Eating Time as a Genetic Indicator of Methane Emissions and Feed Efficiency in Australian Maternal Composite Sheep

Previous studies have shown reduced enteric methane emissions (ME) and residual feed intake (RFI) through the application of genomic selection in ruminants. The objective of this study was to evaluate feeding behaviour traits as genetic indicators for ME and RFI in Australian Maternal Composite ewes using data from an automated feed intake facility. The feeding behaviour traits evaluated were the amount of time spent eating per day (eating time; ETD; min/day) and per visit (eating time per event; ETE; min/event), daily number of events (DNE), event feed intake (EFI; g/event) and eating rate (ER; g/min). Genotypes and phenotypes of 445 ewes at three different ages (post-weaning, hogget, and adult) were used to estimate the heritability of ME, RFI, and the feeding behaviour traits using univariate genomic best linear unbiased prediction models. Multivariate models were used to estimate the correlations between these traits and within each trait at different ages. The response to selection was evaluated for ME and RFI with direct selection models and indirect models with ETE as an indicator trait, as this behaviour trait was a promising indicator based on heritability and genetic correlations. Heritabilities were between 0.12 and 0.18 for ME and RFI, and between 0.29 and 0.47 for the eating behaviour traits. In our data, selecting for more efficient animals (low RFI) would lead to higher methane emissions per day and per kg of dry matter intake. Selecting for more ETE also improves feed efficiency but results in more methane per day and per kg dry matter intake. Based on our results, ETE could be evaluated as an indicator trait for ME and RFI under an index approach that allows simultaneous selection for improvement in emissions and feed efficiency. Selecting for ETE may have a tremendous impact on the industry, as it may be easier and cheaper to obtain than feed intake and ME data. As the data were collected using individual feeding units, the findings on this research should be validated under grazing conditions.

Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits

Background

Variants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles.

Results

Whereas a relatively small number of molecular phenotypes were significantly heritable (h² > 0, P < 0.05), their mean heritability ranged from 0.67 to 0.73 for liver and from 0.71 to 0.77 for muscle. Association analysis between molecular phenotypes and SNPs within ± 1 Mb identified many significant cis-eQTL (false discovery rate, FDR < 0.01). The median distance between the eQTL and transcription start sites (TSS) ranged from 68 to 153 kb across the three eQTL types. The number of common variants between geQTL, eeQTL and sQTL within each tissue, and the number of common variants between liver and muscle within each eQTL type were all significantly (P < 0.05) larger than expected by chance. The identified eQTL were significantly (P < 0.05) enriched in GWAS hits associated with 56 carcass traits and fatty acid profiles. For example, several geQTL in muscle mapped to the FAM184B gene, hundreds of sQTL in liver and muscle mapped to the CAST gene, and hundreds of sQTL in liver mapped to the C6 gene. These three genes are associated with body composition or fatty acid profiles.

Conclusions

We detected a large number of significant eQTL and found that the overlap of variants between eQTL types and tissues was prevalent. Many eQTL were also QTL for meat traits. Our study fills a gap in the knowledge on the regulatory variants and their role in complex traits for the sheep model.

Technical note: validation of an automated feeding system for measuring individual animal feed intake in sheep housed in groups

The development of feeding systems that can individually measure and control feed intake in a group-housed environment would allow a greater understanding of sheep intake without compromising animal welfare and behavior through the removal of social interactions between sheep. This study validated an automated feeding system for measuring feed intake of individual sheep when housed in groups. Validation of the feeding system was conducted during three separate experiments. The validation sampling involved the activation of four individual “feed events,” whereby four separate samples weighing approximately 50, 100, 200, and 400 g were removed from each feeder, with each feed event being linked to a specific radio frequency identification (RFID) tag. The feeder validation experiments evaluated the ability of the feeding system to 1) create a unique feed event every time a sample of pellets was collected from the feeder, 2) link the feed event to the correct RFID, and 3) accurately record the weight of feed that was manually removed. All feed events were initiated and logged in the feeding system with 100% of the events being linked to the correct test RFID. Concordance correlation coefficients between the feeding system-recorded feed weight and the manually removed weight were 0.99 within all three experiments. There was also no overall and little level-dependent bias between the weights measured by the feeding system and weights measured on the external scales. These results indicate the stability of the feeding system over time and consistency between the feeders within and across the three experiments. In conclusion, the automated feeding system developed for measuring individual animal feed intake was able to detect and record the unique electronic RFID associated with unique feed events and accurately capture the weight of feed removed. Furthermore, there was no change in the accuracy of the system from the start to the end of experimental periods, and the amount of feed removed in the feed event (or meal size) did not impact the accuracy of the results.

