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Efficacy of single pass UVC air treatment for the inactivation of coronavirus, MS2 coliphage and Staphylococcus aureus bioaerosols
Get PDFPublication history: Accepted - 20 April 2022; Published online - 26 April 2022There is strong evidence that SARS-CoV-2 is spread predominantly by airborne transmission, with high viral loads released into the air as respiratory droplets and aerosols from the infected subject. The spread and persistence of SARS-CoV-2 in diverse indoor environments reinforces the urgent need to supplement distancing and PPE based approaches with effective engineering measures for microbial decontamination – thereby addressing the significant risk posed by aerosols. We hypothesized that a portable, single-pass UVC air treatment device (air flow 1254 L/min) could effectively inactivate bioaerosols containing bacterial and viral indicator organisms, and coronavirus without reliance on filtration technology, at reasonable scale. Robust experiments demonstrated UVC dose dependent inactivation of Staphylococcus aureus (UV rate constant (k) = 0.098 m2/J) and bacteriophage MS2, with up to 6-log MS2 reduction achieved in a single pass through the system (k = 0.119 m2/J). The inclusion of a PTFE diffuse reflector increased the effective UVC dose by up to 34% in comparison to a standard Al foil reflector (with identical lamp output), resulting in significant additional pathogen inactivation (1-log S. aureus and MS2, p < 0.001). Complete inactivation of bovine coronavirus bioaerosols was demonstrated through tissue culture infectivity (2.4-log reduction) and RT-qPCR analysis – confirming single pass UVC treatment to effectively deactivate coronavirus to the limit of detection of the culture-based method. Scenario-based modelling was used to investigate the reduction in risk of airborne person-to-person transmission based upon a single infected subject within the small room. Use of the system providing 5 air changes per hour was shown to significantly reduce airborne viral load and maintain low numbers of RNA copies when the infected subject remained in the room, reducing the risk of airborne pathogen transmission to other room users. We conclude that the application of single-pass UVC systems (without reliance on HEPA filtration) could play a critical role in reducing the risk of airborne pathogen transfer, including SARS-CoV2, in locations where adequate fresh air ventilation cannot be implemented.This research was partly funded through the Invest Northern Ireland Innovation Voucher Programme (IV130218200 and IV130232906). We are grateful to the Global Challenges Research Fund (GCRF) UK Research and Innovation (SAFEWATER; EPSRC Grant Reference EP/P032427/1) for supporting Mr Arsalan Afkhami, Dr William J Snelling and Dr Jeremy W.J. Hamilton. Research at AFBI is funded by US-Ireland Research and Development Partnership in Agriculture grants BRDC-Seq and BRDC-URTMVP. We wish to thank Jonathan McMaw at AFBI for acquisition of images
Application of metal oxide semiconductor for detection of ammonia emissions from agricultural sources
Get PDFPublication history: Accepted - 17 November 2022; Published online - 21 November 2022.Agricultural emissions of ammonia (NH3) reduce air quality and biodiversity. Measuring the effectiveness of
mitigations measures requires rapid monitoring tools, however, conventional methods are labour intensive and
costly. This study evaluated the performance of a prototype metal oxide semiconductor (MOS) gas sensor for
monitoring NH3. Conventional methods were used to calibrate sensor conductance. The metal oxide semiconductor
(MOS) gas sensor was calibrated against NH3 released from a 0.1 M phosphate buffer spiked with
ammonium chloride and NH3 released from recently spread cattle slurry. Field measurements using the MOS
sensor were compared with values measuring a Bruker Open Path Air Monitoring System. Sensor conductance
and NH3 concentration were described using single site Langmuir adsorption model. Field calibrations suggest a
higher detection limit above 0.1 ppm and coefficients of determination were 0.93 and 0.89 for sensors 1 and 2,
respectively. For prototypes deployed under field conditions, sensitivities of 2.2 and 2.4 with nonlinearity
constants of 0.53 and 0.51, were found for sensor 1 and 3 respectively. Average R2 values were 0.88 for sensor 1
and 0.92 for sensor 3. The calibrations were used to calculate NH3 concentrations from slurry emissions using
MOS sensor conductance. NH3 concentrations between 0.2 and 1 ppm, were measured with standard deviation
of 20% of verified concentrations. The MOS sensor is sensitive enough to detect NH3 emission from agricultural
sources with concentrations above 0.2 ppm. Low power and cost of MOS sensors are an advantage over existing
techniques.This work was supported by the European Union’s Horizon 2020 Research and Innovation Programme [grant agreement No. 825325]
Evaluation of three methods related to Genome-Wide Association studies for identify gene locus using simulated data
