Dairy Science Commons^™

Characterisation Of Sex Chromosome Aneuploidy In Female Cattle Using Genotype Information, Cliona Ryan

ORBioM (Open Research BioSciences Meeting)

Background

Aneuploidy is a genetic condition characterized by the loss (monosomy) or gain (trisomy) of one or more chromosomes. Aneuploidy affecting the sex chromosomes often leads to infertility. The objective of this study was to estimate the prevalence of sex chromosome aneuploidy in a large juvenile population using routinely available genotype intensity information.

Methods

Genotype and genotype intensity data was available on 145,476 female dairy and beef cattle below 15 months of age at the time of genotyping, with no recorded progeny. Genotype intensity data included the LogR Ratio (LRR), R-value (the sum of X and Y SNP probe intensities), …

The Effect Of Slow-Release Milk Replacer Feeding On Health And Behaviour Parameters In Dairy Breed Calves, Lea Krump, Ríona G. Sayers, Katie Sugrue, Emer Kennedy, Jim O'Mahony, Gearoid Sayers

Department of Biological Sciences Publications

The aim of this research paper was to evaluate the effect of a slow-release milk replacer on health and behaviour of neonatal dairy calves. This was done with the potential benefits to welfare during transport in mind. A total of 15 calves were randomly divided into three groups of 5, namely, a control group fed twice in 24 h with 3 l of a conventional milk replacer, a slow-release group fed once in 24 h with 2 l of conventional milk replacer and 1 litre of a specialised micro-encapsulated feed and an enriched-replacer group fed once in 24h with 3L …

Factors Associated With Intensity Of Technology Adoption And With The Adoption Of 4 Clusters Of Precision Livestock Farming Technologies In Irish Pasture-Based Dairy Systems, P. Palma-Molina, T Hennessy, A. H. O'Connor, S. Onakuse, Niall O'Leary, B. Moran, L. Shalloo

Publications

Precision livestock farming (PLF) technologies have been widely promoted as important tools to improve the sustainability of dairy systems due to perceived economic, social, and environmental benefits. However, there is still limited information about the level of adoption of PLF technologies (percentage of farms with a PLF technology) and the factors (farm and farmer characteristics) associated with PLF technology adoption in pasture-based dairy systems. The current research aimed to address this knowledge gap by using a representative survey of Irish pasture-based dairy farms from 2018. First, we established the levels of adoption of 9 PLF technologies (individual cow activity sensors, …

Genetic Selection For Improved Production Efficiency In The Mature Dairy Herd, Maeve Williams

Theses

Improving dairy cow production efficiency is highly desirable because of its well-documented impact on profitability and sustainability. Long-term gains in dairy cow production efficiency have already been delivered through genetic selection. Nonetheless, achieving further improvements in production efficiency could cement the economic and environmental efficiency of the dairy industry, globally. To date, several components contributing to production efficiency have been overlooked, with many studies focusing on dairy cow production efficiency over short periods rather than lifetime efficiency. Therefore, the objectives of this thesis were to quantify the genetic variance components of complementary dairy cow efficiency metrics; including dry matter intake, …

Genetic Variations In The Myostatin Gene Among Irish Cattle Breeds, Cliona Ann Ryan

ORBioM (Open Research BioSciences Meeting)

No abstract provided.

The Effect Of Concentrate Supplementation On Milk Production And Cow Traffic In Early And Late Lactation In A Pasture-Based Automatic Milking System, John Shortall, Cathriona Foley, Roy D. Sleator, Bernadette O'Brien

Department of Biological Sciences Publications

The objective of this experiment was to establish the effect of low-concentrate (LC) and high-concentrate (HC) supplementation in the early and late periods of lactation on milk production and cow traffic in a pasture-based automatic milking (AM) system. In total, 40 cows (10 primiparous and 30 multiparous) were randomly assigned to one of the two treatments. The experimental periods for the early and late lactation trials extended from 23 February to 12 April 2015 and 31 August to 18 October 2015, respectively (49 days in each trial period). The early lactation supplement levels were 2.3 and 4.4 kg/cow per day …

Development Of A Grass Measurement Optimisation Tool To Efficiently Measure Herbage Mass On Grazed Pastures, D. J. Murphy, B. O'Brien, Michael D. Murphy

Publications

Accurate and efficient estimation of herbage mass is essential for optimising grass utilisation and increasing profit for pasture farming. There is no definitive sampling protocol for grass measurement on Irish pastures. This paper presents the Grass Measurement Optimisation Tool (GMOT), designed to generate measurement protocols that optimise for time and accuracy. The GMOT was designed in the form of a decision support tool that generates interactive paddock maps that guide the farmer on how to optimally measure their pastures in a random stratified manner based on GPS co-ordinates, resulting in accurate non-biased estimations of mean herbage mass. Rising plate meter …

Photovoltaic Systems On Dairy Farms: Financial And Renewable Multi-Objective Optimization (Farmoo) Analysis, Michael Breen, J. Upton, Michael D. Murphy

Publications

No abstract provided.

