The Animal Bioscience Centre Research

Digestion and the efficiency of conversion of food into product

5781
Mitigation strategies for methane emissions by dairy cows in Irish Milk production systems
01-Jan-2008 to 30-Jun-2011
John Murphy (Moorpark, (Project leader), Sinead Waters, Padraig O’Kiely (Teagasc, Grange), Tommy Boland and Evelyn Doyle (University College Dublin), Tianhai Yan (AFBINI)

The overall objective of this project is to find mitigation strategies for methane emissions from the Irish dairy herd. The ABD is involved in several parts of this project. Firstly, a study of the effect of breed and diet on methanogenic microbial populations in cattle rumen will be carried out. Molecular techniques such as real time PCR and RFLP will be used on rumen contents samples to examine and quantify methanogenic microbial populations in the rumen of cattle. Different breeds will be compared to determine whether there is a genetic component(s) associated with the variation in composition of such microbial populations. In addition, effects of different feeding regimes on numbers of methanogenic microbes in the rumen will also be studied. The findings from these studies will hopefully have use in breeding programmes and feeding strategies to reduce methane emissions from cattle.

 

5928
Examination of the molecular control of feed intake and energetic efficiency in cattle
01 Jan 09 to 31 Dec 2014
Sinead Waters (Project leader), Richard Dewhurst (Animal Bioscience Centre), Mark McGee (Grange), Frank Buckley (Moorepark) Chris Creevey (Animal Bioscience Centre), David Kenny, (University College Dublin), Dermot Morris (Teagasc, Athenry).

Cattle with poor energetic efficiency have a higher cost of production and a greater environmental footprint. Traditional measures of energetic efficiency such as feed conversion rate (FCR) or feed conversion efficiency (FCE) have been confounded with maturity patterns, body size, composition of gain and appetite of cattle leading to the selection of breeding animals with increased mature size and thus, higher maintenance requirements and costs. Net feed efficiency (NFE), a measure of energetic efficiency, is calculated as the difference between an animal’s actual feed intake and expected requirements based on weight and growth rate. Regulation of feed intake is influenced by an interaction between physical and chemical properties of the diet and complex anatomical, neural and endocrine processes within the animal. Recent advances in genome wide association studies present opportunities for the identification of animals that predispose towards enhanced energetic efficiency. The selection of animals based on NFE is difficult using genome wide association studies for many reasons, including the complex nature of the trait, the costs associated with the generation of a sufficiently large sample population, and the fact that NFE may vary at different times in the animal’s life. In an attempt to gain an understanding of biological mechanisms controlling NFE, the aim of this proposal is to apply next generation transcriptomic sequencing and bioinformatic tools to identify key genes and metabolic/neural pathways influencing energetic efficiency. This data will assist in the discovery of potential biomarkers including single nucleotide polymorphisms for feed efficiency, leading to increased genetic improvement and profitability in Irish cattle production.

Animal Product Quality

5759
Examination of the expression of genes associated with muscle growth and development in beef cattle of varying breeds with high or low growth rate potentials
01-Jan-2008 to 31-Dec-2010
Sinead Waters (Project leader), Sean Doyle and Kay Ohlendieck (National University of Ireland Maynooth), David Kenny (University College Dublin), Gerry Keane (Teagasc, Grange)

Skeletal muscle development is a critical trait to the biological and economic efficiency of beef cattle production. Not only the quantity but also the quality of the muscle produced dictates the value of the animal in terms of meat production potential. Muscle production is a function, not only of the management system under which the animal is reared but also its genetic potential determined at conception. Consequently, detailed molecular knowledge of the regulation of muscle growth, fibre type and extra cellular matrix deposition will be important for optimal beef production systems in the future. Currently a genetic resource, in the form of young beef cattle selected on the basis of sire EPD for either high or low growth rate potential exists at Grange (RMIS 5470), which has been made available for molecular studies. This study proposes to examine the expression of candidate genes associated with muscle growth and development in beef cattle of varying breeds at a number of time points from 15 months of age to slaughter. The ability to determine key genes regulating muscle cell differentiation and proliferation will provide fundamental information on molecular mechanisms controlling growth rate and allow the future discovery of single nucleotide polymorphisms (SNP) associated with muscle growth rate and hence the development of genetic tests to identify animals with superior growth rate potential at an early age. This will considerably increase both the accuracy and intensity of selection as well as shorten the generation interval in beef cattle breeding. This proposal is consistent with project themes of the Animal Bioscience programme.

