The introduction of Next Generation Sequencing (NGS) has revolutionized population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by again sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximize cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild. +
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The ethanol production capacity from sugars and lignocellulosic biomass hydrolysates by Thermoanaerobacter strain AK5 was studied in batch cultures. The strain converts various carbohydrates to acetate, ethanol, hydrogen, and carbon dioxide. Maximum ethanol yields on glucose and xylose were 1.70 and 1.35 mol (mol sugars)−1, respectively. Increased initial glucose concentration inhibited glucose degradation and end-product formation leveled off at 30 mM. Cultivation of the strain with decreased liquid – gas (LG) ratios on glucose resulted in a shift to more acetate and less ethanol. End-product formation from glucose was further manipulated by adding extracellular electron acceptor (thiosulfate) or using a coculture of hydrogenotrophic methanogen. In both cases, the hydrogen-scavenging systems resulted in a dramatic shift from ethanol to acetate. Ethanol production from 4.5 g L–1 of complex biomass hydrolysates (grass, hemp, wheat straw, newspaper, and cellulose) pretreated with acid (0.50% H2SO4), alkali (0.50% NaOH), and without acid / alkali (control) and the enzymes Celluclast and Novozymes 188 (0.1 mL g–1 dry weight (dw); 70 and 25 U g–1 of Celluclast and Novozyme 188, respectively) was investigated. Highest ethanol yields (27.5 mM; 5.5 mM (g biomass)−1) were obtained on cellulose but lowest on hemp leafs (5.1 mM; 0.8 mM g–1). Chemical pretreatment increased ethanol yields substantially from lignocellulosic biomass but not from cellulose. The most-pronounced increase was on straw hydrolysates, where ethanol production increased from 5.5 mM to 15.2 mM on alkali-pretreated biomass. Ethanol yields were increased from 5.5 mM to 7.7 mM g–1 on cellulose by decreasing the hydrolyzate concentration to 2.25 g L–1, because of incomplete glucose degradation in the higher-loaded system.
AsaP1 is a toxic aspzincin metalloendopeptidase secreted by the fish pathogen Aeromonas salmonicida subsp. achromogenes. The protease is highly immunogenic and antibodies against AsaP1 evoke a passive protection against infection with A. salmonicida subsp. achromogenes. The protease is expressed as 37 kDa pre-pro-protein and processed to an active enzyme of 19 kDa in A. salmonicida subsp. achromogenes. Recombinant expression of AsaP1rec in E. coli results in a protease of 22 kDa that is not secreted. AsaP1rec induces comparable pathological changes in Atlantic salmon (Salmo salar L.) to native AsaP1wt. The aim of the study was to construct AsaP1 toxoids by exchanging catalytically important amino acids in the active site region of the protease.
Four different AsaP1 mutants (AsaP1E294A, AsaP1E294Q, AsaP1Y309A, and AsaP1Y309F) were successfully constructed by one step site directed mutagenesis, expressed in E. coli BL21 C43 as pre-pro-proteins and purified by His-tag affinity chromatography and gel filtration. Three of the resulting mutants (AsaP1E294A, AsaP1E294Q, and AsaP1Y309A) were not caseinolytic active and were detected as unprocessed pre-pro-proteins of 37 kDa. Caseinolytic active AsaP1rec and a mutant with reduced activity, AsaP1Y309F, were processed to a size of 22 kDa. Furthermore, AsaP1rec is able to process the inactive mutants to the mature size of 22 kDa, allowing the conclusion that AsaP1 is autocatalytically processed.
All four mutants AsaP1E294A, AsaP1E294Q, AsaP1Y309A and AsaP1Y309F are non-toxic in fish but induce a specific anti-AsaP1 antibody response in Arctic charr (Salvelinus alpinus L.) and are therefore true toxoids and possible vaccine additives.
Lumpfish (Cyclopterus lumpus L. 1758) are widely distributed on both sides of the North Atlantic. They are a commercially important species, but stock size estimates have declined since the mid-1980s in Canada, Norway and Iceland. Little is known about the biology of this species, in particular the breeding migrations and population structure which are fundamental for effective management. This paper describes the development and characterization of twenty-two polymorphic microsatellite loci using next generation sequencing. The number of alleles per locus ranged from 3 to 27 in two geographically distant North Atlantic populations, with observed and expected heterozygosities ranging between 0.0625–0.979 and 0.0618–0.946, respectively. These loci are an important resource that will allow assessment of the population genetic structure of this species, and contribute to its appropriate management.
A thermophilic, aerobic, Gram-stain-negative, filamentous bacterium, strain PRI-4131T, was isolated from an intertidal hot spring in Isafjardardjup, NW Iceland. The strain grew chemo-organotrophically on various carbohydrates. The temperature range for growth was 40–65 ° C (optimum 55 ° C), the pH range was pH 6.5–9.0 (optimum pH 7.0) and the NaCl range was 0–3 % (w / v) (optimum 0.5 %) . Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PRI-4131T represented a distinct lineage within the class Caldilineae of the phylum Chloroflexi. The highest levels of sequence similarity, about 91 %, were with Caldilinea aerophila STL-6-O1T and Caldilinea tarbellica D1-25-10-4T. Fermentative growth was not observed for strain PRI-4131T, which, in addition to other characteristics, distinguished it from the two Caldilinea species. Owing to both phylogenetic and phenotypic differences from the described members of the class Caldilineae , we propose to accommodate strain PRI-4131T in a novel species in a new genus, Litorilinea aerophila gen. nov., sp. nov. The type strain of Litorilinea aerophila is PRI-4131T (= DSM 25763T = ATCC BAA-2444T).