Feed Efficiency And Carcass Metrics In Growing Cattle, David N. Kelly, Craig Murphy, Roy D. Sleator, Michelle M. Judge, Stephen B. Conroy, Donagh P. Berry

Department of Biological Sciences Publications

Some definitions of feed efficiency such as residual energy intake (REI) and residual gain (RG) may not truly reflect production efficiency. The energy sinks used in the derivation of the traits include metabolic live-weight; producers finishing cattle for slaughter are, however, paid on the basis of carcass weight, as opposed to live-weight. The objective of the present study was to explore alternative definitions of REI and RG which are more reflective of production efficiency, and quantify their relationship with performance, ultrasound, and carcass traits across multiple breeds and sexes of cattle. Feed intake and live-weight records were available on 5,172 …

Modelling And Simulation Of Renewable Technologies For Economic And Environmental Analysis And Optimization Of Dairy Farms, Michael Christopher Breen

Theses

The aim of this thesis was to develop a dairy optimisation platform to optimise investments in dairy farm technology and changes to on-farm management practices and electricity tariffs, in order to maximise profitability and minimise environmental impacts. Increased dairy herd sizes and milk production levels in Ireland as well as changing regulations concerning emissions, renewable penetration and energy efficiency have necessitated a means of financial decision support for farmers. Therefore this body of work focused on the creation of a comprehensive method for optimising dairy farm technology selection, management practices and electricity tariffs. The measures which could be implemented on …

Inhibition Of Listeria Monocytogenes By Human Gut Bacteria, Patrycja Sylvia Olesky

Masters

Listeria monocytogenes is a foodborne pathogen, which continues to be problematic to the food industry due to its ability survive within food products and persist within food processing environments. The growing trend towards natural food preservatives and antimicrobial agents increases the need for the development of novel, natural anti-Listeria agents. Evidence presented in the literature suggests that the human gut microbiota is a reservoir of novel antimicrobial agents. It was therefore hypothesized that novel anti-Listeria agents are produced by human gut-derived bacteria. The objective of this study was to isolate and characterize gut bacteria with anti-Listeria monocytogenes activity. A total …

Daily And Seasonal Trends Of Electricity And Water Use On Pasture-Based Automatic Milking Dairy Farms, John Shortall, Bernadette O'Brien, Roy D. Sleator, J. Upton

Department of Biological Sciences Publications

The objective of this study was to identify the major electricity and water-consuming components of a pasture-based automatic milking (AM) system and to establish the daily and seasonal consumption trends. Electricity and water meters were installed on 7 seasonal calving pasture-based AM farms across Ireland. Electricity-consuming processes and equipment that were metered for consumption included milk cooling components, air compressors, AM unit(s), auxiliary water heaters, water pumps, lights, sockets, automatic manure scrapers, and so on. On-farm direct water-consuming processes and equipment were metered and included AM unit(s), auxiliary water heaters, tubular coolers, wash-down water pumps, livestock drinking water supply, and …

The Effect Of Dairy Cow Breed On Milk Production, Cow Traffic And Milking Characteristics In A Pasture-Based Automatic Milking System, John Shortall, Cathriona Foley, Roy D. Sleator, Bernadette O'Brien

Dept. of Biological Sciences Preprints

Despite the increasing frequency of integrated automatic milking (AM) and pasture-based systems, there is limited knowledge available on the suitability of different dairy cow breeds to these systems. Thus, the objective of this experiment was to establish the performance of three breeds in a pasture-based AM system with respect to milk production, cow traffic and milking characteristics. The breeds examined were Holstein Friesian (HF), Jersey x HF (JEX) and Norwegian Red x HF (NRX), all of which have been previously identified as being compatible with conventional milking pasture-based systems. The experiment was conducted in mid-lactation and variables measured included milking …

Predicting Energy And Water Consumption On Dairy Farms Through Statistical Analysis And Machine-Learning Methods, Philip Shine

Theses

With the abolishment of milking quotas across all European Union member states in April 2015, dairy farmers must adjust their farming practises to minimise milk production costs to adequately prepare for potential periods of reduced revenue. Milk production is an intense energy and water consuming process. Coupled with challenging European greenhouse gas reduction targets and legislation regarding the prevention of groundwater pollution and deterioration, increasing the production of milk in Ireland must be met with the sustainable consumption of on-farm energy and direct water resources, to ensure the future monetary and environmental sustainability of Ireland’s dairy industry. Thus, this body …

The Use Of Machine Learning To Detect Suckling In Pre-Weaned Calves, Sukumar Katamreddy