Animal Reproductive Biology

5517
Uterine gene expression in cows of high and low fertility
01-Jan-2006 to 31-Dec-2009
Sinead Waters (Project leader), David Kenny (University College Dublin), Dermot Morris and Michael Diskin (Teagasc, Athenry)

Cow conception rate is a major component of reproductive and production efficiency in beef and dairy herds. There is evidence of repeatable differences between cows in conception rate and of genetic variability for conception rate and cow sustainability. Furthermore, it has been shown that conception rate or embryo survival rate is critically dependent on an optimum uterine environment prior to implantation. The critical period is the first two weeks after fertilisation when the embryo is totally dependent on the uterine fluid for its nutrition. The objective of this proposal is to (i) establish the uterine gene expression basis for differences in embryo survival rate, and (ii) to produce data that may help identify genetic markers for embryo survival/conception rate in cattle which may be exploitable at industry level. The new knowledge generated by this proposal will enhance our understanding of cow fertility and will quantify the extent of gene expression differences existing for an important trait like uterine function.

5677
The effect of stage of cycle and steroid environment on the uterine proteome of the cow and differences from plasma
01-Oct-2007 to 30-Sep-2010
Dermot Morris (Project leader), Michael Dunn (University College Dublin)

Early embryo loss is one of the greatest factors affecting fertility in the dairy and beef herds. Uterine function and the need to maintain an adequate supply of growth factors, binding and transport proteins to support adequate embryo growth and development until implantation has potentially the greatest influence on this loss. From previous studies we now know that uterine function can be affected by changes in nutrition and that uterine gene expression is sensitive to small changes in the steroidal environment. It is the translation and expression of these genes as proteins within the cell, however, that ultimately defines its function. With a potential order of magnitude increase in the number of proteins expressed as a result of alternate splicing and post translational modification, it is the study of these proteins in the post genomic era that hold the key to associating protein form with function. This project sets out to use state of the art proteomic and bioinformatic techniques to characterise for the first time the low molecular proteome of the bovine uterus, how this is affected by changes in systemic progesterone and by stage of cycle. This project also aims to identify uterine specific or uterine predominant proteins and functional pathways implicated in embryo growth and survival.

This is a collaborative project between Athenry and the Proteomic Research Centre of the UCD Conway Institute of Biomolecular & Biomedical Research, UCD.

5679
Uterine and embryo gene expression of cows with high and low polyunsaturated fatty acid concentrations
01-Sep-2006 to 31-Dec-2009
Sinead Waters (Project leader), David Kenny (University College Dublin), Claire Wathes (Royal Veterinary College London), Ailish Hynes (National University of Ireland Galway), Dermot Morris (Teagasc, Athenry)

The inclusion of polyunsaturated fatty acids (PUFAs), specifically those from the omega-3 family, has been reported to positively influence dairy cow fertility, though the mechanism(s) involved are as yet unclear. Most evidence suggests that the omega-3 family cause a reduction in uterine produced prostaglandin F2a with a consequent maintenance of systemic concentrations of progesterone, essential for the initiation and maintenance of pregnancy. Omega-3 PUFAs act as precursors for series 3 prostaglandins which are less biologically active than series 2 (PGF2a). An increase in the series 3 at the expense of series 2 prostaglandins has been proposed as a possible reason for the inhibitory effect of PUFAs on PGF2a synthesis. Another possible mechanism proposed is that Interferon-tau expressed by the pre-implantation embryo may inhibit PGF2a synthesis by altering lipid metabolism and reducing the availability of arachidonic acid for PGF2a synthesis.

