Genetic variability of muscle biological characteristics of young Limousin bulls

Genetic parameters of 4 muscle biological characteristics (protein to DNA ratio (Pro/DNA), lactate dehydrogenase (LDH) activity, isocitrate dehydrogenase (ICDH) activity and the proportion of type I myosin heavy chains (MHC I)), in the Semitendinosus and the Longissimus thoracis, were estimated simultaneously with average daily gain (ADG), 480-d final weight (FW), carcass lean and fat contents (CL% and CF% respectively) in a sample of young Limousin bulls tested in station. The data came from 144 animals, the progeny of 15 sires. Sire and residual variances and covariances were estimated u using an expectation maximization restricted maximum likelihood (EM-REML) procedure applied to a multitrait mixed model. Heritability coefficients of production traits, ADG, FW, CL% and CF%, were 0.19, 0.49, 0.39 and 0.43, respectively, while heritability coefficients of muscle characteristics, Pro/DNA, LDH, ICDH and MHC I, were 0.11, 0.26, 1.03 and 0.35 respectively, in the Semitendinosus muscle and 0.29, 0.31, 0.28 and 0.41, respectively, in the Longissimus thoracis muscle. In both muscles, the oxidative activity of the ICDH appeared to be genetically associated with the proportion of type I myosin heavy chains and opposed to the glycolytic activity of the LDH. The LDH activity was clearly associated with higher muscle-to-fat ratio, while the opposite relationship was observed between that ratio and the ICDH activity or the MHC I proportion.Les paramètres génétiques de 4 caractéristiques biologiques - le rapport protéines /ADN (Pro/DNA), les activités de la lactate déshydrogénase (LDH) et de l’isocitrate déshydrogénase (ICDH) et la proportion en chaînes lourdes de myosine lente (MHC I) - des muscles Semitendinosus et Longissimus thoracis, et ceux du gain moyen quotidien (ADG), du poids vif finaL à 480 j (FW) et des teneurs de la carcasse en muscles et en dépôts adipeux (CL% and CF% respectivement), ont été estimés simultanément à partir d’un échantillon de taurillons Limousins contrôlés en station. Le fichier comprenait 144 veaux issus de 15 pères testés sur descendance. Les variances et covariances paternelles et résiduelles ont été estimées par la méthode du maximum de vraisemblance restreinte, avec l’algorithme d’espérance-maximisation, appliquée à un modèle mixte multicaractère (EM-REML). Les coefficients d’héritabilité des variables de production, ADG, FW, CL% et CF%, s’élevaient respectivement à 0,19, 0,49, 0,39 et 0,43, tandis que les coefficients d’héritabilité des caractéristiques musculaires, Pro/DNA, LDH, ICDH et MHC I, valaient respectivement 0,11, 0,26, 1,03 et 0,35 dans le muscle Semitendinosus et 0,29, 0,31, 0,28 et 0,41 dans le muscle Longissimus thoracis. Dans les 2 muscles, l’activité oxidative de l’ICDH était génétiquement associée à la proportion de myosine lente et opposée à l’activité glycolytique du LDH. Cette activité du LDH était positivement corrélée avec le rapport muscles / dépôts adipeux, alors qu’une relation inverse était observée avec l’activité de l’ICDH et la proportion de MHC I

PaCTS 1.0: A Crowdsourced Reporting Standard for Paleoclimate Data

The progress of science is tied to the standardization of measurements, instruments, and data. This is especially true in the Big Data age, where analyzing large data volumes critically hinges on the data being standardized. Accordingly, the lack of community-sanctioned data standards in paleoclimatology has largely precluded the benefits of Big Data advances in the field. Building upon recent efforts to standardize the format and terminology of paleoclimate data, this article describes the Paleoclimate Community reporTing Standard (PaCTS), a crowdsourced reporting standard for such data. PaCTS captures which information should be included when reporting paleoclimate data, with the goal of maximizing the reuse value of paleoclimate data sets, particularly for synthesis work and comparison to climate model simulations. Initiated by the LinkedEarth project, the process to elicit a reporting standard involved an international workshop in 2016, various forms of digital community engagement over the next few years, and grassroots working groups. Participants in this process identified important properties across paleoclimate archives, in addition to the reporting of uncertainties and chronologies; they also identified archive-specific properties and distinguished reporting standards for new versus legacy data sets. This work shows that at least 135 respondents overwhelmingly support a drastic increase in the amount of metadata accompanying paleoclimate data sets. Since such goals are at odds with present practices, we discuss a transparent path toward implementing or revising these recommendations in the near future, using both bottom-up and top-down approaches