Theses

The weaning of cattle is a process which is known to be labour intensive and to have stressful effects on both cow and calf Common methods used in the weaning process include the temporary removal of a mother from the calf and manual observation and intervention. Early and speedy weaning is known to have a number of benefits, including health benefits for both cow and calf, additional weight gains for the calves as well as reduced labour and feed requirements. The process known as Two-Stage Weaning is recognised to be an effective low-stress approach to weaning in which the calf …

An Optimal Milk Production Model Selection And Configuration System For Dairy Cows, Fan Zhang

PhDs

Milk production forecasting in the dairy industry has been an independent research topic since the early 20th century. The accurate prediction of milk yield can benefit both the processor (creameries) and the producer (dairy farmer) through developing short-term production schedules, planning long-term road maps, facilitating trade and investment in the dairy industry, improving business operations, optimising the existing infrastructure of the dairy industry, and reducing operating costs. Additionally, due to the innate characteristics of the milk production process, the accurate prediction of milk yield has been a challenging issue in the dairy industry. With the abolishment of EU milk quotas …

Is Tb Testing Associated With Increased Blood Interferon-Gamma Levels?, Aideen E. Kennedy, Jim O'Mahony, Noel Byrne, John Macsharry, Riona G. Sayers

Department of Biological Sciences Publications

The Republic of Ireland reports a relatively low prevalence of Johne’s disease (JD) compared to international counterparts. Postulated reasons for this include a lower average herd size and a grass-based production system. Ireland also engages in high levels of bovine tuberculosis (bTB) testing. As interferon-gamma (IFN-γ) is believed to play a key role in protecting against JD, it is our hypothesis that administration of purified protein derivative (PPD), as part of the bTB test, is associated with a systemic increase in IFN-γ production, which may potentially limit clinical progression of the disease. We studied 265 cows (202 Friesian and 63 …

Automating The Milking Process Within A Grass-Based System, John Shortall

Theses

The successful integration of automatic milking (AM) and grazing has resulted in AM becoming a feasible alternative to conventional milking (CM) in pasture-based systems. The objective of this thesis was to establish (i) the social, environmental and economic effects of adopting AM technology and (ii) the factors affecting cow traffic, which once the AM is adopted, can also impact on the sustainability of AM. A theme across this thesis is the examination of AM in the context of a seasonal pasture-based milk production system. Electricity and water meters were installed on seven AM fanns. Milking and livestock/^miscellaneous processes were the …

Low Cost, Multi-Purpose Genotyping Panels For Dairy And Beef Cattle, Michelle Judge

Theses

rhe selection of animals based on DNA has revolutionised animal breeding, but the associated high cost of obtaining genotypes has limited its uptake. The objective of this thesis was to develop a low-cost, low-density, multi-purpose genotyping panel for the procurement of reliable genotype information, and to quantify the long-term consequences of using such low-density genotype panels in breeding programs. The objectives were achieved through a combination of real-life cattle genotype data and simulations to mimic a cattle population. The in-silico development of genotype panels was based on actual genotypes from up to 58,705 beef cattle. Alternative novel strategies were used …

The Development Of New Molecular Tools To Detect Mycobacterium Avium Subspecies Paratuberculosis From A Bovine Faecal Environment By Real-Time Pcr, Marcel De Kruijf

Theses

The slow-growing intracellular pathogen Mycobacterium avium subspecies paratuberculosis (MAP) causes Johne’s disease in domesticated and wild ruminants. Johne’s disease inflicts severe annual economic losses to the dairy industry worldwide. This thesis is divided into five chapters that consist of a literature review' chapter and four experimental chapters focusing on MAP strain genotyping and the development of novel molecular MAP detection tools using real-time PCR. Chapter 1 describes published information regarding MAP characteristics, Johne’s disease, MAP genomes, available MAP detection methods, MAP epidemiology and genotyping.

To efficiently control and monitor MAP infection, molecular t>ping of MAP strains provides extensive knowledge …

Investment Appraisal Of Automatic Milking And Conventional Milking Technologies In A Pasture-Based Dairy System, John Shortall, Laurence Shalloo, Cathriona Foley, Roy D. Sleator, Bernadette O'Brien

Department of Biological Sciences Publications

The successful integration of automatic milking (AM) systems and grazing has resulted in AM becoming a feasible alternative to conventional milking (CM) in pasture-based systems. The objective of this study was to identify the profitability of AM in a pasture-based system, relative to CM herringbone parlors with 2 different levels of automation, across 2 farm sizes, over a 10-yr period following initial investment. The scenarios which were evaluated were (1) a medium farm milking 70 cows twice daily, with 1 AM unit, a 12-unit CM medium-specification (MS) parlor and a 12-unit CM high-specification (HS) parlor, and (2) a large farm …

Analysis Of Johne’S Disease Elisa Status And Associated Performance Parameters In Irish Dairy Cows, A. E. Kennedy, N. Byrne, A. B. Garcia, Jim O'Mahony, R. G. Sayers

Department of Biological Sciences Publications

Infection with Mycobacterium avium subspecies paratuberculosis (MAP) has been associated with reductions in milk production in dairy cows and sub optimal fertility. The aim of this study was to highlight the production losses associated with testing MAP ELISA positive in Irish dairy cows. Secondary objectives included investigation of risk factors associated with testing MAP ELISA positive. A survey of management practices on study farms was also conducted, with examination of associations between management practices and herd MAP status.