The objective of this study is to examine the effect of dietary omega-3 fatty acids on global patterns of gene expression in uterine and embryo tissue in cows. Uterine gene expression profiles will be determined using a 23,000 character Affymetrix GeneChip® Bovine Genome Array. Uterine expression of candidate genes known to be involved in PGF2a biosynthesis will be analysed using quantitative real time RT-PCR. In addition, the effect of dietary omega-3 fatty acids on the expression of genes related to apoptosis (Bax), maternal recognition of pregnancy (IFN-tau) and differentiation and implantation (LIF, LR-beta) in embryos will be analysed by quantitative real time RT-PCR. Gene expression profiles will subsequently be related to changes in omega-3 fatty acid concentration and in turn to embryo survival rates. The knowledge generated by this proposal will quantify the extent of gene expression differences existing for an important trait like uterine function and will in this way enhance our understanding of cow fertility. Furthermore, this information is essential for the proper formulation of cattle diets that may increase cow fertility .

5756
Identification of the effects of short-term dietary restriction on gene expression in the anterior pituitary, hypothalamic, preoptic and the ventromedial hypothalamus tissues of cattle
01-Jan-2008 to 31-Dec-2011
Michael Diskin (Project leader)

Reproductive efficiency is a key factor governing economic performance of both beef and dairy herds and is of particular importance to seasonal calving systems. Nutrition is widely accepted to play a fundamental role in the modulation of reproductive events in all species including cattle. Even short term energy restriction can have major effect on ovarian function and embryo survival. The underlying biological mechanisms by which nutrition affects reproductive efficiency in dairy and beef cattle are poorly delineated. Because of the difficulty in studying both dairy and beef cows in the post partum period (access, cost, complexity of variables) we have developed a repeatable short-term dietary restricted heifer model to characterise the short term effects of NEB on endocrine, physiological and metabolic variables. We now propose to use the same well-defined model to establish the effects of short-term NEB on gene expression profiling in a number of key organs involved in the nutrition-reproduction axis (anterior pituitary, hypothalamic, preoptic and the ventromedial hypothalamus)as well as metabolomics fingerprinting of follicle fluid and blood to describe and establish biomarkers for animal nutritional status, sensitivity to dietary restriction or negative energy balance and or predictive of reproductive status or success. This project proposes to use a combination of global and targeted molecular techniques in associated with emdocrinological and physiological measurements to elucidate the complex interplay between nutrient, hormone and gene expression on the reproductive process. Specifically the obejectives of the project are to screen tissues of the hypothalamic-pituitary-ovarian axis to determine the effect of nutrient restriction on gene expression within these critical organs. Furthermore, metabolic profiling of follicular fluid and blood will provide information on the concentrations of important metabolites and hormones known to influence reproductive events.

5812
Identification of uterine proteomic and genomic differences in dairy heifers with different levels of embryo survival rate
01-Jan-2008 to 31-Dec-2010
Michael Diskin (Project leader)

Selecting female replacements carrying the desired milk production and processing genes and their encoded proteins is a technological aim and a key future economic goal of profitable milk production. To date, animals are selected with reference to desirable phenotypic traits identified in the maternal and paternal lines based on population genetics. However, to reach the future desired economic goal it is important to identify key genes regulating reproductive efficiency and to develop genotyping methods to allow these to be identified and become part of a commercial genotyping service. The aim of this project is to use heifers of proven high or low fertility with a view to beginning to identify ‘fertility genes’ or other biomarkers in cattle for future commercial use. Dairy heifers (n=120) of known genetic background and normal reproductive characteristics will be inseminated, scanned for pregnancy at Day 28 and re-programmed to return to oestrus and be re-inseminated on a further 3 occasions. Each heifer will then be ascribed an embryo survival score based on their cumulative embryo survival rate over the 4 rounds and heifers in the upper and lower 10-12 percentiles will be designated as “high” or “low” fertility groups, respectively, and retained for characterisation. Based on heritability estimates of 0.03 to 0.07 for conception rate with corresponding repeatability estimates of 0.06 and 0.1 the expected genetic difference in conception rate between the low and high groups would be in the order of 10 to 21% points following 4 rounds of repeated inseminations, based on the above heritability and repeatability estimates for conception rate. Uterine fluid and blood plasma will be collected from 8 “low” and 8 “ high” fertility dairy heifers based on the outcome of 4 rounds of insemination. The uterine fluid will be harvested on Days 7 and 15 of successive oestrus cycles, respectively, by catheterisation of each uterine horn and flushing with saline. Flushings will be subjected to proteomic analysis based on MudPIT (Multidimensional Protein Identification Technology), a technique for the separation and identification of complex protein and peptide mixtures. Endometrial tissue samples will be collected from heifers from each of the “high” (n=8) and “low” (n=8) fertility groups immediately following slaughter and total RNA will be isolated from the tissue and processed for array hybridisation. Microarray technology will be used to compare profiles of uterine gene expression in order to identify potential genes regulating key aspects of embryo survival and fertility. This will be facilitated using the Affymetrix 23K bovine GeneChip® master array This project will build on existing basic and applied expertise in both participating institutions.

