Studies on Pre-slaughter Handling of Pigs and its Relationship to Meat Quality

End of Project ReportsTwo quality defects of pork which are affected by preslaughter handling are PSE (Pale Soft Exudative) and DFD (Dark Firm Dry) meat. The incidence of PSE pork is mainly a function of the breed of pig but short-term stressful handling before slaughter and feeding too close to slaughter are also involved. DFD meat is a result of prolonged stressful handling. PSE meat is pale and uneven in colour and exudes fluid making it unattractive in the retail display while dark meat appears stale and is prone to bacterial spoilage. After slaughter muscle metabolism continues and muscle glycogen is converted to lactic acid reducing meat pH. Prolonged stress results in glycogen depletion, pre-slaughter feeding results in elevated levels. Colour may be assessed subjectively by eye or objectively by a meter colour but pH of the meat is closely related to colour and measurement of pH at 45 minutes post-slaughter is frequently used to predict ultimate colour and pH. The objective of this study was to examine pre-slaughter handling practices and their relationship with meat quality (pH, colour). In the first trial, a survey of the amounts of stomach contents in pigs at slaughter in two factories found similar amounts to comparable surveys in France and the UK. It was concluded that most pigs had been fasted for an adequate time before delivery. The relationship between the amount of stomach contents and meat quality in this survey was poor. In the second trial, pigs from the Moorepark herd fed by either a computerised wet feeding system or an ad libitum dry feed system were slaughtered after overnight fasting or with feed available up to loading for transport to the factory, two to three hours before slaughter. There was no difference between feeding systems in meat colour or pH but fasted pigs, on both feeding systems, had darker meat and meat of a higher pH. In the third and fourth trials a survey of transport vehicles was carried out and meat quality of pigs delivered in modern and old-type vehicles was compared. Most trucks examined (78%) were four years old or more. Few had modern hydraulic lifting gear for the top decks. Space allowances during transportation were generally adequate but delays in unloading could, in warm weather, cause stress on pigs. There was little evidence for an effect of vehicle on meat quality parameters but day to day variation in carcass temperature and pH suggested a need for further research on factory influences on meat quality. Feeding of Magneium Aspartate to pigs for the last 5 days prior to slaughter has been shown, in Australia, to have a beneficial effect on meat colour and drip loss. In the final trial in this study Mg Asp had no effect on meat quality parameters.European Union Structural Funds (EAGGF

Bridging the Gap – Enhancing Private Investment in Future Infrastructure Provision

This research enhances understanding of the infrastructure investment landscape within six countries, Canada, China, India, Singapore, the UK and the US. We find differences in maturity, transparency and openness to international investment across the six countries Through a comprehensive series of interviews with investors, developers, policy makers and advisers we highlight the importance of governments as ‘facilitators’ of private infrastructure investment; providing strategic vision, sustained political commitment and, perhaps most importantly, active project pipelines. The protracted and uncertain nature of infrastructure development pipelines and the complexities in governance frameworks that support infrastructure provision have been considerable barriers to enhanced private investment. Our research has shown that more efficient procurement and investment models for greenfield projects would also enhance private sector investment flows, which in turn would contribute to the re-allocation of the societal and economic benefits associated with new infrastructure provision

Effect of Pre-and Post-weaning Nutrition and Management on Performance of Weaned Pigs to circa 35 kg.

End of Project ReportThe objective of this project was to examine the factors affecting performance (growth rate, appetite, feed conversion efficiency) of pigs in the stage from weaning to 35 kg liveweight. The study involved three stages, creep feeding during the suckling period, management during the first weaner stage (c. 4 weeks from weaning or 6 kg to 15 kg liveweight) and management during the second weaner stage (c. 15 kg to 35 kg liveweight. Creep feed intake before weaning was low c. 2.5 to 3.0 kg per litter but where it was consumed the response in terms of feed conversion efficiency was good with litter weight increasing in weight by about 1.1 kg for each 1 kg creep consumed. Milk replacer in liquid form was very readily consumed but its preparation and feeding is very laborious. Weaning weight was poorly related to post weaning performance and weaning age seemed to be more critical which is probably a reflection of the greater maturity of older animals. In the first weaner stage, feeding of cooked cereal containing diets was found to have little benefit in pig performance. Acidification of feeds is likely to have only a minor influence on pig performance. An experiment on choice feeding of starter and link feeds did not confirm that smaller pigs require a higher quality diet and, in a choice situation will eat a greater proportion of the more nutrient dense diet. In the second weaner stage, comparison of three commercial weaner feeds with a cereal based control diet showed good performance on all four diets. Pigs fed a high lysine weaner diet grew better in the weaner stage but by slaughter those pigs fed the low lysine weaner diet, after all pigs were fed a common finisher diet, had overtaken them. The high lysine group did, however, have leaner carcasses. Residual effects of early nutrition need to be investigated in more detail including the effect of pregnancy feeding on prenatal development and the relationship between prenatal growth and postnatal growth, in particular development of muscle.European Union Structural Funds (EAGGF

