The MEGGASENSE platform constructs relational databases of DNA or protein sequences. The default functional analysis uses 14 106 hidden Markov model (HMM) profiles based on sequences in the KEGG database. The Solr search engine allows sophisticated queries and a BLAST search function is also incorporated. These standard capabilities were used to generate the SCATT database from the predicted proteome of Streptomyces cattleya. The implementation of a specialized metagenome database (AMYLOMICS) for bioprospecting of carbohydrate-modifying enzymes is described. In addition to standard assembly of reads, a novel 'functional' assembly was developed, in which screening of reads with the HMM profiles occurs before the assembly. The AMYLOMICS database incorporates additional HMM profiles for carbohydrate-modifying enzymes and it is illustrated how the combination of HMM and BLAST analyzes helps identify interesting genes. A variety of different proteome and metagenome databases have been generated by MEGGASENSE.
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The European Virus-X project explores the virus genomes contained in extreme environments: geothermal hot springs in Iceland, large marine funds of the North Atlantic… for molecular biology applications.
The estimated number of viruses on Earth extends far beyond the estimated number of stars in the Observable Universe. Each type of organism, unicellular or multicellular, can potentially be infected by them. Even in the most extreme environments, such as geothermal hot water sources, we find, at temperatures near 100 ° C, viruses that live and propagate by infecting the bacteria that thrive in these conditions.
The viruses carry in them the genes necessary for their propagation by the infection of their host cell. Despite the sequencing of genomes of very numerous organisms during the last ten years, those viruses remain largely mysterious. Ditto for the function of proteins coded by viral genomes. Pourta…
Class Ascetosporea (Rhizaria; Endomyxa) comprises many parasites of invertebrates. Within this group, recent group ‐ specific environmental DNA (eDNA) studies have contributed to the establishment of the new order Mikrocytida, a new phylogeny and characterization of Paramyxida, and illuminated the diversity and distribution of haplosporidians. Here, we use general and lineage ‐ specific PCR primers to investigate the phylogenetic “gap” between haplosporidians and their closest known free ‐ living relatives, the testate amoeba Gromia and reticulate amoeba Filoreta. Within this gap are Paradinium spp. parasites of copepods, which we show to be highly diverse and widely distributed in planktonic and benthic samples. We reveal a robustly supported radiation of parasites, ENDO ‐ 3, comprised of Paradinium and three further clades (ENDO ‐ 3a, ENDO ‐ 3b and SPP). A further environmental group, ENDO ‐ 2, perhaps comprising several clades, branches between this radiation and the free ‐ living amoebae. Early diverging haplosporidians were also amplified, often associated with bivalves or deep ‐ sea samples. The general primer approach amplified an overlapping set of novel lineages within ENDO ‐ 3 and Haplosporida, whereas the group ‐ specific primer strategy, targeted to amplify from the earliest known divergent haplosporidians to Gromia, generated greater sequence diversity across part of this phylogenetic range.
The rock ptarmigan (Lagopus muta) is a popular game bird in Iceland, but the population has endured a long-term decline. A hunting ban was enforced in 2003, but 2 years later hunting was allowed again with added restrictions. The aim of this study was to investigate the effects of a change in hunting regulations on the ptarmigan population in northeast Iceland, 1998–2013, using a population reconstruction model and to estimate the abundance of juveniles and adults, natural survival, and harvest mortality. The estimated abundance at the beginning of the hunting season ranged from 42,000 (95% CI = 36,000–49,000) birds in 2002 to 158,000 (95% CI = 105,000–250,000) in 1998. The natural survival of adult rock ptarmigan was density dependent and ranged from 36% to 65% (95% CI = 30–75%). Survival for juveniles was constant and was estimated to be 19% (95% CI = 18–20%). We included a change point in the model to account for a change in the harvest mortality that could have occurred with the changes in the hunting regulations. The results indicated that the change in hunting regulations did reduce ptarmigan harvest mortality and changed the harvest strategies of hunters. Inclusion of a change point in models is useful for managers to test if a change in regulations had an effect on the target population. © 2018 The Wildlife Society.
Rhodothermus marinus, a marine aerobic thermophile, was first isolated from an intertidal hot spring in Iceland. In recent years, the R. marinus strain PRI 493 has been genetically modified, which opens up possibilities for targeted metabolic engineering of the species, such as of the carotenoid biosynthetic pathway. In this study, the carotenoids of the R. marinus type-strain DSM 4252T, strain DSM 4253, and strain PRI 493 were characterized. Bioreactor cultivations were used for pressurized liquid extraction and analyzed by ultra-high performance supercritical fluid chromatography with diode array and quadropole time-of-flight mass spectrometry detection (UHPSFC-DAD-QTOF / MS). Salinixanthin, a carotenoid originally found in Salinibacter ruber and previously detected in strain DSM 4253, was identified in all three R. marinus strains, both in the hydroxylated and nonhydroxylated form. Furthermore, an additional and structurally distinct carotenoid was detected in the three strains. MS / MS fragmentation implied that the mass difference between salinixanthin and the novel carotenoid structure corresponded to the absence of a 4-keto group on the ß-ionone ring. The study confirmed the lack of carotenoids for the strain SB-71 (ΔtrpBΔpurAcrtBI ':: trpB) in which genes encoding two enzymes of the proposed pathway are partially deleted. Moreover, antioxidant capacity was detected in extracts of all the examined R. marinus strains and found to be 2–4 times lower for the knock-out strain SB-71. A gene cluster with 11 genes in two operons in the R. marinusDSM 4252T genome was identified and analyzed, in which several genes were matched with carotenoid biosynthetic pathway genes in other organisms.
