Genomic sequencing analysis reveals copy number variations and their associations with economically important traits in beef cattle.

Copy number variation (CNV) represents a major source of genetic variation, which may have potentially large effects, including alternating gene regulation and dosage, as well as contributing to gene expression and risk for normal phenotypic variability. We carried out a comprehensive analysis of CNV based on whole genome sequencing in Chinese Simmental beef cattle. Totally, we found 9313 deletion and 234 duplication events, covering 147.5 Mb autosomal regions. Within them, 257 deletion events of high frequency overlapped with 193 known RefGenes. Among these genes, we observed several genes were related to economically important traits, like residual feed intake, immune responding, pregnancy rate and muscle differentiation. Using a locus-based analysis, we identified 11 deletions and 1 duplication, which were significantly associated with three traits including carcass weight, tenderloin and longissimus muscle area. Our sequencing-based study provided important insights into investigating the association of CNVs with important traits in beef cattle.

Ontogenetic scaling of pelvic limb muscles, tendons and locomotor economy in the ostrich (Struthio camelus).

In rapidly growing animals there are numerous selective pressures and developmental constraints underpinning the ontogenetic development of muscle-tendon morphology and mechanical properties. Muscle force generating capacity, tendon stiffness, elastic energy storage capacity and efficiency were calculated from muscle and tendon morphological parameters and in vitro tendon mechanical properties obtained from a growth series of ostrich cadavers. Ontogenetic scaling relationships were established using reduced major axis regression analysis. Ostrich pelvic limb muscle mass and cross-sectional area broadly scaled with positive allometry, indicating maintained or relatively greater capacity for maximum isometric force generation in larger animals. The length of distal limb tendons was found to scale with positive allometry in several tendons associated with antigravity support and elastic energy storage during locomotion. Distal limb tendon stiffness scaled with negative allometry with respect to body mass, with tendons being relatively more compliant in larger birds. Tendon material properties also appeared to be size-dependent, suggesting that the relative increased compliance of tendons in larger ostriches is due in part to compensatory distortions in tendon material properties during maturation and development, not simply from ontogenetic changes in tendon geometry. Our results suggest that the previously reported increase in locomotor economy through ontogeny in the ostrich is due to greater potential for elastic energy storage with increasing body size. In fact, the rate of this increase may be somewhat greater than the conservative predictions of previous studies, thus illustrating the biological importance of elastic tendon structures in adult ostriches.

Muscle quality as a complementary prognostic tool in conjunction with sarcopenia assessment in younger and older individuals.

PURPOSE: This pilot study investigated differences in lean tissue mass, muscle strength, muscle quality (strength per unit of muscle mass; MQ), and functional performance in healthy younger and older individuals. The most robust predictors of appendicular lean mass (ALM) were then determined in each group. METHODS: Fifty younger (18-45 years) and 50 older (60-80 years) participants completed tests of upper and lower body strength alongside body composition by dual-energy X-ray absorptiometry from which upper- and lower-body MQ were estimated. Available cut-points for older people were used to determine low upper-body MQ in both groups. Low lower-body MQ was determined as at least two standard deviations below the mean of the younger group. Functional performance was assessed by gait speed. Sarcopenia was identified using two established definitions. RESULTS: Upper and lower body strength, ALM, lower-body MQ and gait speed were significantly higher in the younger group (all p < 0.002). Sarcopenia was identified in 2-4% of the older group. Low upper-body MQ was evident in 32% and 42% of the younger and older group, respectively. Low lower-body MQ was observed in 4% of younger participants, and 50% of older participants. In both groups, the most robust predictors of ALM were upper and lower body strength (young R2 = 0.74, 0.82; older R2 = 0.68, 0.72). CONCLUSIONS: Low MQ despite low prevalence rates of sarcopenia in both groups suggests a need for age-specific MQ cut-points. Muscle quality assessments might be useful complementary prognostic tools alongside existing sarcopenia definitions.

The effect of micronutrient supplementation on growth and hepatic metabolism in diploid and triploid Atlantic salmon (Salmo salar) parr fed a low marine ingredient diet.