PaCTS 1.0: A Crowdsourced Reporting Standard for Paleoclimate Data

The progress of science is tied to the standardization of measurements, instruments, and data. This is especially true in the Big Data age, where analyzing large data volumes critically hinges on the data being standardized. Accordingly, the lack of community-sanctioned data standards in paleoclimatology has largely precluded the benefits of Big Data advances in the field. Building upon recent efforts to standardize the format and terminology of paleoclimate data, this article describes the Paleoclimate Community reporTing Standard (PaCTS), a crowdsourced reporting standard for such data. PaCTS captures which information should be included when reporting paleoclimate data, with the goal of maximizing the reuse value of paleoclimate data sets, particularly for synthesis work and comparison to climate model simulations. Initiated by the LinkedEarth project, the process to elicit a reporting standard involved an international workshop in 2016, various forms of digital community engagement over the next few years, and grassroots working groups. Participants in this process identified important properties across paleoclimate archives, in addition to the reporting of uncertainties and chronologies; they also identified archive-specific properties and distinguished reporting standards for new versus legacy data sets. This work shows that at least 135 respondents overwhelmingly support a drastic increase in the amount of metadata accompanying paleoclimate data sets. Since such goals are at odds with present practices, we discuss a transparent path toward implementing or revising these recommendations in the near future, using both bottom-up and top-down approaches

Effects of the total replacement of fish-based diet with plant-based diet on the hepatic transcriptome of two European sea bass (Dicentrarchus labrax) half-sibfamilies showing different growth rates with the plant-based diet

Background: Efforts towards utilisation of diets without fish meal (FM) or fish oil (FO) in finfish aquaculture have been being made for more than two decades. Metabolic responses to substitution of fishery products have been shown to impact growth performance and immune system of fish as well as their subsequent nutritional value, particularly in marine fish species, which exhibit low capacity for biosynthesis of long-chain poly-unsaturated fatty acids (LC-PUFA). The main objective of the present study was to analyse the effects of a plant-based diet on the hepatic transcriptome of European sea bass (Dicentrarchus labrax). Results: We report the first results obtained using a transcriptomic approach on the liver of two half-sibfamilies of the European sea bass that exhibit similar growth rates when fed a fish-based diet (FD), but significantly different growth rates when fed an all-plant diet (VD). Overall gene expression was analysed using oligo DNA microarrays (GPL9663). Statistical analysis identified 582 unique annotated genes differentially expressed between groups of fish fed the two diets, 199 genes regulated by genetic factors, and 72 genes that exhibited diet-family interactions. The expression of several genes involved in the LC-PUFA and cholesterol biosynthetic pathways was found to be up-regulated in fish fed VD, suggesting a stimulation of the lipogenic pathways. No significant diet-family interaction for the regulation of LC-PUFA biosynthesis pathways could be detected by microarray analysis. This result was in agreement with LC-PUFA profiles, which were found to be similar in the flesh of the two half-sibfamilies. In addition, the combination of our transcriptomic data with an analysis of plasmatic immune parameters revealed a stimulation of complement activity associated with an immunodeficiency in the fish fed VD, and different inflammatory status between the two half-sibfamilies. Biological processes related to protein catabolism, amino acid transaminations, RNA splicing and blood coagulation were also found to be regulated by diet, while the expression of genes involved in protein and ATP synthesis differed between the half-sibfamilies. Conclusions: Overall, the combined gene expression, compositional and biochemical studies demonstrated a large panel of metabolic and physiological effects induced by total substitution of both FM and FO in the diets of European sea bass and revealed physiological characteristics associated with the two half-sibfamilies

Replacement of Marine Fish Oil with de novo Omega-3 Oils from Transgenic Camelina sativa in Feeds for Gilthead Sea Bream (Sparus aurata L.)

Omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA) are essential components of the diet of all vertebrates and. The major dietary source of n-3 LC-PUFA for humans has been fish and seafood but, paradoxically, farmed fish are also reliant on marine fisheries for fish meal and fish oil (FO), traditionally major ingredients of aquafeeds. Currently, the only sustainable alternatives to FO are vegetable oils, which are rich in C18 PUFA, but devoid of the eicosapentaenoic (EPA) and docosahexaenoic acids (DHA) abundant in FO. Two new n-3 LC-PUFA sources obtained from genetically modified (GM) Camelina sativa containing either EPA alone (ECO) or EPA and DHA (DCO) were compared to FO and wild-type camelina oil (WCO) in juvenile sea bream. Neither ECO nor DCO had any detrimental effects on fish performance, although final weight of ECO-fed fish (117 g) was slightly lower than that of FO- and DCO-fed fish (130 and 127 g, respectively). Inclusion of the GM-derived oils enhanced the n-3 LC-PUFA content in fish tissues compared to WCO, although limited biosynthesis was observed indicating accumulation of dietary fatty acids. The expression of genes involved in several lipid metabolic processes, as well as fish health and immune response, in both liver and anterior intestine were altered in fish fed the GM-derived oils. This showed a similar pattern to that observed in WCO-fed fish reflecting the hybrid fatty acid profile of the new oils. Overall the data indicated that the GM-derived oils could be suitable alternatives to dietary FO in sea bream