IAP-26-048

Uncovering environmental and artificial light impacts on domestic animals

Naturally occurring variation in environmental sunlight is a reliable external cue that plants and animals use for adaptive daily and seasonal changes in physiology and health. Increased availability of artificial light at night (ALAN) is known to have detrimental impacts on wild animals. However, our understanding of the impacts of artificial lighting on domesticated animals is poor. This project has three visions. First, we know that different light wavelengths impact laboratory animals. Using this extensive scientific literature, the project will use high resolution spectrophotometry to measure light environments across domestic livestock housing conditions. Using the wide range of barns available at Cochno Farm and University partners (e.g., Meldrum Farm), the student will collect light measurements to capture the variation in photopic and melanopic lux. Moreover, we know that the retina in animals detects and generates physiological responses to the different light wavelengths. The second vision seeks to examine the amount and distribution of light receptors (i.e., photoreceptors) in the retina from cattle (both dairy and beef), sheep and poultry. The students will conduct molecular and cellular assays to evaluate the expression of multiple photoreceptors. The findings generated from this project will significantly improve our understanding of not only which light wavelengths are detected by some domestic animals, but also the potential role of specific retinal photoreceptors for the integration of light information. Moreover, traditional housing environments consist of large barns with limited roof and door lighting. Polytunnels are becoming more frequently used housing environments due to the cheaper costs to erect, and absence of building permits. Polytunnels provide many housing benefits for livestock as the light environment is better matched to natural conditions compared to traditional barns. The third vision is to determine the impact of polytunnel versus traditional barns on animal physiology and health. The overall output will be a comprehensive survey of light wavelengths used across agricultural settings and identify the precise retinal photoreceptors that integrate wavelength-specific information for the regulation of physiology and health in domestic animals.

The studies will use multiple University and farm locations (e.g., University Cochno Farm and University partner farms). All light environments will be assessed using advanced NanoLambda Nsp32 Spectrometry to delineate the power and lux across light wavelengths critical for colour vision (i.e., S/M cones), irradiance light (i.e. rhodopsin) and biological rhythms (i.e., melanopsin). Animal studies will be conducted between January to April and September to December to experimentally evaluate the impact of vernal and autumnal changes in daylength on animal physiology and health. The rationale is to examine light wavelengths prior, during and post birth/egg laying periods. The student will use a range of dependent measures of physiological and health (e.g., calving/lambing success, milk colostrum, egg laying). The student will use a series of common molecular and cellular assays to examine the expression and distribution of photoreceptors in animal retina. Finally, the student will also examine relative abundance of bacteria in the different conditions to assess the light environment on potential health factors.

There are four overall aims:
1) to capture the range in light environments used across agricultural settings (e.g., barns, coops, polytunnels).
2) To determine offspring survival (e.g., single, twin triplets), birth rate, and colostrum quality (i.e. antibody) in animals housed in different light environments (i.e. traditional barns), and polytunnels.
3) To examine the impact of different light environments on animal physiology (e.g., retinal photoreceptor) and health (e.g., faecal microbiome).
4) To examine the relative abundance of zoonotic bacteria (E coli, Staphylococcus spp., Streptococcus spp. and Salmonella Spp) across traditional barns and polytunnels.

Assessment of light environments
Spectrophotometer recordings from traditional barns and polytunnels will be examined at the University of Glasgow Cochno Farm, St Andrews LuckyEwe Farm and affiliated partners (e.g. Arnprior Farms). Light levels will be surveyed continuously for 4 days during the spring, summer, autumn and winter periods. The power, rhodopic (~500nm), melanopic (~485nm), and cone-opic (i.e. S- (~430nm) and M-cone (~530nm)) lux will be averaged and compared across barns and polytunnels. Light environments will be compared across different traditional barns (e.g., open sided, roof lighting). Polytunnel environments will serve as a natural lighting condition comparison.

Animals and Experimental Design
The study will take advantage of common animal husbandry practice at Cochno Farm, LuckyEwe and Arnprior Farms. EasyCare sheep are housed at Cochno Farm and reliably birth between March and April. Angus-cross cattle are maintained at Poultry will be housed at St. Andrews University and conducted under the supervision of Prof. Karen Spencer. Animal studies will occur between January and May to capture the period before, during and after the birthing season. Cows/Ewes will be pseudorandomly assigned (based on number of lambs [e.g., singlet, twin, or triplets]) to either a polytunnel or traditional barn prior. The student will compare birth rates in the different light environments (i.e. polytunnel versus traditional barns). Additional dependent measures will include the number of animals (i.e. singlet, twin, and triplets).

