New evidence for habitat specific selection in Wadden Sea Zostera marina populations revealed by genome scanning using SNP and microsatellite markers

Eelgrass Zostera marina is an ecosystem-engineering species of outstanding importance for coastal soft sediment habitats that lives in widely diverging habitats. Our first goal was to detect divergent selection and habitat adaptation at the molecular genetic level; hence, we compared three pairs of permanently submerged versus intertidal populations using genome scans, a genetic marker-based approach. Three different statistical approaches for outlier identification revealed divergent selection at 6 loci among 46 markers (6 SNPs, 29 EST microsatellites and 11 anonymous microsatellites). These outlier loci were repeatedly detected in parallel habitat comparisons, suggesting the influence of habitat-specific selection. A second goal was to test the consistency of the general genome scan approach by doubling the number of gene-linked microsatellites and adding single nucleotide polymorphism (SNP) loci, a novel marker type for seagrasses, compared to a previous study. Reassuringly, results with respect to selection were consistent among most marker loci. Functionally interesting marker loci were linked to genes involved in osmoregulation and water balance, suggesting different osmotic stress, and reproductive processes (seed maturation), pointing to different life history strategies. The identified outlier loci are valuable candidates for further investigation into the genetic basis of natural selection

A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment

<p>Abstract</p> <p>Background</p> <p>Technological advances have lead to the rapid increase in availability of single nucleotide polymorphisms (SNPs) in a range of organisms, and there is a general optimism that SNPs will become the marker of choice for a range of evolutionary applications. Here, comparisons between 300 polymorphic SNPs and 14 short tandem repeats (STRs) were conducted on a data set consisting of approximately 500 Atlantic salmon arranged in 10 samples/populations.</p> <p>Results</p> <p>Global F_STranged from 0.033-0.115 and -0.002-0.316 for the 14 STR and 300 SNP loci respectively. Global F_STwas similar among 28 linkage groups when averaging data from mapped SNPs. With the exception of selecting a panel of SNPs taking the locus displaying the highest global F_STfor each of the 28 linkage groups, which inflated estimation of genetic differentiation among the samples, inferred genetic relationships were highly similar between SNP and STR data sets and variants thereof. The best 15 SNPs (30 alleles) gave a similar level of self-assignment to the best 4 STR loci (83 alleles), however, addition of further STR loci did not lead to a notable increase assignment whereas addition of up to 100 SNP loci increased assignment.</p> <p>Conclusion</p> <p>Whilst the optimal combinations of SNPs identified in this study are linked to the samples from which they were selected, this study demonstrates that identification of highly informative SNP loci from larger panels will provide researchers with a powerful approach to delineate genetic relationships at the individual and population levels.</p

Elementär lärobok i geoteknik

(1) Geologisk översikt; (2) Jordarternas indelning och egenskaper; (3) Tjälproblem; (4) Fältundersökningar; (5) Deformeringsproblem; (6) Jordtryck; (7) Stabilitetsproblem; (8) Förstärkningsåtgärder; (9) Erosio

Clinical and genetic studies in a family with a novel mutation in the sepiapterin reductase gene

OBJECTIVES: Sepiapterin reductase deficiency is a rare, but treatable inherited disorder of tetrahydrobiopterin and neurotransmitter metabolism. This disorder is most probably underdiagnosed. To date, only 44 cases have been described in the literature. We present the clinical and genetic investigations in a family with a complex movement disorder. MATERIALS AND METHODS: We examined two affected sisters and three healthy family members. The cerebrospinal fluid was analyzed for neurotransmitter and pterins, and the sepiapterin reductase gene (SPR) was sequenced. RESULTS: The sisters had a complex movement disorders with dystonia and diurnal fluctuations. Both had oculogyric crises, and the older sister also hypersomnia. Both sisters had raised prolactin levels twice above the reference level. One sister had a dramatic response to levodopa, the other responded, but developed dyskinesia despite low doses. Both patients improved dramatically over time with levodopa (2.3 and 1.5 mg/kg/day). Very low levels of homovanillic acid and 5-hydroxyindoleacetic acid and increased levels of sepiapterin and dihydrobiopterin were measured in the cerebrospinal fluid before treatment. DNA analyses revealed a novel homozygous mutation in exon 2 in the SPR gene, c.364A>G/p.(Tyr123Cys), located in a highly conserved region in the gene. Both parents and the healthy sister were carriers for the same mutation. CONCLUSIONS: A new homozygous mutation in the SPR gene was found in two sisters with dopa-responsive dystonia. This important and treatable neurotransmitter disorder must be considered in patients with a complex movement disorder with diurnal fluctuations with or without intellectual impairment. Patients with these symptoms should undergo levodopa trial, cerebrospinal fluid investigations, and genetic analyses

Targeted high throughput sequencing in hereditary ataxia and spastic paraplegia

<div><p>Hereditary ataxia and spastic paraplegia are heterogeneous monogenic neurodegenerative disorders. To date, a large number of individuals with such disorders remain undiagnosed. Here, we have assessed molecular diagnosis by gene panel sequencing in 105 early and late-onset hereditary ataxia and spastic paraplegia probands, in whom extensive previous investigations had failed to identify the genetic cause of disease. Pathogenic and likely-pathogenic variants were identified in 20 probands (19%) and variants of uncertain significance in ten probands (10%). Together these accounted for 30 probands (29%) and involved 18 different genes. Among several interesting findings, dominantly inherited <i>KIF1A</i> variants, p.(Val8Met) and p.(Ile27Thr) segregated in two independent families, both presenting with a pure spastic paraplegia phenotype. Two homozygous missense variants, p.(Gly4230Ser) and p.(Leu4221Val) were found in <i>SACS</i> in one consanguineous family, presenting with spastic ataxia and isolated cerebellar atrophy. The average disease duration in probands with pathogenic and likely-pathogenic variants was 31 years, ranging from 4 to 51 years. In conclusion, this study confirmed and expanded the clinical phenotypes associated with known disease genes. The results demonstrate that gene panel sequencing and similar sequencing approaches can serve as efficient diagnostic tools for different heterogeneous disorders. Early use of such strategies may help to reduce both costs and time of the diagnostic process.</p></div

Pedigree structures of families with <i>KIF1A</i> variants.

<p>(a) Pedigree structure of family HCT-024 (III-7) with a c.80T>C, p.(Ile27Thr) variant in <i>KIF1A</i>. The filled symbols indicate affected individuals. The striped symbol indicates an individual that was initially classified as a non-affected individual, but after clinical re-examination was also found to be possibly affected. (b) Pedigree structure of family of HCT-026 (IV-6) with a c.22G>A, p.(Val8Met) variant. The symbols with a question mark are not confirmed regarding the phenotype. The diamond shaped symbols indicate masked gender. A line crossing a symbol represents a deceased individual. Probands are labelled with ‘P’.</p