Sexually dimorphic gene expression in bovine conceptuses at the initiation of implantation

In cattle, maternal recognition of pregnancy occurs on Day 16 via secretion of interferon tau (IFNT) by the conceptus. The endometrium can distinguish between embryos with different developmental competencies. In eutherian mammals, X-chromosome inactivation (XCI) is required to ensure an equal transcriptional level of most X-linked genes for both male and female embryos in adult tissues, but this process is markedly different in cattle than mice. We examined how sexual dimorphism affected conceptus transcript abundance and amino acid composition as well as the endometrial transcriptome during the peri-implantation period of pregnancy. Of the 5132 genes that were differentially expressed on Day 19 in male compared to female conceptuses, 2.7% were located on the X-chromosome. Concentrations of specific amino acids were higher in the uterine luminal fluid of male compared to female conceptuses, while female conceptuses had higher transcript abundance of specific amino acid transporters (SLC6A19 and SLC1A35). Of note, the endometrial transcriptome was not different in cattle gestating a male or a female conceptus. These data support the hypothesis that, far from being a blastocyst specific phenomenon, XCI is incomplete before and during implantation in cattle. Despite differences in transcript abundance and amino acid utilization in male versus female conceptuses, the sex of the conceptus itself does not elicit a different transcriptomic response in the endometrium

Influence of the Intestinal Microbiota on Colonization Resistance to Salmonella and the Shedding Pattern of Naturally Exposed Pigs

[EN] Salmonella colonization and infection in production animals such as pigs are a cause for concern from a public health perspective. Variations in susceptibility to natural infection may be influenced by the intestinal microbiota. Using 16S rRNA compositional sequencing, we characterized the fecal microbiome of 15 weaned pigs naturally infected with Salmonella at 18, 33, and 45 days postweaning. Dissimilarities in microbiota composition were analyzed in relation to Salmonella infection status (infected, not infected), serological status, and shedding pattern (nonshedders, single-point shedders, intermittent-persistent shedders). Global microbiota composition was associated with the infection outcome based on serological analysis. Greater richness within the microbiota postweaning was linked to pigs being seronegative at the end of the study at 11 weeks of age. Members of the Clostridia, such as Blautia, Roseburia, and Anaerovibrio, were more abundant and part of the core microbiome in nonshedder pigs. Cellulolytic microbiota (Ruminococcus and Prevotella) were also more abundant in noninfected pigs during the weaning and growing stages. Microbial profiling also revealed that infected pigs had a higher abundance of Lactobacillus and Oscillospira, the latter also being part of the core microbiome of intermittent-persistent shedders. These findings suggest that a lack of microbiome maturation and greater proportions of microorganisms associated with suckling increase susceptibility to infection. In addition, the persistence of Salmonella shedding may be associated with an enrichment of pathobionts such as Anaerobiospirillum. Overall, these results suggest that there may be merit in manipulating certain taxa within the porcine intestinal microbial community to increase disease resistance against Salmonella in pigs. IMPORTANCE Salmonella is a global threat for public health, and pork is one of the main sources of human salmonellosis. However, the complex epidemiology of the infection limits current control strategies aimed at reducing the prevalence of this infection in pigs. The present study analyzes for the first time the impact of the gut microbiota in Salmonella infection in pigs and its shedding pattern in naturally infected growing pigs. Microbiome (16S rRNA amplicon) analysis reveals that maturation of the gut microbiome could be a key consideration with respect to limiting the infection and shedding of Salmonella in pigs. Indeed, seronegative animals had higher richness of the gut microbiota early after weaning, and uninfected pigs had higher abundance of strict anaerobes from the class Clostridia, results which demonstrate that a fast transition from the suckling microbiota to a postweaning microbiota could be crucial with respect to protecting the animalsSIThis study was funded by the Food Institutional Research Measure (FIRM) administered by the Department of Agriculture Food and the Marine (DAFM). H.A. is a postdoctoral researcher supported by the Juan de la Cierva Postdoctoral Trainee Program of the Spanish Ministry of Economy and Competitiveness (IJCI-2016-30795). H.A. was funded by the PiGutNet COST action (FA1401) for a Short-Term Scientific Mission at INRA’s GABI laboratory (Jouy-en-Josas, France). We gratefully acknowledge the Central Veterinary Research Laboratory (CVRL) Backweston for their expert help with the serological analyses. H.A. participated in the study design, sample collection and processing, data analysis, and manuscript writing. F.C.L. participated in study design and manuscript correction. J.E. participated in data analysis and manuscript revision. P.D.C. and F.C. participated in microbiome sequencing and manuscript revision. O.O. performed part of the data analysis and manuscript revision. H.L. and K.W. participated in sample collection and processing. G.D. and P.G.L. participated in the study design and manuscript correction. G.E.G. participated in the study design, data analysis, and manuscript writin