An alternative approach for sustainable sheep meat production: implications for food security

Background

A pelleted diet containing camelina hay (CAMH) or camelina meal (CAMM) as a supplement along with a control pellet (CONT) diet formulated with commonly available feeds during summer was used to investigate an alternative pathway for sustainable meat production. Sustainable meat production was based on a simple estimation of income from meat produced versus feed costs if animals were fed for an extended period over summer compared to early slaughter at the beginning of summer. Eighty maternal composite wether lambs (Composite) based on Coopworth genetics and 80 pure Merino wether yearlings were divided into 10 groups within breed (n = 8) using stratified randomisation based on liveweights. Following 1 week of adaptation to experimental diets, animals were fed experimental diets for up to10 weeks.

Results

Animals were slaughtered after either 8, 9 or 10 weeks of full feeding when the average liveweight of diet/genetic combination reached a weight appropriate for either ‘heavy lamb’ or ‘heavy hogget’ production, which occurred between 8 and 10 weeks of full feeding. There was no diet × breed interactions except for dressing percentage (DP), where Composite lambs fed the CAMH diet had the greatest DP (48.1 ± 0.35) and the Merino yearlings fed the CAMM diet the lowest DP (45.8 ± 0.33). Composite lambs gained 17.6–20.3 kg and Merino yearlings gained 10.7–12.9 kg liveweight. Based on their DP, this resulted in the production of approximately 8.3–9.5 kg additional carcass weight in Composites and 4.9–5.7 kg in Merinos, which in turn produced greater profit per Composite lamb and a small profit per Merino yearling.

Conclusions

Composite lambs fed CAMM and CAMH had 5% greater carcass weights at slaughter compared to the CONT group, but dietary treatments did not change carcass weight of Merino yearlings at slaughter. The extended feeding approach offered the producer an estimated economic gain of AUD $20.00 to $25.00 when yearly average prices were used (Method 1) and AUD $40.00 to $47.70 when pre- and post-summer average prices were used (Method 2) per Composite lambs, but extra carcass gain did not result in the same profit per Merino yearling. Among the Composites, the profit for animals fed the CAMH and CAMM were AUD $2.75 to $4.50 greater than CONT group when full year average prices were applied while AUD $3.50 to $5.50 greater than CONT group when pre- and post-summer average prices were applied. However, we acknowledge a combination approach of extended feeding for a portion of animals already on ground and selling the remaining animals pre-summer with joining of additional ewes is the most likely strategy. Considering the scenario of extended feeding for 3 weeks, based on the growth rates observed for Composite lambs, if an additional 2 kg carcass weight per animal can be gained for 50% of the 22 million lambs slaughtered in Australia (= 11 million animals), it would potentially supply an additional 22 million kg of lamb carcasses produced per annum. This is equivalent to producing an extra 1 million lamb carcasses per annum weighing 22 kg each. Feeding Composite lambs for an extended period and selling Merino yearlings pre-summer may be a good option due to faster growth rate of Composites that may help quick turn-over to market.

Understanding the impact of sire lean meat yield breeding value on carcass composition, meat quality, nutrient and mineral content of Australian lamb

Advances in genomics and technology measuring body composition are now allowing sheep producers to select directly for increased lean meat yield (LMY) using Australian Sheep Breeding Values (ASBV). This experiment evaluated the impact of sire LMY ASBV on carcass composition, meat quality, nutrient and mineral content for lambs reared at pasture and finished in a feedlot. A 1% unit increase in sire LMY ASBV resulted in progeny that were leaner (0.8%) and had less fat (1.0%) on carcass. There was also a 0.2% reduction in the intramuscular fat content, a 3.2 N increase in meat toughness determined by shear force at day 5 ageing, a reduction in the redness of the fresh meat and a lower iron content. It is concluded that Australian sheep producers will need to incorporate ASBVs for other aspects of meat quality when selecting sires with increased LMY to avoid deterioration in meat quality, nutritional content of lamb and fresh meat colour.

Understanding the action of muscle iron concentration on dark cutting: An important aspect affecting consumer confidence of purchasing meat

We investigated the association of muscle iron concentration, in addition to ultimate pH (pHU), on dark meat formation in sheep of different breeds fed forage-based diets. At 1 h simulated display, redness of meat (a*-value) increased (P < .0001) by about 3 units as the iron concentration increased from 10 to 22 mg/kg of meat, whereas the a*-value decreased by 2 units as pHU increased from 5.5 to 6.2 in fresh meat (P < .0001). After 90 days storage the corresponding responses were about 2 units increase for iron concentration and about 1 unit decrease for pHU, respectively. The results clearly show that increased muscle iron concentration was strongly associated with reduced dark cutting in fresh and stored meat evaluated at 1 h simulated display. We conclude that it may be desirable to measure iron concentration, along with pHU, for evaluation of the potential for carcasses to produce dark cutting meat, and for the meat to turn brown during display.

