We describe an emerging initiative – the ‘Functional Annotation of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.
Flokkur: Greinar
The effects of dietary lipid oxidation on fish are diverse and contradictory. In this study, herring oil was oxidized to five different levels (peroxide values (POV): 20.44, 182.97, 56.12, 33.27 and 0.00 meq kg− 1) and used to formulate five experimental diets. Juvenile Arctic charr (Salvelinus alpinus, mean body mass ± SD: 2.41 ± 0.11 g) were reared on the five diets for 67 days. In another experiment, juvenile Nile tilapia (Oreochromis niloticus) (1.71 ± 0.40 g) were reared on three diets formulated with oxidized oils having POV of 19.55, 447.27 and 32.72 respectively, for 90 days. Growth responses were monitored in quadruplicate groups of 60 individuals of Arctic charr and 100 for Nile tilapia, respectively. The activities of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx) were only studied in Arctic charr.
At the end of the study, the Arctic charr group reared on a diet with oils in the primary oxidation state had significantly lower body mass and specific growth rate, but higher hepatosomatic index compared to the rest of the groups. The activities of CAT and GPx increased with dietary lipid oxidation while that of SOD remained fairly stable. In Nile tilapia, both final body mass and condition factor were significantly lower in the group fed fresh oil than in the groups fed oxidized oils. Fillet lipid content decreased with lipid oxidation while ash and protein did not differ amongst tilapia groups. The results suggest that Arctic charr are more susceptible to lipid oxidation than are Nile tilapia. These differences may be the result of species differences in tolerance to oxidized lipids, variable lipid intake or access to vitamin E/tocopherol in feed.
Unstable conditions are commonly encountered during industrial storage and transportation of frozen fish. Temperature stress and fluctuations may increase the amount of unfrozen water in the muscle and enzymatic activity and lipid oxidation can thus still take place during frozen storage. The aim of this study was to investigate the changes of characteristics of different muscle types of herring at unstable modelled conditions during storage and transportation. Compositional changes, lipid oxidation and lipid hydrolysis were monitored in light and dark muscle of Atlantic herring (Clupea harengus), during frozen storage, as affected by temperature stress (samples were stored at − 25 °C for 2 months, then stressed at − 12 °C for 1 month, followed by storage at a stable − 25 °C for the remaining storage duration), and compared to samples stored at a stable − 25 °C for 14 months. The dark muscle was more sensitive to lipid oxidation than the light muscle, leading to faster degradation. Increased lipid oxidation and lipid hydrolysis were observed in temperature-stressed samples of both muscle types. The study demonstrated the importance of avoiding temperature stress during industrial frozen storage and transportation to improve the quality and shelf life of frozen herring products. Removal of dark muscle by deep skinning could benefit both processors and customers regarding the shelf life and nutritional value of the light herring muscle.
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 specialised 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 analyses helps identify interesting genes. A variety of different proteome and metagenome databases have been generated by MEGGASENSE.
Le projet européen Virus-X explore les génomes de virus contenusdans des milieux extrêmes : sources chaudes géothermiques en Islande, grands fonds marins de l’Atlantique Nord… Les membres du consortium tentent à présent de repérer les enzymes pouvant constituer de nouveaux ou de meilleurs outils pour des applications de biologie moléculaire.
Le nombre estimé de virus sur Terre dépasse de loin le nombre estimé d’étoiles dans l’Univers observable. Chaque type d’organisme, unicellulaire ou multicellulaire, peut potentiellement être infecté par eux. Même dans les environnements les plus extrêmes, tels que les sources d’eau chaude géothermiques, on trouve, à des températures proches de 100 °C, des virus qui vivent et se propagent en infectant les bactéries qui prospèrent dans ces conditions.
Les virus portent en eux les gènes nécessaires à leur propagation par l’infection de leur cellule hôte. Malgré le séquençage de génomes de très nombreux organismes au cours des dix dernières années, ceux des virus restent en grande partie mystérieux. Idem pour la fonction des protéines codées par les génomes viraux. 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 analyses (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 shows 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.