Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing

BACKGROUND: Approximately half of the mitochondrial genome inherent within 546 individual Atlantic salmon (Salmo salar) derived from across the species' North Atlantic range, was selectively amplified with a novel combination of standard PCR and pyro-sequencing in a single run using 454 Titanium FLX technology (Roche, 454 Life Sciences). A unique combination of barcoded primers and a partitioned sequencing plate was employed to designate each sequence read to its original sample. The sequence reads were aligned according to the S. salar mitochondrial reference sequence (NC_001960.1), with the objective of identifying single nucleotide polymorphisms (SNPs). They were validated if they met with the following three stringent criteria: (i) sequence reads were produced from both DNA strands; (ii) SNPs were confirmed in a minimum of 90% of replicate sequence reads; and (iii) SNPs occurred in more than one individual. RESULTS: Pyrosequencing generated a total of 179,826,884 bp of data, and 10,765 of the total 10,920 S. salar sequences (98.6%) were assigned back to their original samples. The approach taken resulted in a total of 216 SNPs and 2 indels, which were validated and mapped onto the S. salar mitochondrial genome, including 107 SNPs and one indel not previously reported. An average of 27.3 sequence reads with a standard deviation of 11.7 supported each SNP per individual. CONCLUSION: The study generated a mitochondrial SNP panel from a large sample group across a broad geographical area, reducing the potential for ascertainment bias, which has hampered previous studies. The SNPs identified here validate those identified in previous studies, and also contribute additional potentially informative loci for the future study of phylogeography and evolution in the Atlantic salmon. The overall success experienced with this novel application of HT sequencing of targeted regions suggests that the same approach could be successfully applied for SNP mining in other species

Gout in immigrant groups: a cohort study in Sweden

Our aim was to study the association between country of birth and incidence of gout in different immigrant groups in Sweden. The study population included the whole population of Sweden. Gout was defined as having at least one registered diagnosis in the National Patient Register. The association between incidence of gout and country of birth was assessed by Cox regression, with hazard ratios (HRs) and 95% confidence intervals (95% CI), using Swedish-born individuals as referents. All models were conducted in both men and women, and the full model was adjusted for age, place of residence in Sweden, educational level, marital status, neighbourhood socio-economic status and co-morbidities. The risk of gout varied by country of origin, with highest estimates, compared to Swedish born, in fully adjusted models among men from Iraq (HR 1.82, 95% CI 1.54–2.16), and Russia (HR 1.69, 95% CI 1.26–2.27), and also high among men from Austria, Poland, Africa and Asian countries outside the Middle East; and among women from Africa (HR 2.23, 95% CI 1.50–3.31), Hungary (HR 1.98, 95% CI 1.45–2.71), Iraq (HR 1.76, 95% CI 1.13–2.74) and Austria (HR 1.70, 95% CI 1.07–2.70), and also high among women from Poland. The risk of gout was lower among men from Greece, Spain, Nordic countries (except Finland) and Latin America and among women from Southern Europe, compared to their Swedish counterparts. The increased risk of gout among several immigrant groups is likely explained by a high cardio-metabolic risk factor pattern needing attention

Regional mtDNA SNP differentiation in European Atlantic salmon (Salmo salar): an assessment of potential utility for determination of natal origin

Abstract Verspoor, E., Consuegra, S., Fridjonsson, O., Hjorleifsdottir, S., Knox, D., Olafsson, K., Tompsett, S., Wennevik, V., and Garciá de Leániz, C. 2012. Regional mtDNA SNP differentiation in European Atlantic salmon (Salmo salar): an assessment of potential utility for determination of natal origin. – ICES Journal of Marine Science, 69: 1625–1636. The Atlantic salmon, Salmo salar, shows geographically structured differentiation at various classes of molecular genetic variation, among and within river stocks. Nuclear microsatellite locus variation at multiple loci has been exploited for more than a decade as a marker for the continental origin of fish caught at sea in distant-water fisheries. However, a simpler, more cost-effective, but still accurate, assignment can be obtained using a single microsatellite locus in combination with a mitochondrial DNA (mtDNA) single-nucleotide polymorphism (SNP) detected by restriction enzyme digestion. Following on from this, a preliminary study was made of the potential for using mtDNA SNP variation to enhance the resolving power and cost-effectiveness of within-continent assignment of European salmon as determined using microsatellites. Variation in 20 mtDNA regions, encompassing ∼43% of this genome, in 330 salmon from 29 rivers across Europe, was analysed. High levels of inter-individual and inter-river variation were found, as well as evidence of regional differentiation paralleling observed microsatellite differentiation. The observations indicate scope for using mtDNA SNPs along with microsatellites for genetically based assignment of European salmon to region and river of natal origin, but further study is needed.</jats:p

Rupture process of the 2004 Sumatra-Andaman earthquake.