Development of VISNIR predictive regression models for ultimate pH, meat tenderness (shear force) and intramuscular fat content of Australian lamb

This study investigated the effectiveness of visible-near-infrared (VISNIR) spectroscopy at classifying Australian lamb for: a) ultimate pH (pH 24), b) meat tenderness (i.e. shear force at day 5 of ageing, SF5) and c) intramuscular fat (IMF) content at 24 h post-slaughter using a custom-made handheld probe coupled with the ASD Labspec Pro instrument. VISNIR predictive regression models were developed. In the loin muscle (M. longissimus thoracis et lumborum), the models classified the predicted pH 24, SF5 and IMF content at above or below a threshold value with 94%, 98% and 88% accuracy, respectively. The observed difference between the actual and predicted value (i.e. the standard error of cross validation, SECV) for ultimate pH and IMF content are approaching accuracies required to attain highly reliable Meat Standards Australia grading standards. However, further development is required to improve the SECV for SF5.

Milk-derived ribonuclease 5 preparations induce myogenic differentiation in vitro and muscle growth in vivo

Ribonuclease 5, also known as angiogenin, is a stable and abundant ribonuclease in milk whey protein, which is able to regulate several cellular functions, including capillary formation, neuron survival, and epithelial cell growth. Ribonuclease 5 is important for protein synthesis directly stimulating rRNA synthesis in the nucleolus. Here, we show that biologically active RNase5 can be purified from bovine milk. Furthermore, we show that milk-derived RNase5 directly stimulates muscle cell differentiation in vitro, inducing C2C12 cell differentiation and myogenesis. When supplemented into the diet of healthy adult mice, milk-derived RNase5 preparations promoted muscle weight gain and grip strength. Collectively, these data indicate that milk-derived RNase5 preparations exhibit a novel role in skeletal muscle cell function.

Peanut allergens alter intestinal barrier permeability and tight junction localisation in Caco-2 cell cultures

BACKGROUND/AIMS

Allergen absorption by epithelia may play an important role in downstream immune responses. Transport mechanisms that can bypass Peyer's patches include transcellular and paracellular transport. The capacity of an allergen to cross via these means can modulate downstream processing of the allergen by the immune system. The aim of this study was to investigate allergen-epithelial interactions of peanut allergens with the human intestinal epithelium.

METHODS

We achieved this using the human Caco-2 cell culture model, exposed to crude peanut extract. Western and immunofluorescence analysis were used to identify the cellular and molecular changes of peanut extract on the intestinal epithelium.

RESULTS

Following exposure of Caco-2 cells to peanut extract, binding of the peanut allergens Ara h 1 and Ara h 2 to the apical cellular membrane and transcytosis across the monolayers were observed. Additionally, the co-localisation of the transmembrane tight junction proteins occludin, JAM-A and claudin-1, with the intracellular adhesion protein ZO-1 was modified.

CONCLUSION

Disruption of Caco-2 barrier integrity through tight junction disruption may enable movement of peanut proteins across the intestinal epithelium. This accounts for peanut's increased allergenicity, compared to other food allergens, and provides an explanation for the potency of peanut allergens in immune response elicitation.

A disintegrin and metalloprotease-12 is type I myofiber specific in Bos taurus and Bos indicus cattle

A disintegrin and metalloproteinase-12 (ADAM12) is involved in the regulation of myogenesis and adipogenesis and is of interest as a potential target to manipulate skeletal muscle development and intramuscular fat (IMF) deposition in cattle to increase beef yield and improve meat quality. The longissimus thoracis muscle (LM) and semitendinosus muscle (STM) from 5 Bos taurus (Angus) and 5 Bos indicus (Brahman) cattle were collected for histological and ADAM12 gene and protein expression analysis. Myofiber typing was used to determine if ADAM12 expression patterns related to differences in muscling and IMF deposition, which are influenced by proportions of the different myofiber types. The STM was found to contain a higher proportion of glycolytic myofibers than the LM, which contained a greater proportion of oxidative myofibers (myofiber ratio of glycolytic to more oxidative types in LM and STM of 1.1 and 3.5, respectively; P < 0.05). ADAM12 gene expression, fluorescent immunohistochemical staining for ADAM12, and image analysis found ADAM12 to be greater in the LM (P < 0.05). Regression analysis found a strong, positive relationship for the distribution of ADAM12 against the proportion of type I myofibers (P < 0.05, r(2) = 0.86). These findings suggest ADAM12 is upregulated in muscles with more slow-oxidative myofibres, such as the LM, and is linked to type I myofibers in cattle. ADAM12 may be important in the regulation and maintenance slow myofibers in the LM muscle.