Blood samples were collected from 4188 breeding animals on 22 farms. Samples were ELISA tested using the ID Screen Paratuberculosis Indirect Screening …

Analysis Of Johne's Disease Elisa Status And Associated Performance Parameters In Irish Dairy Cows, A. E. Kennedy, N. Byrne, A. B. Garcia, Jim O'Mahony, R. G. Sayers

Department of Biological Sciences Publications

Background

Infection with Mycobacterium avium subspecies paratuberculosis (MAP) has been associated with reductions in milk production in dairy cows and sub optimal fertility. The aim of this study was to highlight the production losses associated with testing MAP ELISA positive in Irish dairy cows. Secondary objectives included investigation of risk factors associated with testing MAP ELISA positive. A survey of management practices on study farms was also conducted, with examination of associations between management practices and herd MAP status.

Blood samples were collected from 4188 breeding animals on 22 farms. Samples were ELISA tested using the ID Screen Paratuberculosis Indirect …

An Investigation Of The Use Of Natural Agents To Control Mycobacteria, Olga Lesniak

Theses

Economic losses that are caused by Mycobacterium avium paratuberculosis (MAP) infections represent a major obstacle for farmers and also for the dairy industry. In order to control the population of MAP, alternative control agents must be investigated. One of the studies described in this thesis focused on using a bacteriophage therapy based approach to assess its efficacy on simulated industrial environments and food models. Another study described in this thesis investigated the antimicrobial effects of parsley and garlic on a range of mycobacteria species. Both studies used conventional microbiological methods such as plaque assays, AlamarBlue assay (MABA) and growth curves, …

Development And Validation Of Gas Chromatographic Methods For Free Fatty Acid Determination In Dairy Products, David Mannion

Theses

Quantification of free fatty acids (FFA) in dairy products by gas chromatography flame ion'^ation detection is an important requirement for qua'ity, research, nutritional, authenticity and legislative purposes. Common procedures are typically variants of either the fatty acid methyl esterification (FAME) or direct on-column injection methods developed more than two decades ago. This study involved the development of an alternative novel derivatization method using butylation, incorporating automation, reducing solvent usage that is applicable for a wide range of dairy products. The accuracy, precision, linearity, limits of detection and limits of quantification of all three methods were assessed for the quantification of …

A Tail Of Two Phages: Genomic And Functional Analysis Of Listeria Monocytogenes Phages Vb_Lmos_188 And Vb_Lmos_293 Reveal The Receptor-Binding Proteins Involved In Host Specificity, Aidan Casey, Kieran Jordan, Horst Neve, Aidan Coffey, Olivia Mcauliffe

Department of Biological Sciences Publications

The physical characteristics of bacteriophages establish them as viable candidates for downstream development of pathogen detection assays and biocontrol measures. To utilize phages for such purposes, a detailed knowledge of their host interaction mechanisms is a prerequisite. There is currently a wealth of knowledge available concerning Gram-negative phage-host interaction, but little by comparison for Gram-positive phages and Listeria phages in particular. In this research, the lytic spectrum of two recently isolated Listeria monocytogenes phages (vB_LmoS_188 and vB_LmoS_293) was determined, and the genomic basis for their observed serotype 4b/4e host-specificity was investigated using comparative genomics. The late tail genes of these …

Phages Of Non-Diary Lactococci: Isolation And Characterization Of Phi L47, A Phage Infecting The Grass Isolate Lactococcus Lactis Ssp Cremoris Dpc6860, Daniel Cavanagh, Caitríona M. Guinane, Horst Neve, Aidan Coffey, R. Paul Ross, Gerald F. Fitzgerald, Olivia Mcauliffe

Department of Biological Sciences Publications

Lactococci isolated from non-dairy sources have been found to possess enhanced metabolic activity when compared to dairy strains. These capabilities may be harnessed through the use of these strains as starter or adjunct cultures to produce more diverse flavor profiles in cheese and other dairy products. To understand the interactions between these organisms and the phages that infect them, a number of phages were isolated against lactococcal strains of non-dairy origin. One such phage, ΦL47, was isolated from a sewage sample using the grass isolate L. lactis ssp. cremoris DPC6860 as a host. Visualization of phage virions by transmission electron …