The effects of low marine ingredient diets supplemented with graded levels (L1, L2, L3) of a micronutrient package (NP) on growth and metabolic responses were studied in diploid and triploid salmon parr. Diploids fed L2 showed significantly improved growth and reduced liver, hepatic steatosis, and viscerosomatic indices, while fish fed L3 showed suppressed growth rate 14 weeks post feeding. In contrast, dietary NP level had no effect on triploid performance. Whole body mineral composition, with exception of copper, did not differ between diet or ploidy. Whole fish total AAs and N-metabolites showed no variation by diet or ploidy. Free circulating AAs and white muscle N-metabolites were higher in triploids than diploids, while branch-chained amino acids were higher in diploids than triploids. Diploids had higher whole body α-tocopherol and hepatic vitamins K1 and K2 than triploids. Increased tissue B-vitamins for niacin and whole-body folate with dietary NP supplementation were observed in diploids but not triploids, while whole body riboflavin was higher in diploids than triploids. Hepatic transcriptome profiles showed that diploids fed diet L2 was more similar to that observed in triploids fed diet L3. In particular, sterol biosynthesis pathways were down-regulated, whereas cytochrome P450 metabolism was up-regulated. One­carbon metabolism was also affected by increasing levels of supplementation in both ploidies. Collectively, results suggested that, for optimised growth and liver function, micronutrient levels be supplemented above current National Research Council (2011) recommendations for Atlantic salmon when fed low marine ingredient diets. The study also suggested differences in nutritional requirements between ploidy.

Rabbit meat production and consumption: State of knowledge and future perspectives.

Since the 1970s, in some European countries rabbit meat production has progressively become a highly specialized industry, which has made Europe the second (after China) largest rabbit meat producer in the world. However, the industry is currently facing a critical period due to structural weaknesses, progressive and constant reductions in consumption, and raising criticism related to welfare conditions and other ethical issues. This trend is questioning the future of the rabbit meat industry, which could lead to the loss of knowledge and technical expertise acquired over decades of major investments and research efforts (a valuable cultural and professional heritage for future generations). In the present review, we provide an overview of the rabbit meat industry, market and value chain, we depict consumer's attitude towards rabbit meat, highlighting strengths and weaknesses, and factors driving their current purchase behavior. Finally, we will attempt to outline possible strategies to ensure a sustainable future for the production of rabbits for commercial meat purposes.

Use of olive leaves (whether or not fortified with sodium selenate) in rabbit feeding: Effect on performance, carcass and meat characteristics, and estimated indexes of fatty acid metabolism.

Sixty New Zealand White weaned rabbits were divided into three groups and subjected to different dietary treatments: a standard diet for the control (C), a standard feed supplemented with 10% of plain olive leaves (OL) and a standard feed supplemented with 10% of selenium-fortified olive leaves (100 mg/L of foliar spray sodium selenate solution; SeOL). The productive performance was recorded at the time of slaughter (after 35 days); the carcass and meat traits were determined and estimated indexes of fatty acid metabolism were calculated. No significant differences were found on the rabbit productive performance and the physical-chemical characteristics of the meat. Both group of rabbits on the enriched diet showed leaner and thinner carcasses and a higher meat concentration of oleic acid. The estimated index of Δ5 + Δ6-desaturase, starting from n-6 fatty acids, was lower in both groups supplemented with leaves. The use of selenium-fortified olive leaves, positively affected the lipid oxidative stability of rabbit meat.

Effect of diet and packaging system on the oxidative status and polyunsaturated fatty acid content of rabbit meat during retail display.

The aim of this study was to evaluate the combined effect of two dietary lipid sources (sunflower vs. linseed oil) and three packaging methods (PVC film - BAG vs. modified atmosphere CO2 20% + 80% O2 - MAP vs. and vacuum - VAC) on the oxidative status and polyunsaturated fatty acid content of rabbit loins (Longissimus thoracis et lumborum muscle), at days 1, 4 and 10 of simulated retail display. The diet, storage time and packaging method affected the oxidative status of rabbit meat under retail display. As expected, storage time, independently on the other factors, significantly reduced the antioxidant content of loin meat. Accordingly, TBARs values significantly increased during storage, as well as the dietary supplementation of linseed. The fatty acid profile of the fresh loin closely respected that of the diets. At day 10, oxidative status and fatty acid profile of MAP samples could be yet considered optimal.

Dietary supplementation of branched-chain amino acids increases muscle net amino acid fluxes through elevating their substrate availability and intramuscular catabolism in young pigs.