The 26 December 2004 Sumatra-Andaman earthquake initiated slowly, with small slip and a slow rupture speed for the first 40 to 60 seconds. Then the rupture expanded at a speed of about 2.5 kilometers per second toward the north northwest, extending 1200 to 1300 kilometers along the Andaman trough. Peak displacements reached approximately 15 meters along a 600-kilometer segment of the plate boundary offshore of northwestern Sumatra and the southern Nicobar islands. Slip was less in the northern 400 to 500 kilometers of the aftershock zone, and at least some slip in that region may have occurred on a time scale beyond the seismic band

Induced seismicity risk analysis of the hydraulic stimulation of a geothermal well on Geldinganes, Iceland

The rapid increase in energy demand in the city of Reykjavik has posed the need for an additional supply of deep geothermal energy. The deep-hydraulic (re-)stimulation of well RV-43 on the peninsula of Geldinganes (north of Reykjavik) is an essential component of the plan implemented by Reykjavik Energy to meet this energy target. Hydraulic stimulation is often associated with fluid-induced seismicity, most of which is not felt on the surface but which, in rare cases, can be a nuisance to the population and even damage the nearby building stock. This study presents a first-of-its-kind pre-drilling probabilistic induced seismic hazard and risk analysis for the site of interest. Specifically, we provide probabilistic estimates of peak ground acceleration, European microseismicity intensity, probability of light damage (damage risk), and individual risk. The results of the risk assessment indicate that the individual risk within a radius of 2km around the injection point is below 0.1 micromorts, and damage risk is below 10-2 for the total duration of the project. However, these results are affected by several orders of magnitude of variability due to the deep uncertainties present at all levels of the analysis, indicating a critical need in updating this risk assessment with in situ data collected during the stimulation. Therefore, it is important to stress that this a priori study represents a baseline model and starting point to be updated and refined after the start of the project

Full-Waveform based methods for Microseismic Monitoring Operations: An Application to Natural and Induced Seismicity in the Hengill Geothermal Area, Iceland

Geothermal systems in the Hengill volcanic area, SW Iceland, started to be exploited for electrical power and heat production since the late 1960s. Today the two largest operating geothermal power plants are located at Nesjavellir and Hellisheiði. This area is a complex tectonic and geothermal site, located at the triple junction between the Reykjanes Peninsula (RP), the Western Volcanic Zone (WVZ), and the South Iceland Seismic Zone (SISZ). The region is seismically highly active with several thousand earthquakes located yearly. The origin of such earthquakes may be either natural or anthropogenic. The analysis of microseismicity can provide useful information on natural active processes in tectonic, geothermal and volcanic environments as well as on physical mechanisms governing induced events. Here, we investigate the microseismicity occurring in Hengill area, using a very dense broadband seismic monitoring network deployed in Hellisheiði since November 2018, and apply sophisticated full-waveform based method for detection and location. Improved locations and first characterization indicate that it is possible to identify different types of microseismic clusters, which are associated with either production/injection or the tectonic setting of the geothermal area

Soft stimulation treatment of geothermal well RV-43 to meet the growing heat demand of Reykjavik

Reykjavik is almost entirely heated by geothermal energy. Yet, recent growth of the city significantly increased the heat demand. Past experiences in Iceland's capital region showed that hydraulic stimulation of existing geothermal wells is suited to improve hydraulic performance and energy supply. However, fluid injection may also trigger felt or even damaging earthquakes, which are of concern in populated areas and pose a significant risk to stimulation operations. Consequently, soft stimulation concepts have been developed to increase geothermal well performance while minimizing environmental effects such as induced seismicity. In a demonstration project of hydraulic soft stimulation in October 2019, more than 20.000 m³ of water were injected into well RV-43 in Reykjavik in multiple stages and with different injection schemes. The hydraulic performance of the well was improved without inducing felt seismicity. An a priori seismic risk assessment was conducted and for the first time the risk was continuously updated by an adaptive traffic light system supported by a sophisticated realtime microseismic monitoring. Our results confirm that it is possible to improve the performance of geothermal wells in Reykjavik and worldwide with acceptable technical, economic, and environmental risks. Here we provide an overview of the entire stimulation project including site description, stimulation design, zonal isolation, logging, seismic risk assessment and mitigation measures, realtime seismic, hydraulic and chemical monitoring, and stimulation results and challenges