Animal Health

5741
Improved control of respiratory disease in weaned calves through development of new nanoparticle vaccines
01-Jan-2008 to 31-Dec-2010
Bernadette Earley (Project leader), Brian Adair and Simon Docherty (AFBINI).

Viral pneumonia is a major and persistent problem in calf production in Ireland, causing severe disease, often with permanent disability and frequently death. For this reason respiratory disease causes substantial economic losses to calf production in Ireland running to millions of euros on an annual basis. Outbreaks of disease are most often initiated by viruses and the most important virus involved is bovine respiratory syncytial virus (BRSV). Secondary bacterial infection often follows the virus infection, and treatment of the disease invariably involves the use of antibiotics, which increases the likelihood of the emergence of antibiotic-resistant organisms, posing a risk to human health. The best way to protect against infection would be to stimulate strong specific immunity by vaccination at the site of virus infection in the upper respiratory tract. The currently approved vaccines are administered mainly parenterally and whilst they generate strong systemic immune responses, they fail to stimulate adequate immunity at the site of infection. With recent advances in our understanding of immunity in the respiratory tract and in vaccine delivery and targeting, it is now possible to contemplate the development of a new generation of vaccines, based on nanotechnology, which are aimed at stimulating long lasting immunity in the respiratory tract, and preventing the establishment of virus infections and therefore the development of severe respiratory disease. In previous studies carried out at Teagasc, working in collaboration with colleagues in the Agri-Food and Biosciences Institute (AFBINI) at Veterinary Sciences Division, Belfast, we have produced nanoparticle vaccines which encapsulate BRSV peptides, and have demonstrated antigenicity following inoculation into calves. We now wish to build on these studies, by fine tuning the formulation of the particles, then to select formulations which give rise to optimal stimulation in in vitro experiments with bovine dendritic cells, and then to investigate immunogenicity and antigenicity following vaccination of weaned calves.

5742
Effects of abrupt weaning and truck transportation of beef calves on physiological mediators of the stress response and gene expression
01-Jan-2008 to 31-Dec-2010
Bernadette Earley (Project leader), Sean Doyle (National University of Ireland, Maynooth) and Patty Weber (Michigan State University, USA).

Physiological, cytokine gene expression and responses of the immune system to stressors are poorly understood yet it is reasonable to assume that their economic impact is significant in terms of reduced immune responsiveness in the bovine. Stress management in cattle has three major components: 1), management of the cause of stress; 2), understanding the biological basis of the stress immune axes and 3), alleviation of the stress response. The hypothesis of this study is that weaning and truck transportation induce physiologically relevant stress responses that heighten neutrophil inflammatory status via altered expression of genes involved in key cell-cell adhesion, programmed cell death, bactericidal, and tissue remodeling pathways. The three objectives of this study are to examine the effects of abrupt weaning and truck transportation of beef calves on: (1) physiological mediators of the stress response (serum cortisol, dehydroepiandrosterone (DHEA), adrenaline, noradrenaline, and acute phase proteins); (2) indicators of neutrophil immunocompetence (counts, apoptosis rate, phagocytic index, surface expression of L-selectin, CD18, Fas, TLR-2, TLR-4, TLR-9, and intracellular levels of CD14, IL-8, MMP-9, BPI, mitochondrial cytochrome b, TGF-beta1, PPAR-gamma, IkK-alpha, and GR alpha); and (3) the neutrophil transcriptome. The long term goal of this work is to elucidate a cluster of stress-responsive neuroendocrine and immunocompetence biomarkers for weaning and transportation stressors that will be used in the future for development of novel diagnostics and therapies to identify and treat stress in newly arrived feedlot cattle at heightened risk of bovine respiratory disease.