Branched-chain amino acids (BCAA) have been clearly demonstrated to have anabolic effects on muscle protein synthesis. However, little is known about their roles in the regulation of net AA fluxes across skeletal muscle in vivo. This study was aimed to investigate the effect and related mechanisms of dietary supplementation of BCAA on muscle net amino acid (AA) fluxes using the hindlimb flux model. In all fourteen 4-week-old barrows were fed reduced-protein diets with or without supplemental BCAA for 28 d. Pigs were implanted with carotid arterial, femoral arterial and venous catheters, and fed once hourly with intraarterial infusion of p-amino hippurate. Arterial and venous plasma and muscle samples were obtained for the measurement of AA, branched-chain α-keto acids (BCKA) and 3-methylhistidine (3-MH). Metabolomes of venous plasma were determined by HPLC-quadrupole time-of-flight-MS. BCAA-supplemented group showed elevated muscle net fluxes of total essential AA, non-essential AA and AA. As for individual AA, muscle net fluxes of each BCAA and their metabolites (alanine, glutamate and glutamine), along with those of histidine, methionine and several functional non-essential AA (glycine, proline and serine), were increased by BCAA supplementation. The elevated muscle net AA fluxes were associated with the increase in arterial and intramuscular concentrations of BCAA and venous metabolites including BCKA and free fatty acids, and were also related to the decrease in the intramuscular concentration of 3-MH. Correlation analysis indicated that muscle net AA fluxes are highly and positively correlated with arterial BCAA concentrations and muscle net BCKA production. In conclusion, supplementing BCAA to reduced-protein diet increases the arterial concentrations and intramuscular catabolism of BCAA, both of which would contribute to an increase of muscle net AA fluxes in young pigs.

Carbohydrate intake and resistance-based exercise: are current recommendations reflective of actual need?

Substantial research has been completed examining the impact of carbohydrate (CHO) intake on endurance exercise, whereas its role in resistance-based exercise performance, adaptation and cell signalling has yet to be fully characterised. This empirical shortcoming has precluded the ability to establish specific CHO recommendations for resistance exercise. This results in recommendations largely stemming from findings based on endurance exercise and/or anecdotal evidence despite the distinct energetic demands and molecular responses mediating adaptation from endurance- and resistance-based exercise. Moreover, the topic of CHO and exercise has become one of polarising nature with divergent views - some substantiated, others lacking evidence. Current literature suggests a moderately high daily CHO intake (3-7 g/kg per d) for resistance training, which is thought to prevent glycogen depletion and facilitate performance and adaptation. However, contemporary investigation, along with an emerging understanding of the molecular underpinnings of resistance exercise adaptation, may suggest that such an intake may not be necessary. In addition to the low likelihood of true glycogen depletion occurring in response to resistance exercise, a diet restrictive in CHO may not be detrimental to acute resistance exercise performance or the cellular signalling activity responsible for adaptation, even when muscle glycogen stores are reduced. Current evidence suggests that signalling of the mammalian target of rapamycin complex 1, the key regulatory kinase for gene translation (protein synthesis), is unaffected by CHO restriction or low muscular glycogen concentrations. Such findings may call into question the current view and subsequent recommendations of CHO intake with regard to resistance-based exercise.

Detection of four polymorphisms in 5' upstream region of PNPLA2 gene and their associations with economic traits in pigs.

As an important triglyceride hydrolase in mammalian cells, patatin-like phospholipase domain-containing 2 (PNPLA2) predominantly performs the first step in triglyceride hydrolysis. The objective of this study was to detect and evaluate the effects of mutations in the 5' upstream region of porcine PNPLA2 gene with fat deposition and carcass traits. Four single nuclear polymorphisms were identified, including g.161969 T>C, g.161962 A>G, g.161953 C>G and g.161904 G>T, and subsequently genotyped in five pure breeds. Three haplotypes were constructed, including H1(CGGT), H2(TACG) and H3(CACT), which were the most abundant haplotypes in Duroc (0.75), Landrace (0.78) and Chinese indigenous breeds (>0.73), respectively. Duroc individuals with the H1H1 diplotype always exhibited the lowest feed conversion ratio (FCR) (P < 0.05), while H2H2 had the thickest backfat thickness (P < 0.05). Landrace individuals with H2H3 had lower backfat thickness (P < 0.05), higher muscle thickness (P < 0.05) and estimated lean meat percentage (P < 0.05) than those with diplotype H2H2 and H3H3. Luciferase assay indicated pGL3-basic-H2 had the highest activity and pGL3-basic-H1 had the lowest activity in driving reporter gene transcription in HEK293 cells in vitro. In H1 haplotype, two GR binding sites and an ERα binding site were predicted to be introduced. While in H2 and H3, there were other transcriptional factor binding sites predicted in H2 and H3, such as Sp1, AP-2 and CAC-binding proteins, which were broadly expressed transcription factors and capable of contributing to basal promoter activity. The reduced basal promoter activity of H1 may be due to the lack of inducement for GR and ERα binding sites in HEK293 cells. The identified functional polymorphisms provide new evidence of PNPLA2 as an important candidate gene for fat deposition and carcass traits in pigs.

