Category: Branches

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Davíð Gíslason

Project Manager

davidg@matis.is

Genetic introgression of domesticated plants and animals into wild populations occurs globally. Such introgression disrupts adaptive potential, reduces fitness in wild populations and threatens intraspecific genetic variation. The best-documented case of farmed introgression into wild populations is that of the Atlantic salmon (Salmo salar). Norway is the world’s largest producer of farmed Atlantic salmon, and the industry is growing in Iceland and other countries. In Norway, genetic introgression resulting from farmed escapees breeding with wild conspecifics has been documented in approximately two-thirds of 250 salmon populations studied. This comprehensive quantification has been possible due to a panel of genetic markers diagnostic of farmed introgression. Improved genomic resources, continued selection and genetic drift in the farmed breeding lines, as well as new breeding lines in commercial production, call for an updated tool to quantify farmed genetic introgression. Here, we present second-generation panels of genetic markers diagnostic of farmed introgression in Norway and the first panels of genetic markers diagnostic of farmed introgression in Iceland. We show that these diagnostic markers provide increased power to detect introgression compared to the first-generation panel, as well as increased power compared to a genome-wide marker set. Improved accuracy will benefit the ongoing monitoring of farmed introgression and facilitate research into the ecological and functional effects of farmed introgression in wild populations.

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Hildur Inga Sveinsdóttir

Project Manager

hilduringa@matis.is

Growing fish consumption worldwide has driven fish processors to introduce innovative seafood products with extended shelf-life and desirable organoleptic properties. Atlantic mackerel (Scomber scombrus) enters the Icelandic catching waters during a well-fed and fatty stage during summer, providing several challenges for its processing and utilization for human consumption. This study investigates the impact of freezing this well-fed and fatty deep-skinned Atlantic mackerel fillets before and after smoking, prior to canning to assess its suitability for processing of smoked and canned products for human consumption. Physicochemical and organoleptic properties of canned fillets were evaluated after 1 and 12 months of storage at room temperature. The formation of primary oxidation products (peroxide value, PV) was similar in both cases, while the secondary oxidation products (thiobarbituric acid reactive substances, TBARS) were notably lower when the fillets were smoked before freezing. Additionally, PV and TBARS levels were significantly reduced in all canned mackerel samples after prolonged storage compared to those stored for a shorter period. However, lipid oxidation and hydrolysis were minimal after both treatments, indicating that these factors do not pose a significant issue for these products. Instrumental texture analysis and product evaluation of canned mackerel revealed more favourable characteristics (firmer fillets, nor mushy) when fillets were frozen first and then hot-smoked (FSC). In contrast, fillets that were smoked first and then frozen (SFC), irrespective of the canning storage time, exhibited a mushy texture and appearance, which could negatively impact consumer acceptance. Therefore, freezing prior to hot-smoking may represent a better option if the fillets are intended for canning.

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Epigenetic studies are commonly conducted on DNA from tissue samples. However, tissues are ensembles of cells that may each have their own epigenetic profile, and therefore inter-individual cellular heterogeneity may compromise these studies. Here, we explore the potential for such confounding on DNA methylation measurement outcomes when using DNA from whole blood. DNA methylation was measured using pyrosequencing-based methodology in whole blood (n = 50–179) and in two white blood cell fractions (n = 20), isolated using density gradient centrifugation, in four CGIs (CpG Islands) located in genes HHEX (10 CpG sites assayed), KCNJ11 (8 CpGs), KCNQ1 (4 CpGs) and PM20D1 (7 CpGs). Cellular heterogeneity (variation in proportional white blood cell counts of neutrophils, lymphocytes, monocytes, eosinophils and basophils, counted by an automated cell counter) explained up to 40% (p<0.0001) of the inter-individual variation in whole blood DNA methylation levels in the HHEX CGI, but not a significant proportion of the variation in the other three CGIs tested. DNA methylation levels in the two cell fractions, polymorphonuclear and mononuclear cells, differed significantly in the HHEX CGI; specifically the average absolute difference ranged between 3.4–15.7 percentage points per CpG site. In the other three CGIs tested, methylation levels in the two fractions did not differ significantly, and/or the difference was more moderate. In the examined CGIs, methylation levels were highly correlated between cell fractions. In summary, our analysis detects region-specific differential DNA methylation between white blood cell subtypes, which can confound the outcome of whole blood DNA methylation measurements. Finally, by demonstrating the high correlation between methylation levels in cell fractions, our results suggest a possibility to use a proportional number of a single white blood cell type to correct for this confounding effect in analyses.