Sampling schedule
Liquid colostrum samples will be collected twice from February to the end of April. This period captures the levels during and after the calving/lambing period. Colostrum will be collected 48hr after calving/lambing (e.g., mid-March) and then after another 2-weeks (early April). 15mL of colostrum will be collected via Udderly EZ Sheep Milker 48 hours and 2-weeks after lambing. Calf/lambs will be faecal sampled in the first 48 hours of life and faecal microbiome measured. We will conduct DNA extraction and amplicon metagenomics (e.g. 16s RNA). Retinal samples will be obtained from local abattoirs and collected in March, June, September and December. Daily and seasonal changes in photoreceptor expression will be analysed in addition to retinal distribution. Bacterial swabs of surfaces (e.g., water/food containers, fencing) will be collected biweekly and abundance will be measured using common culture media used in the Ormsby lab.

Year 1

The student will obtain the necessary animal licence training and graduate student academic and training courses. The student will complete the first year literature review which will establish the introductory chapter for their thesis. This document should lead to a first author review publication. The sheep and cattle projects will commence in the second term. All dependent measure from bacterial sampling, through animal physiology and welfare will be completed by the end of May. June and July will consist of molecular and cellular, and hormonal assays. The first data chapter of the thesis should be completed by the end of September. The student will gain presentation skills through participation in the School seminar series, and specific research theme series. The student will meet with the supervisory team on a weekly basis online, and face to face once each term.

Year 2

The student will continue to enroll in graduate courses for academic development. The student will start the second animal study in collaboration with supervisory team at the Unversity of St Andrews. All dependent measures associated with physiological and behavioural outcomes in response to light treatments will be completed by the winter break. In the second term, the student will complete the molecular and cellular and hormonal assays. The aim will be for the student to complete two data chapter before the end of April. Moreover, the student will be encourage to attend and present in the British Society for Neuroendocrinology and British & Irish Society for Animal Science conferences. During the spring and summer periods, the student will be supported to write their own research projects for grant funding from the British Society for Neuroendocrinology and Genetics Society. The purpose here is to develop grant writing skills and potentially broaden the scope of the student research directions. The student will continue to develop presentation skills through participation in the School seminar series, and specific research theme series. The student will continue to meet regularly (i.e. weekly) with the supervisory team.

Year 3

The Autumn term will involve the final project to assess the impact of housing conditions (e.g., artificial light, traditional barns, and polytunnels) on livestock physiology and welfare. All dependent measures will be collected by the end of the second term. The molecular and cellular, and hormonal assays will be completed by the end of the term. The student will be encouraged to attend and present in the British Society for Neuroendocrinology and British & Irish Society for Animal Science conferences. The student will continue to develop presentation skills through participation in the School seminar series, and specific research theme series. The student will continue to meet regularly (i.e. weekly) with the supervisory team.

Year 3.5

The student will have the Autumn term to complete the final data chapter and thesis conclusions. The student will continue to present in National and International conferences and School seminar series. The student will be encouraged and support to develop their curriculum vitae and online profile to facilitate securing employment (e.g., post-doctoral researcher) position. Moreover, the student will be supported to develop their potential fellowship applications

This studentship will expose the student to broad fields of research including: neuroanatomy, bioinformatics, molecular neuroscience, physiology, and animal behaviour. The student will develop skills in light measurement and subsequently handling large datasets for graphical presentation, interpretation and statistical analyses. The student will also learn tissue dissection followed by molecular assays (e.g., qPCR) and cellular analyses (e.g., histological assays). The students are encouraged to develop other in vivo, in vitro or in silico approaches to examine the relationship between light detection and livestock welfare through small research project grant applications. The student will take the lead role in data collection, interpretation and drafting manuscripts. The supervisory team maintains an open-door policy for trainees and will welcome requests for assistance at each step. The students will develop oral presentation skills and directly participate in knowledge exchange activities with end-users (e.g. Arnprior Farms). This will provide the student with hands-on experience discussing research and impacts for local farmers. The student will have the opportunity to participate in other dissemination activities (i.e. Royal Highland Show) and have experience to interact with the wider farming community and end-users. Students will also be encouraged to engage other scientists in the respective institutes to foster their own collaborations and widen their network. Lastly, the student will be encouraged to present their research at a national conference and local veterinary researchers.