Effect of Dietary Restriction and Subsequent Re-Alimentation on the Transcriptional Profile of Bovine Skeletal Muscle.

Compensatory growth (CG), an accelerated growth phenomenon which occurs following a period of dietary restriction is exploited worldwide in animal production systems as a method to lower feed costs. However the molecular mechanisms regulated CG expression remain to be elucidated fully. This study aimed to uncover the underlying biology regulating CG in cattle, through an examination of skeletal muscle transcriptional profiles utilising next generation mRNA sequencing technology. Twenty Holstein Friesian bulls were fed either a restricted diet for 125 days, with a target growth rate of 0.6 kg/day (Period 1), following which they were allowed feed ad libitum for a further 55 days (Period 2) or fed ad libitum for the entirety of the trial. M. longissimus dorsi biopsies were harvested from all bulls on days 120 and 15 of periods 1 and 2 respectively and RNAseq analysis was performed. During re-alimentation in Period 2, previously restricted animals displayed CG, growing at 1.8 times the rate of the ad libitum control animals. Compensating animals were also more feed efficient during re-alimentation and compensated for 48% of their previous dietary restriction. 1,430 and 940 genes were identified as significantly differentially expressed (Benjamini Hochberg adjusted P < 0.1) in periods 1 and 2 respectively. Additionally, 2,237 genes were differentially expressed in animals undergoing CG relative to dietary restriction. Dietary restriction in Period 1 was associated with altered expression of genes involved in lipid metabolism and energy production. CG expression in Period 2 occurred in association with greater expression of genes involved in cellular function and organisation. This study highlights some of the molecular mechanisms regulating CG in cattle. Differentially expressed genes identified are potential candidate genes for the identification of biomarkers for CG and feed efficiency, which may be incorporated into future breeding programmes.

Short term supplementation rates to optimise vitamin E concentration for retail colour stability of Australian lamb meat.

The relationship between vitamin E supplementation rate and colour stability was investigated using 70 mixed sex 6-8 month old crossbred lambs. An initial group of 10 were slaughtered, while the remainder were fed a pellet ration containing either 30, 150, 275 or 400 IU vitamin E/kg ration or on green pasture for 56 days. After slaughter, carcases were halved; one side packed fresh (5 days) and the other in CO2 (21 days), both at 2°C. Five muscles were set for retail display for 96 h. The oxy/metmyoglobin ratio was measured every 12 h. Colour stability increased with increasing muscle vitamin E until an apparent maximum effect for vitamin E concentration (3.5-4.0mg α-tocopherol/kg tissue) was reached beyond which no further response was evident. This was reached within 3-4 weeks (275 IU treatment), and meat from these lambs should reach 60 h retail display with a satisfactory surface colour. This effect was most apparent in aerobic muscle types and meat aged post slaughter.

Stable carbon and nitrogen isotopes as a potential tool to differentiate pork from organic and conventional systems.