Fecal Microbiota Transplantation in Gestating Sows and Neonatal Offspring Alters Lifetime Intestinal Microbiota and Growth in Offspring

Previous studies suggest a link between intestinal microbiota and porcine feed efficiency (FE). Therefore, we investigated whether fecal microbiota transplantation (FMT) in sows and/or neonatal offspring, using inocula derived from highly feed-efficient pigs, could improve offspring FE. Pregnant sows were assigned to control or FMT treatments and the subsequent offspring to control treatment, FMT once (at birth), or FMT four times (between birth and weaning). FMT altered sow fecal and colostrum microbiota compositions and resulted in lighter offspring body weight at 70 and 155 days of age when administered to sows and/or offspring. This was accompanied by FMT-associated changes within the offspring?s intestinal microbiota, mostly in the ileum. These included transiently higher fecal bacterial diversity and load and numerous compositional differences at the phylum and genus levels (e.g., Spirochaetes and Bacteroidetes at high relative abundances and mostly members of Clostridia, respectively), as well as differences in the abundances of predicted bacterial pathways. In addition, intestinal morphology was negatively impacted, duodenal gene expression altered, and serum protein and cholesterol concentrations reduced due to FMT in sows and/or offspring. Taken together, the results suggest poorer absorptive capacity and intestinal health, most likely explaining the reduced body weight. An additive effect of FMT in sows and offspring also occurred for some parameters. Although these findings have negative implications for the practical use of the FMT regime used here for improving FE in pigs, they nonetheless demonstrate the enormous impact of early-life intestinal microbiota on the host phenotype.publishersversionPeer reviewe

Zebrafish Ciliopathy Screen Plus Human Mutational Analysis Identifies C21orf59 and CCDC65 Defects as Causing Primary Ciliary Dyskinesia

Primary ciliary dyskinesia (PCD) is caused when defects of motile cilia lead to chronic airway infections, male infertility, and situs abnormalities. Multiple causative PCD mutations account for only 65% of cases, suggesting that many genes essential for cilia function remain to be discovered. By using zebrafish morpholino knockdown of PCD candidate genes as an in vivo screening platform, we identified c21orf59, ccdc65, and c15orf26 as critical for cilia motility. c21orf59 and c15orf26 knockdown in zebrafish and planaria blocked outer dynein arm assembly, and ccdc65 knockdown altered cilia beat pattern. Biochemical analysis in Chlamydomonas revealed that the C21orf59 ortholog FBB18 is a flagellar matrix protein that accumulates specifically when cilia motility is impaired. The Chlamydomonas ida6 mutant identifies CCDC65/FAP250 as an essential component of the nexin-dynein regulatory complex. Analysis of 295 individuals with PCD identified recessive truncating mutations of C21orf59 in four families and CCDC65 in two families. Similar to findings in zebrafish and planaria, mutations in C21orf59 caused loss of both outer and inner dynein arm components. Our results characterize two genes associated with PCD-causing mutations and elucidate two distinct mechanisms critical for motile cilia function: dynein arm assembly for C21orf59 and assembly of the nexin-dynein regulatory complex for CCDC65

Effects of Feeding Bt MON810 Maize to Pigs for 110 Days on Peripheral Immune Response and Digestive Fate of the cry1Ab Gene and Truncated Bt Toxin

peer-reviewedBackground: The objective of this study was to evaluate potential long-term (110 days) and age-specific effects of feeding genetically modified Bt maize on peripheral immune response in pigs and to determine the digestive fate of the cry1Ab gene and truncated Bt toxin. Methodology/Principal Findings: Forty day old pigs (n = 40) were fed one of the following treatments: 1) isogenic maize-based diet for 110 days (isogenic); 2) Bt maize-based diet (MON810) for 110 days (Bt); 3) Isogenic maize-based diet for 30 days followed by Bt maize-based diet for 80 days (isogenic/Bt); and 4) Bt maize-based diet (MON810) for 30 days followed by isogenic maize-based diet for 80 days (Bt/isogenic). Blood samples were collected during the study for haematological analysis, measurement of cytokine and Cry1Ab-specific antibody production, immune cell phenotyping and cry1Ab gene and truncated Bt toxin detection. Pigs were sacrificed on day 110 and digesta and organ samples were taken for detection of the cry1Ab gene and the truncated Bt toxin. On day 100, lymphocyte counts were higher (P<0.05) in pigs fed Bt/isogenic than pigs fed Bt or isogenic. Erythrocyte counts on day 100 were lower in pigs fed Bt or isogenic/Bt than pigs fed Bt/isogenic (P<0.05). Neither the truncated Bt toxin nor the cry1Ab gene were detected in the organs or blood of pigs fed Bt maize. The cry1Ab gene was detected in stomach digesta and at low frequency in the ileum but not in the distal gastrointestinal tract (GIT), while the Bt toxin fragments were detected at all sites in the GIT. Conclusions/Significance: Perturbations in peripheral immune response were thought not to be age-specific and were not indicative of Th 2 type allergenic or Th 1 type inflammatory responses. There was no evidence of cry1Ab gene or Bt toxin translocation to organs or blood following long-term feeding.The research leading to these results has received funding from the European Union’s Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 211820 and the Teagasc Walsh Fellowship programme

