Tracking Down Disease Pathways
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PIC Update: February 2011
Tracking down the different ways disease can enter the food production system is not as clear cut as it may seem – especially when there are many steps along the way from farm gate to dinner plate. Speedy analysis would make a difference not only to animal and human health, but also to the environment and economy.
Prof. Deborah Stacey, Director of the Department of Computing and Information Science at the University of Guelph, is looking for a better way for administrators and researchers to plan for and respond to the spread of animal diseases, based on the numerous paths diseases can take.
And to her, the answer is the Shared Hierarchical Academmic Research Computing Network (SHARCNET), a network of high performance supercomputers linked across universities in southern Ontario.
Stacey and her research team are developing free, open-source software that can be modified to suit individual situations when problems arise. Their new software is designed using a “scale-free” network of “hubs” (instead of a random network) to simulate possible distributions of flocks along the food supply chain.
A hub might be a large chicken operation or meat processing plant that distributes poultry to several supermarket chains. The idea is to illustrate the possible distribution paths poultry could take. In a simulated disease outbreak, epidemiologists can study the differences in disease spread that are caused by various distributions or contact networks.
The software also allows researchers to account for many variable elements, such as farm location, the method of transportation, and whether a related disease is airborne. All of these elements can either influence or trigger the spread of a disease.
Stacey says that being able to model the wide variety of these possible paths a disease may take with the help of their new software program will allow government health agencies to study different scenarios and plan for an emergency.
The information will help determine the best course of action – quarantine, vaccination or culling an infected flock – and the possible effect on the plan’s effectiveness and economic viability.
“The models can’t predict where the infections are going to go, but what we can do is help inform epidemiologists and ministry officials so that they can develop policies if there is an infection,” says Stacey.
Joey Sabljic is a student writer with the University of Guelph’s Student Promoting Academic Research Knowledge (SPARK). Also involved in this study are computer science masters students Joel Francis and Sarah Ahmad.
Stacey’s research is supported by OMAFRA, the Canadian Food Inspection Agency and the Chemical, Biological Radiological-Nuclear Research and Technology.
This article was originally published in the University of Guelph’s Research magazine, 2010 Agri-Food Yearbook Edition.
By Tim Nelson, Executive Director
The majority of the research funded through PIC will hit the farm sector a good 10 to 15 years after the work is completed. This means that for the work to be relevant into the future it needs to be developed with a mindset that the results will be implemented 20-30 years from now. “Guessing” what the market will want and what the industry will look like 30 years from now is quite a challenge, as we try to decide what resources, both human and physical, we will need to utilize for the research that will be implemented 20 years after its completion. This is an imprecise process; however, it’s an important one. The feather boards are currently undertaking this process and we’ll report on their thoughts in the March issue of Canadian Poultry magazine. In the meantime, for you poultry sages out there: if you have opinions of our industry’s future science needs, as always, we’d appreciate your opinions.
This year has started with a bang. The first Science in the Pub was held in early January, examining the role of science in farm safety. At the beginning of this month, the Producer Updates were held in Belleville and St. Catharines, Ont.
Also this month are additional Growing Forward meetings. There are more Growing Forward meetings in February wherein producers can take the one-day workshop to be eligible for up to $10,000 in government funds to enhance their biosecurity system(s). There’s still time to register for these events; please see our website at www.poultryindustrycouncil.ca.
We’ll keep you posted throughout the year as other events unfold and look forward to another positive and busy year of research and education delivery for the poultry industry in Ontario.
Efficient evaluation for profitability
Steve Miller and Lindsay Case, University of Guelph
Body conformation is important in the turkey industry, as a substantial proportion of total production is further processed. Breast meat is the highest value component of the further processed carcass. As a result, breast meat yield has a significant effect on profitability, such that conformation and breast meat size has been a selection objective for many years. Together with substantial increases in growth rate and body size, moderate breast meat yield improvements have been achieved.
Selection for conformation has traditionally been on subjective breast conformation score (taking into account size, distribution, chest shape and spread of muscle). Using subjective measures is inherently difficult – there may be differences within and between scorers, and one scorer’s measures may change over time. Objective measures have also been used as selection criteria (including chest width, breast circumference, indentation height from keel to breast and ultrasound muscle depth).
In practice, selection criteria depend on the accuracy, speed and cost of measurements taken. In order to optimally use this type of information, the poultry industry needs a strategy that accounts for ease of measurement, cost and genetic response. Steve Miller, Ben Wood (Hybrid Turkeys) and PhD student Lindsay Case, and their research team at the University of Guelph, have been studying the use of ultrasound as a non-invasive measure of breast meat yield. Their aim is to increase the accuracy of the information used to select for breast meat yield, thereby increasing the selection response within a breeding program.
Measurements were taken on 719 hens from a female breeding line and on 657 hens from a male breeding line. The research team developed a technique in which they took two ultrasound images of each bird (lengthwise and widthwise). Conformation of each bird was measured by a trained scorer, and both methods were compared for accuracy in estimating breast meat yield. Heritability of traits was also calculated.
Their findings? Ultrasound traits showed increased heritability compared to conformation score – meaning the use of this technique should enable more rapid genetic progress. Overall, the research team has shown that ultrasound technology can be useful in increasing the efficiency of breast meat yield measurement in the live turkey. The results of this study can ultimately be used to increase profitability of turkey production with downstream value benefits for the consumer.
Deborah Stacey has been with the School of Computer Science at the University of Guelph since 1988. She has been the director of the school since 2006.
Her areas of research are ontologies for software composition, simulation of disease spread in animals and the application of artificial neural networks and genetic algorithms for data analysis. Her area of teaching expertise is software design and software engineering.
She has collaborated with the Canadian Food Inspection Agency, the Public Health Agency of Canada and the United States Department of Agriculture.
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