BACKGROUND: Isotopic discrimination, dietary composition and feeding regime determine the carbon and nitrogen stable isotope ratios of animals. Accordingly, measurement of the stable isotope ratios of carbon and nitrogen can be a potential method to identify patterns of pork production. RESULTS: In the current study, we investigated the carbon and nitrogen isotopic ratio in pork from organic and conventional systems. The average carbon and nitrogen isotope ratios for various organic tissues, including hair, blood and defatted meat, were higher than those of conventionally raised ones. The discriminant analysis results based on the combination of carbon and nitrogen isotopic ratios in defatted meat reached a 100% correct classification. Furthermore, the variation in carbon and nitrogen stable isotope ratios of retail organic and conventional pork has been studied over 1 year. The results suggested that organic pork had a higher δ(13) C value than that of the conventional pork in all but three fortnights. Grouping of the δ(15) N data showed that the δ(15) N value in organic pork was higher than that of the conventional one throughout the whole year. CONCLUSION: The method established in the present study provides a potential detection that can be highly valuable to prevent fraudulent labelling of organic pork. © 2015 Society of Chemical Industry.

Hidden Markov induced Dynamic Bayesian Network for recovering time evolving gene regulatory networks.

Dynamic Bayesian Networks (DBN) have been widely used to recover gene regulatory relationships from time-series data in computational systems biology. Its standard assumption is 'stationarity', and therefore, several research efforts have been recently proposed to relax this restriction. However, those methods suffer from three challenges: long running time, low accuracy and reliance on parameter settings. To address these problems, we propose a novel non-stationary DBN model by extending each hidden node of Hidden Markov Model into a DBN (called HMDBN), which properly handles the underlying time-evolving networks. Correspondingly, an improved structural EM algorithm is proposed to learn the HMDBN. It dramatically reduces searching space, thereby substantially improving computational efficiency. Additionally, we derived a novel generalized Bayesian Information Criterion under the non-stationary assumption (called BWBIC), which can help significantly improve the reconstruction accuracy and largely reduce over-fitting. Moreover, the re-estimation formulas for all parameters of our model are derived, enabling us to avoid reliance on parameter settings. Compared to the state-of-the-art methods, the experimental evaluation of our proposed method on both synthetic and real biological data demonstrates more stably high prediction accuracy and significantly improved computation efficiency, even with no prior knowledge and parameter settings.

Meat quality assessment from young goats fed for long periods with castor de-oiled cake.

Diet can influence both the qualitative and quantitative traits of ruminant meat. This study evaluated the effects of castor de-oiled cake on the meat of mixed-breed male goat kids. After 165days of diet treatment, no alterations (p>0.05) were observed in the in vivo performance, anatomic components, dissection and proximate composition of the Longissimus dorsi muscle, as well as in the color and pH of the carcasses. However, diet had an effect (p<0.05) on energy metabolites, fatty acid profile, and expression of certain proteins of the Longissimus dorsi muscle. To conclude, this study showed that the establishment of castor de-oiled cake diet for a long period to goats led to alterations in meat quality, without compromising its consumption qualities.

Is the future of meat palatable? Perceptions of in vitro meat as evidenced by online news comments.

OBJECTIVE: To understand current public perceptions of in vitro meat (IVM) in light of its potential to be a more environmentally sustainable alternative to conventional meat. DESIGN: A qualitative content analysis of the comments made on online news articles highlighting the development of IVM and the world's first IVM hamburger in August 2013. SETTING: News article comment sections across seven US-based online news sources (The New York Times, The Los Angeles Times, The Washington Post, The Wall Street Journal, USA Today, Cable News Network and National Public Radio). SUBJECTS: Four hundred and sixty-two commenters who made eight hundred and fourteen publicly available online comments addressing IVM. RESULTS: Key themes in commenter perceptions of IVM included environmental and public health benefits, but also negative themes such as IVM's status as an unnatural and unappealing food. Overall, the tone of comments was more negative than positive. CONCLUSIONS: Findings suggest that while the environmental and public health motivations for developing and in turn consuming IVM resonate with some segments of the population, others find that reasoning both uncompelling and problematic. Concerns about IVM as an unnatural and risky product also appear to be a significant barrier to public acceptance of IVM. Supporters of IVM may wish to begin to develop a regulatory strategy for IVM to build public trust and explore messaging strategies that cast IVM as a new technology with benefits to individuals rather than primarily a solution to global challenges. Those in the public health nutrition field can make an important contribution to the emerging public discussion about IVM.

Muscle fibre size optimisation provides flexibility for energy budgeting in calorie-restricted coho salmon transgenic for growth hormone.