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Björn Þór Aðalsteinsson

Research Group Leader

bjornth@matis.is

Epigenetic mechanisms modulate genome function by writing, reading and erasing chromatin structural features. These have an impact on gene expression, contributing to the establishment, maintenance and dynamic changes in cellular properties in normal and abnormal situations. Great effort has recently been undertaken to catalogue the genome-wide patterns of epigenetic marks-creating reference epigenomes-which will deepen our understanding of their contributions to genome regulation and function with the promise of revealing further insights into disease etiology. The foundation for these global studies is the smaller scale experimentally-derived observations and questions that have arisen through the study of epigenetic mechanisms in model systems. One such system is genomic imprinting, a process causing the mono-allelic expression of genes in a parental-origin specific manner controlled by a hierarchy of epigenetic events that have taught us much about the dynamic interplay between key regulators of epigenetic control. Here, we summarize some of the most noteworthy lessons that studies on imprinting have revealed about epigenetic control on a wider scale. Specifically, we will consider what these studies have revealed about: the variety of relationships between DNA methylation and transcriptional control; the regulation of important protein-DNA interactions by DNA methylation; the interplay between DNA methylation and histone modifications; and the regulation and functions of long non-coding RNAs.

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The paternally expressed imprinted retrotransposon-like 1 (Rtl1) is a retrotransposon-derived gene that has evolved a function in eutherian placentation. Seven miRNAs, including miR-127, are processed from a maternally expressed antisense Rtl1 transcript (Rtl1as) and regulate Rtl1 levels through RNAi-mediated post-transcriptional degradation. To determine the relative functional role of Rtl1as miRNAs in Rtl1 dosage, we generated a mouse specifically deleted for miR-127. The miR-127 knockout mice exhibit placentomegaly with specific defects within the labyrinthine zone involved in maternal-fetal nutrient transfer. Although fetal weight is unaltered, specific Rtl1 transcripts and protein levels are increased in both the fetus and placenta. Phenotypic analysis of single (ΔmiR-127/Rtl1 or miR-127/ΔRtl1) and double (ΔmiR-127/ΔRtl1) heterozygous miR-127- and Rtl1-deficient mice indicate that Rtl1 is the main target gene of miR-127 in placental development. Our results demonstrate that miR-127 is an essential regulator of Rtl1, mediated by a trans-homologue interaction between reciprocally imprinted genes on the maternally and paternally inherited chromosomes.

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AbstractPw1/Peg3 is an imprinted gene expressed from the paternally inherited allele. Several imprinted genes, including Pw1/Peg3, have been shown to regulate overall body size and play a role in adult stem cells. Pw1/Peg3 is expressed in muscle stem cells (satellite cells) as well as a progenitor subset of muscle interstitial cells (PICs) in adult skeletal muscle. We therefore examined the impact of loss-of-function of Pw1/Peg3 during skeletal muscle growth and in muscle stem cell behavior. We found that constitutive loss of Pw1/Peg3 function leads to a reduced muscle mass and myofiber number. In newborn mice, the reduction in fiber number is increased in homozygous mutants as compared to the deletion of only the paternal Pw1/Peg3 allele, indicating that the maternal allele is developmentally functional. Constitutive and a satellite cell-specific deletion of Pw1/Peg3, revealed impaired muscle regeneration and a reduced capacity of satellite cells for self-renewal. RNA sequencing analyses revealed a deregulation of genes that control mitochondrial function. Consistent with these observations, Pw1/Peg3 mutant satellite cells displayed increased mitochondrial activity coupled with accelerated proliferation and differentiation. Our data show that Pw1/Peg3 regulates muscle fiber number determination during fetal development in a gene-dosage manner and regulates satellite cell metabolism in the adult.