High-Throughput Proteomics Detection of Novel Splice Isoforms in Human Platelets

Alternative splicing (AS) is an intrinsic regulatory mechanism of all metazoans. Recent findings suggest that 100% of multiexonic human genes give rise to splice isoforms. AS can be specific to tissue type, environment or developmentally regulated. Splice variants have also been implicated in various diseases including cancer. Detection of these variants will enhance our understanding of the complexity of the human genome and provide disease-specific and prognostic biomarkers. We adopted a proteomics approach to identify exon skip events - the most common form of AS. We constructed a database harboring the peptide sequences derived from all hypothetical exon skip junctions in the human genome. Searching tandem mass spectrometry (MS/MS) data against the database allows the detection of exon skip events, directly at the protein level. Here we describe the application of this approach to human platelets, including the mRNA-based verification of novel splice isoforms of ITGA2, NPEPPS and FH. This methodology is applicable to all new or existing MS/MS datasets

Porcine Feed Efficiency-Associated Intestinal Microbiota and Physiological Traits: Finding Consistent Cross-Locational Biomarkers for Residual Feed Intake

Publication history: Accepted - 21 May 2019; Published online - 18 June 2019Optimal feed efficiency (FE) in pigs is important for economic and environmental reasons. Previous research identified FE-associated bacterial taxa within the intestinal microbiota of growing pigs. This study investigated whether FE-associated bacteria and selected FE-associated physiological traits were consistent across geographic locations (Republic of Ireland [ROI) [two batches of pigs, ROI1 and ROI2], Northern Ireland [NI], and Austria [AT]), where differences in genetic, dietary, and management factors were minimized. Pigs (n = 369) were ranked, within litter, on divergence in residual feed intake (RFI), and 100 extremes were selected (50 with high RFI and 50 with low RFI) across geographic locations for intestinal microbiota analysis using 165 rRNA amplicon sequencing and examination of FE-associated physiological parameters. Microbial diversity varied by geographic location and intestinal sampling site but not by RFI rank, except in ROI2, where more-feed-efficient pigs had greater ileal and cecal diversity. Although none of the 188 RFI-associated taxonomic differences found were common to all locations/batches, Lentisphaerae, Ruminococcaceae, RF16, Mucispirillum, Methanobrevibacter, and two uncultured genera were more abundant within the fecal or cecal microbiota of low-RFI pigs in two geographic locations and/or in both ROI batches. These are major contributors to carbohydrate metabolism, which was reflected in functional predictions. Fecal volatile fatty acids and salivary cortisol were the only physiological parameters that differed between RFI ranks. Despite controlling genetics, diet specification, dietary phases, and management practices in each rearing environment, the rearing environment, encompassing maternal influence, herd health status, as well as other factors, appears to impact intestinal microbiota more than FE. IMPORTANCE Interest in the role of intestinal microbiota in determining FE in pigs has increased in recent years. However, it is not known if the same FE-associated bacteria are found across different rearing environments. In this study, geographic location and intestinal sampling site had a greater influence on the pig gut microbiome than FE. This presents challenges when aiming to identify consistent reliable microbial biomarkers for FE. Nonetheless, seven FE-associated microbial taxa were common across two geographic locations and/or two batches within one location, and these indicated a potentially "healthier' and metabolically more capable microbiota in more-feed-efficient pigs. These taxa could potentially be employed as biomarkers for FE, although bacterial consortia, rather than individual taxa, may be more likely to predict FE. They may also merit consideration for use as probiotics or could be targeted by dietary means as a strategy for improving FE in pigs in the future.The research leading to these results received funding from the European Union’s Seventh Framework Programme (ECO-FCE project number 311794) for research, technological development, and demonstration independently of any commercial input, financial or otherwise. U.M.M. was funded by the Teagasc Walsh Fellowship program. Gwynneth Halley, who assisted with laboratory work, was funded by a Society for Applied Microbiology Students into Work grant