified species have been shown not to enter or bind to cells, and since resistant cells modify more than non-resistant cells, the modification constitutes a new extracellular mechanism for cisplatin resistance which merits further attention.     

The usage of marker traits in plants for evaluation of resistance of the winter wheat to pest insects

A new method of selection of the winter wheat varieties has been tested for resistance to the pest insects' complex by the traits of plants that are the markers of plant resistance. It makes it possible to use this method from year to year independently of the pests' density.     

Structure and Ubiquitination-Dependent Activation of TANK-Binding Kinase 1

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Highlights? TBK1 forms a dimer structurally distinct from IKKβ ? Structure of TBK1 with inhibitors reveals basis for specific inhibition ? TBK1 is K63 polyubiquitinated on Lys30 in the kinase domain and Lys401 in the scaffold/dimerization domain ? K63-linked ubiquitination of dimerized TBK1 is required for kinase activation and signaling     

Quantitation of minimal residual disease in patients with chronic lymphocytic leukemia using locked nucleic acid-modified, fluorescently labeled hybridization probes and real-time PCR technology

BACKGROUND: The knowledge of biological characteristics of minimal residual disease (MRD) in chronic lymphocytic leukemia (CLL) remains sparse. There are no data available on what level of MRD might be 'safe' without an overt risk of relapse, or whether any such level exists at all. To address this issue in prospective studies, we have developed a quantitative molecular approach to monitor MRD in CLL, which allows the malignant clone to be traced with far higher sensitivity than possible with the techniques available currently. METHOD: To quantify MRD in CLL patients, a novel locked nucleic acid (LNA)-RNA-based quantitative real-time PCR technique was developed. Clone-specific assays were prepared for 62 CLL patients. Thirty patients were followed up molecularly for a median of 250 days (range 69-570 days). All patients were administered chemo/immunotherapy. RESULTS: In three patients, molecular negativity was achieved, as estimated by LNA-based assays. In one patient, a sustained molecular negativity was established by chemo/immunotherapy and the patient remains molecularly negative (322 days). The LNA-based assay enabled us to evaluate MRD in a reproducible manner with the sensitivity of 10(-7). CONCLUSION: LNA-RNA-based quantitative real-time PCR is an effective approach for MRD monitoring with the potential for increased sensitivity compared with standard DNA-based assays used for molecular follow-up.     

House sparrow (Passer domesticus) habitat use in urbanized landscapes

The house sparrow (Passer domesticus) is showing population declines in many parts of Europe, with recent declines being particularly severe in urban areas. To date, relatively little is known about the species’ habitat associations within urbanized landscapes. We report here an investigation of the habitat associations of house sparrows using a survey of 1223 stratified randomly selected 500 × 500-m squares within urbanized landscapes of the UK, defined as at least 25% ‘human cover’. The densities of chirping male house sparrows and of all house sparrows were analysed separately to obtain insights into breeding habitat requirements and general habitat associations, respectively. Multi-model inference showed that residential areas (houses, flats), allotments (areas used for small-scale horticulture) and farm buildings were key predictors of house sparrow density and chirping male density. Separate analyses on landscapes of differing human cover showed similar results. Within residential areas, the increase of house sparrow density with habitat area (on a log scale) was approximately threefold greater when private gardens were present than when they were absent. The model predicted a rapid decline in house sparrow abundance when only a small area of private gardens is converted to continuous housing. Allotments and residential areas with gardens are likely to be under pressure due to increased demand for housing, specifically from the infilling of green space within urban areas. It would seem to be imperative that any action plan to protect urban house sparrow populations should include specific protection of such key habitats. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Is supplementary feeding in gardens a driver of evolutionary change in a migratory bird species?

Human activities are causing rapid environmental change at a global scale. Urbanization is responsible for some of the most extreme human‐altered habitats and is a known driver of evolutionary change, but evidence and understanding of these processes is limited. Here, we investigate the potential underlying mechanisms contributing to the contemporary evolution of migration behaviour in the Eurasian blackcap (Sylvia atricapilla). Blackcaps from central Europe have been wintering in urban areas of Britain with increasing frequency over the past 60 years, rather than migrating south to the Mediterranean. It has been hypothesized that the popularization of providing supplementary foods for wild birds within Britain may have influenced this marked migratory change, but quantifying the selective forces shaping evolutionary changes remains challenging. Using a long‐term national scale data set, we examine both the spatial distribution and interannual variation in blackcap wintering behaviour in Britain in relation to supplementary food availability and local climate. Over a 12‐year period, we show that blackcaps are becoming increasingly associated with the provision of supplementary foods in British gardens, and that the reliability of bird food supplies is influencing their winter distribution at a national scale. In addition, local climatic temperatures and broader scale weather variation are also important determinants of blackcap wintering patterns once they arrive in Britain. Based on our findings, we conclude that a synergistic effect of increased availability of feeding resources, in the form of garden bird food, coupled with climatic amelioration, has enabled a successful new wintering population to become established in Britain. As global biodiversity is threatened by human‐induced environmental change, this study presents new and timely evidence of the role human activities can play in shaping evolutionary trajectories.