Contact

Björn Þór Aðalsteinsson

Research Group Leader

bjornth@matis.is

Seaweed (or macroalgae) produced sustainably at large scale opens opportunities as source of fuels, chemicals and food. The production does not directly compete with terrestrial food production and may make use of anthropogenic sources of carbon dioxide and nitrogen. Seaweed biomass can be transformed into a suitable substrate for fermentation using a biorefinery approach. In this study the entire process of biofuel production from seaweed is described: starting with cultivation and harvest, the seaweed is dried and cut, enzymatically hydrolysed, demineralized, detoxified, and finally fermented into acetone, butanol, and ethanol (ABE). Juvenile Saccharina latissima was directly seeded on AlgaeTex® nets and cultivated in the North East Atlantic off the west coast of Scotland for 6 months. Sun dried seaweed was hydrolysed with different enzymes, looking for optimal glucose release, solid/liquid ratio, and enzyme load. Using Cellic® CTec2 in combination with alginate lyases, approximately 80% of available glucose was released. The hydrolysis was scaled up to 100 L, using only Cellic® CTec2. Part of the hydrolyzate was demineralized using ion-exclusion chromatography, removing over 90% of minerals while recovering 92% of glucose and mannitol. A fraction of the demineralized hydrolysate was additionally detoxified using a hydrophobic resin to remove hydrophobic components to a concentration below detection limit. The three hydrolysates (untreated, demineralized, and demineralized followed by detoxification) were used as substrate for ABE production by a newly developed strain of Clostridium acetobutylicum adapted to grow on S. latissima hydrolyzate. Demineralization reduced the lag phase of fermentation from 72 h (untreated) to 24–48 h. Further detoxification of the hydrolysate led to immediate fermentation, resulting in a yield of 0.23 ± 0.02 g_ABE/g_sugar similar to control fermentation in control medium (0.19 g_ABE/g_sugar).

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Seaweed biomass is an underutilized resource that is rich in polysaccharides, including xylan. Seaweed polysaccharides could be used as a feedstock in industrial microbiology and and for production of prebiotic oligosaccharides and rare monosaccharides – processes that would benefit from the availability of robust enzymes that break down the seaweed polysaccharides. The present study aimed to identify genes encoding endo-xylanases in bacterial genomes and metagenomes sourced from marine thermal environments, and to characterize the respective enzymes. Twelve endo-xylanases were studied which displayed 59 % median maximal sequence similarity to characterized GH10 or GH11 enzymes. Overall, most of the enzymes functioned optimally at high temperatures, in the presence of salt, and at circumneutral pH. Eight enzymes functioned optimally at temperatures of 50°C or higher, and in the most extreme cases at 85°C to 95°C. Six enzymes retained activity after three-hour incubation at 60°C or higher. Ten enzymes displayed improved catalytic function in the presence of salt, and several retained high catalytic function at 10 % NaCl concentration. All the enzymes hydrolyzed xylan from diverse sources, including crude biomass. The study contributes to an increased understanding of the structural diversity of xylanases; it expands the availability of thermostable xylanases of marine origin; and contributes to increased valorization of seaweed biomass.

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Contact

Kolbrún Sveinsdóttir

Project Manager

kolbrun.sveinsdottir@matis.is

Svalbard is situated in the north between mainland Norway and the North Pole. In the coming 10 years, the Snow crab (SC) and Red king crab (RKC) are assumed to establish themselves in the fjords around Svalbard. We have explored conditions for utilizing local SC and RKC in culinary dishes/experiences in Svalbard.

This will contribute to Svalbard’s sustainability as most of the food consumed is transported from mainland Norway. Workshops, test fishery, survey of the tourists’ interest, and development of culinary dishes were performed. Furthermore, we have described the biological, practical, and regulatory conditions for local harvesting, processing, and live holding of the crabs in Svalbard. The survey revealed that most tourists did not know SC or RKC. Still, they were interested in local food, including crabs. Challenges have been identified and solutions proposed to ensure that when SC and RKC are present in the Svalbard fjords, a local, sustainable pot fishery can provide locally caught crabs, offering tourists a “taste of the Arctic”.

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