ROBUSTFISH: NEW POSSIBILITIES FOR GROWTH AND ROBUSTNESS IN ORGANIC AQUACULTURE

The aim of Robustfish project is to answer the following research questions: (1) Is it possible to select robust rainbow trout fry early in development before they enter the more cost intensive steps in the production cycle? (2) Does sustainable (non-fish based) dietary lipid sources affect stress resilience and immune-competence of the fry? (3) Related to (1) and (2): Is improved resistance to RTFS achieved? (4) How will the market respond to a significant increase in production of organic trout, i.e. consumer preferences and competiveness by companies in the value chain? RobustFish will strengthen the development of Danish organic trout production. In this respect the robustness of the fry to diseases is crucial, i.a. RTFS. The robustness of the fry seems to be related to larval developmental rate and to the dietary content of specific Ω-3 fatty acids (HUFAs). Stress and RTFS challenge tests will be performed to investigate if these two factors can be included in strategies to increase the robustness of the fry. Further, the effect of water treatments on health and welfare using approved agents (Pedersen et al., 2013) is tested. RobustFish will create growth – based on organic principles and in a balance between environment, ethics and economy. The efforts will also aim at improving the productivity of the conventional trout farming by a lower prevalence of RTFS, reduced medication and lower environmental impact. Connected to these efforts RobustFish also will provide needed knowledge about market conditions and consumer attitudes, including the competitive effect of increased production (Nielsen et al., 2007). Mapping the existing types of organic aquaculture products in European markets will pave the way for product development and increased market share

Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction

<p>Abstract</p> <p>Background</p> <p>Reliable predictions of Cytotoxic T lymphocyte (CTL) epitopes are essential for rational vaccine design. Most importantly, they can minimize the experimental effort needed to identify epitopes. NetCTL is a web-based tool designed for predicting human CTL epitopes in any given protein. It does so by integrating predictions of proteasomal cleavage, TAP transport efficiency, and MHC class I affinity. At least four other methods have been developed recently that likewise attempt to predict CTL epitopes: EpiJen, MAPPP, MHC-pathway, and WAPP. In order to compare the performance of prediction methods, objective benchmarks and standardized performance measures are needed. Here, we develop such large-scale benchmark and corresponding performance measures and report the performance of an updated version 1.2 of NetCTL in comparison with the four other methods.</p> <p>Results</p> <p>We define a number of performance measures that can handle the different types of output data from the five methods. We use two evaluation datasets consisting of known HIV CTL epitopes and their source proteins. The source proteins are split into all possible 9 mers and except for annotated epitopes; all other 9 mers are considered non-epitopes. In the RANK measure, we compare two methods at a time and count how often each of the methods rank the epitope highest. In another measure, we find the specificity of the methods at three predefined sensitivity values. Lastly, for each method, we calculate the percentage of known epitopes that rank within the 5% peptides with the highest predicted score.</p> <p>Conclusion</p> <p>NetCTL-1.2 is demonstrated to have a higher predictive performance than EpiJen, MAPPP, MHC-pathway, and WAPP on all performance measures. The higher performance of NetCTL-1.2 as compared to EpiJen and MHC-pathway is, however, not statistically significant on all measures. In the large-scale benchmark calculation consisting of 216 known HIV epitopes covering all 12 recognized HLA supertypes, the NetCTL-1.2 method was shown to have a sensitivity among the 5% top-scoring peptides above 0.72. On this dataset, the best of the other methods achieved a sensitivity of 0.64. The NetCTL-1.2 method is available at <url>http://www.cbs.dtu.dk/services/NetCTL</url>.</p> <p>All used datasets are available at <url>http://www.cbs.dtu.dk/suppl/immunology/CTL-1.2.php</url>.</p

Immune epitope database analysis resource (IEDB-AR)

We present a new release of the immune epitope database analysis resource (IEDB-AR, http://tools.immuneepitope.org), a repository of web-based tools for the prediction and analysis of immune epitopes. New functionalities have been added to most of the previously implemented tools, and a total of eight new tools were added, including two B-cell epitope prediction tools, four T-cell epitope prediction tools and two analysis tools