Novel strategies for thawing of pre-rigor frozen Atlantic cod (Gadus morhua) in water with air circulation, applying different and controlled temperatures are presented. After thawing (day 0) and after six days of storage at 2.9 ± 0.6 ° C (day 6), quality parameters (thawing- and drip loss, cooking yield, sensory evaluation, and textural properties), chemical (pH, water content, total volatile basic nitrogen (TVB-N)) and microbiological analyzes (total viable counts (TVC-IA), H2S-producing bacteria (H2S-IA), coliforms, thermo-tolerant coliforms and presumptive E. coli, and Listeria monocytogenes) were performed. The results obtained were compared statistically. Both thawing strategies, thawing at 10 ° C and −0.5 ° C or at constant 10 ° C, preserved good quality fish. The hygienic conditions during the thawing processes were satisfactory and there were no indications of impaired food safety during any of the thawing strategies. No pathogens were detected in any of the cod samples, nor in the thawing media. The results showed that water thawing at −0.5 to 10 ° C is suitable for frozen cod, without compromising quality and safety, and that no significant difference were seen between the selected thawing temperature regimes.
Background: The catch of marine whitefish is typically seasonal, whereas the land based processing industry has a need for all-year stable supply of raw materials. This challenge can be met by applying fish frozen at sea. When using frozen fish the methods employed for thawing may influence the safety and quality of the final product. This study aimed to investigate the applicability of novel thawing strategies in order to provide an all-year supply of high-quality and safe cod products. Results: Comparative investigations of quality and safety factors after thawing in water, with and without air circulation, and contact thawing were performed. The parameters included water-holding capacity, thawing loss, drip loss, cooking yield, sensory evaluation and microbiological analysis (including TVB-N). Water thawing with air circulation provided faster thawing compared to water thawing without air circulation and contact thawing. For all three methods, the quality of the thawed fish was acceptable and the shelf life of the fillets during chilled storage was between 10 and 14 days post-filleting. Conclusion: The results show that controlled freezing of cod, followed by appropriate thawing may provide the processing industry with an all-year delivery of raw materials, without compromising quality and safety of the final product.
A Quality Management Framework to improve quality and harmonization of Total Diet Study practices in Europe was developed within the TDS-Exposure Project. Seventeen processes were identified and hazards, Critical Control Points and associated preventive and corrective measures described. The Total Diet Study process was summarized in a flowchart divided into planning and practical (sample collection, preparation and analysis; risk assessment analysis and publication) phases. Standard Operating Procedures were developed and implemented in pilot studies in five organizations. The flowchart was used to develop a quality framework for Total Diet Studies that could be included in formal quality management systems. Pilot studies operated by four project partners were visited by project assessors who reviewed implementation of the proposed framework and identified areas that could be improved. The quality framework developed can be the starting point for any Total Diet Study center and can be used within existing formal quality management approaches.
Seafood is amongst the most internationally traded food commodities worldwide and it is one of the food groups most likely to be subject to fraud. A number of studies have been conducted where samples from retail-, restaurant- and food service outlets have been tested for species substitution. These studies have mostly focused on specific species, particular types of outlets or confined to some geographical location. The study presented in this paper is the first large-scale attempt to study the rate of fish mislabeling in mass caterer (HoReCa) sector across Europe. A total of 283 samples were collected in 180 mass caterer outlets in 23 European countries. DNA barcoding revealed that 26% of the samples were mislabeled and that 31% of the outlets sold mislabeled seafood. The highest mislabeling rate was observed in Spain, Iceland, Finland and Germany, where close to 50% of the outlets sampled offered mislabeled seafood. Conversely, there was no mislabeling detected in Sweden, Switzerland and Slovakia. The species with the highest mislabeling rates were dusky grouper, butterfish, pike perch, sole, bluefin tuna and yellowfin tuna. In the case of other important fish species in Europe such as hake, cod, haddock and swordfish, mislabeling rates ranged between 14 and 33%. The results of the study show that the majority of the mislabelings are with cheaper fish, such as the presence of Pangasius commonly substituting other species, being labeled as more expensive ones, suggesting economic motivation for mislabeling.
Fishers are often perceived to be poor, and low income levels are used to justify subsidies and other types of direct and indirect income support to maintain coastal communities. In this study fishers' income levels are investigated in four Nordic countries; Denmark, Iceland, Norway and Sweden for different types of fishers and vessels and in comparison to alternative occupations. The most important result is that fishers in these countries are doing relatively well, and only in Sweden is the fishers' average income level below the average national income. Within the fleets, there are substantial differences. Owners of coastal vessels tend to have the lowest income, and also lower than crews. Owners as well as crews on larger vessels tend to do much better and in the largest fishing nations, Iceland and Norway, they do especially well.