5477
Animal welfare index (AWI) scientific assessment of farm animal welfare.
01-Jan-2006 to 31-Dec-2009
Bernadette Earley (Project leader) and Mark Crowe (UCD).

Low investment costs and high production efficiency are vital criteria for future competitiveness in animal production. On-farm assessment of welfare has to be combined with the current scientific knowledge on how animals perceive their social and technical environment. Fundamental studies from different scientific disciplines (i.e., physiology, immunology, pathology and stress physiology) can help to create better assessment parameters and to improve the interpretation of what we can observe on the farm. Animal welfare has become an integrated part of quality assurance programs for sustainable animal production, considering that welfare, health, management, economy, consumer acceptance and environmental impact are depending on each other. For this purpose, welfare assessment via objectively measured indicators provides the knowledge needed to further improve this approach in the future. Today, there is no general consensus on which parameters are most suitable for an overall assessment of animal welfare. Additional major thrusts of this project are to improve the EU animal welfare status through knowledge based strategies and to stimulate science-society dialogue on welfare issues. The aim being to increase societal sustainability of Irish agriculture in a EU framework and to enhance the competitiveness of its animal products through their guaranteed added value.

Resource building

5678
Development of a DNA bank resource for Irish beef cattle
01-Nov-2006 to 1-Nov-2009
Michael Diskin (Project leader), Sinead Waters (Teagasc, Grange), Donagh Berry (Teagasc, Moorepark), Sue Galloway (AgResearch, New Zealand), Brian Wickham, (Irish Cattle Breeding Federation)

The traditional approach to genetic improvement in beef cattle has been through quantitative genetics. In simple terms, this implies that the genetic superiority of animals was derived, usually from progeny records, using statistical methodology comparing animals within similarly managed contemporary groups. In such an approach superiority was measured by the additive effects of all the genes located across the entire genome without any cognizance of individual genes. We have now entered a new era where changes, or polymorphisms in quantitative trait loci or genes of known effects are being identified and licensed for use in breeding programs. The royalties a farmer or breeding organization can pay for the use of such tools will be dictated largely by the response attainable which is determined by factors such as the current frequency in the population/farm, the impact of the polymorphism on important traits and the associated expected profitability realized. Furthermore, it is vital, prior to the inclusion or the recommendation to select on any of these polymorphisms in a breeding program that any possible deleterious effects on other economically or socially important traits is assessed. The objective of this project is to develop a DNA-bank of Irish AI beef sires and beef animals with detailed measures on a wide range of traits in Teagasc research herds. Although, no scientific results or publications are expected within the project proposal, it should be seen as the development of a vital ingredient for future anticipated projects. The resource generated may also be used to quantify the effect of potential candidate genes on important traits.

5686
Design and implementation of a web based microarray analysis system
01-Oct-2007 to 31-Dec-2009
Dermot Morris (Project leader), Ailish Hynes and Aaron Golden (National University of Ireland, Galway)

Microarrays are now widely used for gene expression profiling in many animal science based experiments. Raw data emanating from microarray experiments, however, are very noisy and there are many sources of variation and bias. The raw data needs to be quality assessed and interactively "pre-processed" to minimise or remove this variation before statistical analysis in order to achieve any meaningful result. This requires a combination of visualisation and statistical tools which vary depending on what microarray platform or experimental design was used. A number of stand alone tools based on the statistical software R and Bioconductor routines are readily available for these types of analyses. However, the analysis pipeline is not always clear to the user, and the desired tools are not always available from a single integrated source without resorting to a command- line interface, unfamiliar to most users. A user friendly interface is required to facilitate the pre-processing and analysis of microarray experiments in Teagasc addressing the most common microarray platforms and array formats and following a logical progression through an analysis pipeline that is extensible and capable of addressing current as well as future needs.