Rapport fra RobustFish temadag d. 5. april 2018

Formålet med RobustFish projektet var at: • Styrke udviklingen af økologisk ørredproduktion i Danmark men også til gavn for konventionelt opdræt • Undersøge ørredyngels robusthed i forhold til start-fodrings adfærd, fedtsyreindholdet i foderet og følsomhed over for yngeldødeligheds-syndromet (YDS) • Effekt af vandbehandling med hjælpestoffer • Viden om markedsforhold, forbrugerkendskab, produktudvikling og øget afsætning. Robustfish har adresseret ovennævnte problemstillinger, og på grundlag af opnåede resultater kan der drages følgende konklusioner og deraf følgende anbefalinger og perspektiver for styrkelse af det økologiske opdræt af regnbueørred i Danmark. • Yngel med tidlig fødesøgnings adfærd (swim-up) viste tendens til større robusthed over for de anvendte stress påvirkninger. • Der var ingen statistisk forskel mellem dødelighed forårsaget af YDS-bakterien Flavobacterium psychrophilum og ”Tidlig”, ”Mellem” og ”Sen” swim-up adfærd. • Udskiftning af marine protein kilder (kun 10 % fiskemel i diæterne) med vegetabilske viste negativ effekt på foderindtag, vækst og dødelighed i regnbueørred yngel. • Lavt indhold af flerumættede fedtsyrer (HUFA) i foderet (> 1 % af total fedtsyrer (TFA)) havde tilsyneladende kun lille påvirkning på vækst, foderkonvertering (FK) og enzymatisk aktivitet indtil 100 dage efter startfodring – i foder med optimal marin proteinkilde. • Fedtsyre resultater indikerede, at ørred tilsyneladende kan syntetisere kortere kædede fedtsyrer til HUFA. • De godkendte hjælpestoffer anvendes med større sikkerhed og dambrugerne er blevet fortrolige med produkterne, ligesom fiskene tilsyneladende tilpasser sig de grønne hjælpestoffer. • Behov for optimering af driften med henblik på dels at sikre en bedre og mere stabil vandkvalitet – og derved reducere brugen af hjælpestoffer og dels sikre fiskevelfærd, herunder også vandcirkulation, beluftning, overdækning, mm.). • Det vurderes at der vil være gode muligheder for at opretholde en merpris (20 – 30 %) på økologiske ørreder, og at markedsføring skal fokusere mere på dyrevelfærd end miljø. • Forbrugerne havde en negativ opfattelse af opdrættet fisk, der blev forbundet med noget negativt - på linje med industrialiseret landbrug og i modsætning til ”vile fisk”. • Kun få forbrugere var i stand til at identificere regler for økologisk fisk og ofte sammenblandedes de med MSC, ASC og andre certificeringer. • Der behov for en systematisk kommunikations-/forbrugeroplysningskampagne med fokus på større bevidsthed om ”Økologisk fisk”, der er opdrættet og kontrolleret i forhold til specifikke regler for økologisk akvakultur og at økomærket adskiller sig fra f. eks. miljømærkerne MSC og ASC. • Stigende efterspørgsel efter økologiske produkter i Europa vil være et godt afsætningsmæssigt grundlag for at fastholde målsætningen i regeringens 2020-plan for dansk akvakultur. Det anbefales at der skabes yderligere incitament til omlægning af dambrug til økologisk produktion

Leisure time physical activity in middle age predicts the metabolic syndrome in old age: results of a 28-year follow-up of men in the Oslo study

<p>Abstract</p> <p>Background</p> <p>Data are scarce on the long term relationship between leisure time physical activity, smoking and development of metabolic syndrome and diabetes. We wanted to investigate the relationship between leisure time physical activity and smoking measured in middle age and the occurrence of the metabolic syndrome and diabetes in men that participated in two cardiovascular screenings of the Oslo Study 28 years apart.</p> <p>Methods</p> <p>Men residing in Oslo and born in 1923–32 (n = 16 209) were screened for cardiovascular diseases and risk factors in 1972/3. Of the original cohort, those who also lived in same area in 2000 were invited to a repeat screening examination, attended by 6 410 men. The metabolic syndrome was defined according to a modification of the National Cholesterol Education Program criteria. Leisure time physical activity, smoking, educational attendance and the presence of diabetes were self-reported.</p> <p>Results</p> <p>Leisure time physical activity decreased between the first and second screening and tracked only moderately between the two time points (Spearman's ρ = 0.25). Leisure time physical activity adjusted for age and educational attendance was a significant predictor of both the metabolic syndrome and diabetes in 2000 (odds ratio for moderately vigorous versus sedentary/light activity was 0.65 [95% CI, 0.54–0.80] for the metabolic syndrome and 0.68 [0.52–0.91] for diabetes) (test for trend P < 0.05). However, when adjusted for more factors measured in 1972/3 including glucose, triglycerides, body mass index, treated hypertension and systolic blood pressure these associations were markedly attenuated. Smoking was associated with the metabolic syndrome but not with diabetes in 2000.</p> <p>Conclusion</p> <p>Physical activity during leisure recorded in middle age prior to the current waves of obesity and diabetes had an independent predictive association with the presence of the metabolic syndrome but not significantly so with diabetes 28 years later in life, when the subjects were elderly.</p