This paper describes a quantitative risk – benefit assessment of fish consumption. We compare the net health effect expressed in DALYs of two scenarios. The reference scenario is the current fish intake of the Dutch population, which is less than what is recommended by the health authorities. The alternative scenario describes the health effects if the population consumes 200 g of fish per week, which is close to the recommendation. All health effects due to fish consumption for which there is convincing evidence are incorporated in the assessment. The QALIBRA software (www.qalibra.eu) is used to simulate the two scenarios. The results show there is a net benefit for the population if it consumes 200 g of fish each week.
The fish ingredient N3-docosahexaenoic acid 22: 6 n-3 (DHA) stimulates brain development. On the other hand methylmercury (MeHg) in fish disturbes the developing central nervous system.
In this Context the IQ score in children is considered as an aggregate measure of in utero brain development.
To determine the effect of DHA exposure on prenatal neurodevelopment the maternal DHA intake during pregnancy was compared with its epidemiologically observed effect on the IQ score of children.
For MeHg the maternal intake was converted into its accumulation in the maternal body. The maternal body burden then was compared with its epidemiologically observed relationship with the IQ score.
Taking the MeHg and DHA content of 33 fish species the net effect of these compounds on the IQ score was quantified. For most fish species the adverse effect of MeHg on the IQ score exceeded the beneficial effect of DHA. In the case of long-living predators a negative effect up to 10 points on the IQ score was found.
The results of this study indicate that food interventions aiming at the beneficial effects of fish consumption should focus on fish species with a high DHA content, while avoiding fish species with a high MeHg content.
Low field Nuclear Magnetic Resonance was used in comparison to yield and physicochemical measurements to assess the effects of salt and protein injection on the properties of saithe (Pollachius virens) fillets during chilled and frozen storage. Saithe fillets injected with various combinations of salt, homogenized fish proteins, gelatin and fish protein hydrolyzate, were compared to the properties of untreated fillets. Addition of salt or fish protein hydrolyzate resulted in increased yield after cooking and water holding capacity compared to other treatments. Transversal relaxation data fitting resulted in three water populations with relaxation times of 27–45 ms, 60–99 ms and 187–341 ms. Relaxation times and respective populations showed significant correlation to various physicochemical properties, that muscle water behavior was changed by salt and protein injection and indicated protein denaturation during frozen storage. Fish protein hydrolyzate injected fillets were most stable through storage, while gelatin injected fillets were most denatured during frozen storage.
Effects of added phosphates on retardation of lipid oxidation of salted cod during processing, storage and after rehydration were investigated. Lipid hydrolysis progress and development of color, primary and secondary lipid oxidation products and fluorescence intensities were determined. Added phosphates significantly retarded lipid hydrolysis and lipid oxidation progress, resulting in lower free fatty acid, lipid hydroperoxides (PV), thiobarbituric acid-reactive substances (TBARS) as well as fluorescence intensities (δF or and δF aq). Significant correlation between the lipid oxidation products (PV, TBARS, δF or and δF aq) and yellow / brownish discoloration (b * value) of salted cod was observed. Principal component analysis showed that TBARS, b * value and δF or were the strongest indicators of lipid oxidation during salting and storage.
Contaminants have been determined in blue mussels (Mytilus edulis) at 11 locations around the Icelandic coastline from 1990 to 2010. The aim of the present study was to investigate if there has been a change in concentration of contaminants around the Icelandic coastline for the last two decades and if the concentrations and changes, if present , were consistent between locations. Concentrations of the persistent organic pollutants, p, p′-Dichlorodiphenyldichloroethene (p, p′ -DDE), hexachlorobenzene (HCB), α-hexachlorocyclohexane (α-HCH), polychlorinated biphenyl (PCB-153) and trans-nonachlor, have decreased at most of the sampling locations in Iceland in recent years. However, an increasing trend was found at a few locations that could be explained by anthropogenic activity. The concentration levels of the persistent organics were much lower than found at the Norwegian, USA and Chinese coasts, especially levels of p, p′ -DDE. The concentration of copper and selenium had a consistent pattern of change and concentration between locations over the period which showed a decreasing trend in recent years. The trace elements arsenic, cadmium, mercury and zinc showed more variation in concentration between locations, the concentration of arsenic, mercury and zinc was fairly stable over the period, whereas there were fluctuations in cadmium concentrations. The concentrations of cadmium and zinc were observed to be somewhat higher than found in mussels from Norway, USA and China but values of mercury and lead were much lower in the mussel sampled in Iceland. The higher concentrations of cadmium and zinc can be explained by the volcanic activity in Iceland but no major anthropogenic sources of trace elements are known in Iceland.