Coho salmon (Oncorhynchus kisutch) transgenic for growth hormone (GH) show substantially faster growth than wild-type (WT) fish. We fed GH-transgenic salmon either to satiation (1 year; TF) or the same smaller ration of wild-type fish (2 years; TR), resulting in groups matched for body size to WT salmon. The myotomes of TF and WT fish had the same number and size distribution of muscle fibres, indicating a twofold higher rate of fibre recruitment in the GH transgenics. Unexpectedly, calorie restriction was found to decrease the rate of fibre production in transgenics, resulting in a 20% increase in average fibre size and reduced costs of ionic homeostasis. Genes for myotube formation were downregulated in TR relative to TF and WT fish. We suggest that muscle fibre size optimisation allows the reallocation of energy from maintenance to locomotion, explaining the observation that calorie-restricted transgenics grow at the same rate as WT fish whilst exhibiting markedly higher foraging activity.

Nutritional quality of salmon products available from major retailers in the UK: content and composition of n-3 long-chain PUFA.

In the present study, salmon products available from UK retailers were analysed to determine the levels of n-3 long-chain PUFA (LC-PUFA), a key determinant of nutritional quality. There was a wide variation in the proportions and absolute contents of EPA and DHA in the products. Relatively high contents of 18 : 1n-9, 18 : 2n-6 and 18 : 3n-3, characteristic of vegetable oils (VO), were found in several farmed salmon products, which also had generally lower proportions of EPA and DHA. In contrast, farmed salmon products with higher levels of 16 : 0 and 22 : 1, characteristic of fish oil (FO), had higher proportions of EPA and DHA. Therefore, there was a clear correlation between the levels of VO and FO in feeds and the proportions of n-3 LC-PUFA in products. Although wild salmon products were characterised by higher proportions of n-3 LC-PUFA (20-40%) compared with farmed fish (9-26%), they contained lower total lipid contents (1-6% compared with 7-17% in farmed salmon products). As a result, farmed salmon products invariably had higher levels of n-3 LC-PUFA in absolute terms (g/100 g fillet) and, therefore, delivered a higher 'dose' of EPA and DHA per portion. Overall, despite the finite and limiting supply of FO and increasing use of VO, farmed salmon continue to be an excellent source of and delivery system for n-3 LC-PUFA to consumers.

Hand grip strength and associated factors in non-institutionalised men and women 50 years and older in South Africa.

BACKGROUND: Little is known about the prevalence, predictors and gender differences in hand grip strength of older adults in Africa. This study aims to investigate social and health differences in hand grip strength among older adults in a national probability sample of older South Africans who participated in the Study of Global Ageing and Adults Health (SAGE wave 1) in 2008. METHODS: We conducted a national population-based cross-sectional study with a sample of 3840 men and women aged 50 years or older in South Africa. The questionnaire included socio-demographic characteristics, health variables, and anthropometric measurements. Linear multivariate regression analysis was performed to assess the association of social factors, health variables and grip strength. RESULTS: The mean overall hand grip strength was 37.9 kgs for men (mean age 61.1 years, SD = 9.1) and 31.5 kgs for women (mean age 62.0 years, SD = 9.7). In multivariate analysis among men, greater height, not being underweight and lower functional disability was associated with greater grip strength, and among women, greater height, better cognitive functioning, and lower functional disability were associated with greater grip strength. CONCLUSIONS: Greater height and lower functional disability were found for both older South African men and women to be significantly associated with grip strength.

Bioeconomic model and selection indices in Aberdeen Angus cattle.

A bioeconomic model was developed to calculate economic values for biological traits in full-cycle production systems and propose selection indices based on selection criteria used in the Brazilian Aberdeen Angus genetic breeding programme (PROMEBO). To assess the impact of changes in the performance of the traits on the profit of the production system, the initial values ​​of the traits were increased by 1%. The economic values for number of calves weaned (NCW) and slaughter weight (SW) were, respectively, R$ 6.65 and R$ 1.43/cow/year. The selection index at weaning showed a 44.77% emphasis on body weight, 14.24% for conformation, 30.36% for early maturing and 10.63% for muscle development. The eighteen-month index showed emphasis of 77.61% for body weight, 4.99% for conformation, 11.09% for early maturing, 6.10% for muscle development and 0.22% for scrotal circumference. NCW showed highest economic impact, and SW had important positive effect on the economics of the production system. The selection index proposed can be used by breeders and should contribute to greater profitability.