An independent validation association study of carcass quality, shear force, intramuscular fat percentage and omega-3 polyunsaturated fatty acid content with gene markers in Australian lamb

Previous association studies revealed several single nucleotide polymorphisms (SNPs) that explained the observed phenotypic variation for meat tenderness and long-chain omega-3 polyunsaturated fatty acid (PUFA) content of Australian lamb. To confirm the validity of these associated SNPs at predicting meat tenderness and omega-3 PUFA content, an independent validation study was designed. The OvineSNP50 genotypes of these animals were used to impute the 192 SNP Meat Quality Research (MQR) panel genotypes on nearly 6200 animals from the Cooperative Research Centre for Sheep Industry Innovation Information Nucleus Flock and Sheep Genomics Falkiner Memorial Field Station flock. Association analysis revealed numerous SNP from the 192 SNP MQR panel that were associated with carcass quality - fat depth at the C-site and eye muscle depth; shear force at day 1 and day 5 after slaughter (SF1 and SF5); and omega-3 PUFA content at P<0.01. However, 1 SNP was independently validated for SF5 (i.e. CAST_101781475). The magnitude of the effect of each significant SNP and the relative allele frequencies across Merino-, Maternal- and Terminal-sired progeny was determined. The independently validated SNP for SF5 and the associated SNP with omega-3 PUFA content will accelerate efforts to improve these phenotypic traits in Australian lamb.

Problems associated with determining protein concentration: a comparison of techniques for protein estimations

Although a range of methods are available for determining protein concentration, many scientists encounter problems when quantifying proteins in the laboratory. The most commonly used methods for determining protein concentration in a modern biochemistry laboratory would probably be the Lowry and/or the Bradford protein assays. Other techniques, including direct spectrophotometric analysis and densitometry of stained protein gels, are applied, but perhaps to a lesser extent. However, the reliability of all of the above techniques is questionable and dependent to some extent on the protein to be assayed. In this paper we describe problems we encountered when using some of the foregoing techniques to quantify the concentration of poly(adenosine diphosphate-ribose) polymerase-1 (PARP-1), a nuclear enzyme found in most eukaryotes. We also describe how, by using a fluorescence-based assay and amino acid analysis, we overcame the problems we encountered.

Production, extraction, and purification of human poly(ADP-ribose) polymerase-1 (PARP-1) with high specific activity

Poly(ADP-ribose) polymerase-1 (PARP-1) is a nuclear enzyme involved in a range of activities associated with DNA metabolism and plays a key role in maintaining the integrity of DNA and chromatin structure. As such, this enzyme is likely to provide a useful target when using a rational drug design approach to develop pharmaceutical reagents, including cancer therapeutics. However, there is still a great deal to learn about the mode of action of PARP-1 and therefore efforts are being directed at gaining a better understanding of the relationship between its structure and function. To this end we have developed a rapid and relatively simple approach to producing and purifying PARP-1. Unlike traditional PARP-1 purification protocols, the method described here requires only one chromatography step thus minimizing losses of the enzyme and also avoids the use of a competitive inhibitor-based affinity chromatography step, which is common to several other protocols in the literature. The product of the method described here is high-quality native PARP-1 with a high specific activity and K(m) and V(max) values similar to what is reported by other workers in the field. This protocol is particularly well suited to making PARP-1 in a quantity and of a quality suitable for structure-function studies.

Continuous ambulatory peritoneal dialysis in a program for children with end stage renal disease

Eighteen infants, children, and adolescents were trained in the techniques of continuous ambulatory peritoneal dialysis (CAPD) as a therapy for end stage renal disease (ESRD) at the University of Florida. Fourteen patients successfully continued CAPD 4-24 months, for a total of 193 patient-months. Uremic symptoms were well controlled with blood urea nitrogen concentration (BUN) decreased to between 60 and 80 mg/dl. Parathyroid hormone levels increased but roentgenographic evidence of osteodystrophy improved in most patients. The rate of peritonitis was one episode in 7.7 patient-months. Blood transfusion requirements decreased for patients transferred from in-center hemodialysis to CAPD with no significant decrease in average hematocrits. Caloric intake was adequate and anorexia was usually not a major problem. Children who were evaluated for growth were under 15 years of age, with bone ages less than 12 years, and were using CAPD for longer than 6 months. Their mean growth velocity was 74.7 +/- 20.4% (SD) of the predicted velocity.