No full textPublication history: Accepted - 16 March 2022; Published online - 16 March 2022Introduction: Due to the widespread distribution of SNPs throughout the genome, these markers are widely used in livestock breeding research. These markers were used to predict the disease risk in human, to localize genetic variations responsible for complex traits through genome wide association study (GWAS), and to predict the genetic values of economically important traits in plant and animal breeding (Zhang et al 2015). Mostly whole genome scanning methods are based on two SSGWAS (Single SNP Genome-Wide Association Studies) and multiple markers methods. The SSGWAS method is able to identify a large number of common variables affecting quantitative traits. However, a large proportion of the genetic variance remains to be explained (Shirali et al 2018). In quantitative traits the proportion of phenotypic variance explained by SNPs is related to the number of adjacent SNPs in the genomic region. The heritability created by these genomic regions is defined as the regional heritability. The RHM (Regional Heritability Mapping) method is used to identify small genomic regions. This method can capture more of the missing genetic variation (Nagamine et al 2012). In RHM, a mixed model framework based on Restricted Maximum Likelihood (REML) is used, and two variance components, one contributed by the whole genome and a second one by a specific genomic region, are fitted in the model to estimate genomic and regional heritabilities, respectively (Uemoto et al 2013). Also fastBAT (fast and flexible set-Based Association Test) is a method that performs a fast set-based association analysis (Bakshi et al 2016). The purpose of this study is compare SNPs and regions identified by the Genome-Wide Association methods, compare these results with the simulated QTLs and also investigate and determine the false positive results in each method.
Material and methods: In this study, markers and populations were simulated as a Forward-in-time process using QMSim software (Sargolzaei and Schenkel 2009). For this population, 27586 single nucleotide polymorphisms (SNPs) were counted on 3 pairs of autosomal chromosomes. Simulation was performed in 3 scenarios with 75, 150 and 300 quantitative trait loci (QTL). The minimum and maximum number of SNPs in the analysis after quality control were 19662 and 23817 SNPs, respectively. For each scenario, 10 replicates were simulated, in all scenarios, heritability was 0.2 which corresponded equally to the polygenic and QTLs effects. Whole genomic relationship and pedigree base genetic relationship matrices were used in all 3 methods to estimate genetic parameters. To create the whole genomic relationships matrix, whole genomic additive effects was estimated using all SNPs. Also the additive effect of genomic regions was estimated using the regional genomic relationship matrix. Whole genomic relationships matrix and regional genomic relationship matrix were estimated based on genetic relationships between individuals using SNPs by GCTA software (Yang et al 2011). Pedigree based genetic relationship matrix was created by the kinship relationship between individuals using pedigree package (Coster 2013) of RStudio software (RStudio Inc 2013). To perform RHM and to estimate variance components, windows containing 50 genotyped SNPs were considered. Also windows containing 25 genotyped SNPs to overlap between two consecutive windows throughout the genome were used. SSGWAS analysis were performed by MLMA (Yu et al 2006) method using GCTA software. MLMA results were adjusted based on P-value at 5% significant threshold using Bonferroni correction. To evaluate the results of SSGWAS using fastBAT method, GCTA software was used.
Results and discussion: For each replication after identifying significant SNPs, the genetic variance explained by these SNPs was estimated by equation (Faulkner & McKay 1996). In Table 1, the number of QTLs detected by the SSGWAS method, the MAF of QTLs, the range and mean of genetic variance explained by significant SNPs and QTLs are reported. For 30 replicates of simulation in SSGWAS, 16 QTLs were detected containing 2 QTLs with MAF≤0.1 and other detected QTLs with MAF≥0.1. 107 Significant regions were identified in fastBAT method. In this method, 120 QTLs were detected in 3 scenarios containing 52 QTLs with MAF≤0.1. All QTLs detected in the fastBAT and SSGWAS methods were also detected in the RHM method. In RHM method, 612 regions containing simulated QTLs and number of 316 QTLs with MAF≤0.1 were detected. In all replications, the variance explained by SNPs was equal to the variance explained by QTLs. In SSGWAS, less number of QTLs were detected than the other two methods and the maximum variance explained by QTLs was 14.9%. The criterion used to determine false positive QTLs was the absence of significant QTL in the before and after significant windows containing QTLs. In SSGWAS method the percentage of false positive QTLs was higher than the other two methods. In fastBAT, unlike the other two methods, detected QTLs were not false positive. In table 5 Number of detected QTLs, MAF range of QTLs, range and mean of genetic variance explained by detected QTLs and SNPs in fastBAT are shown. Many QTLs and regions detected by RHM method were not detected by SSGWAS and fastBAT methods. The genetic variance explained by detected QTLs in the RHM was at the range of 7.26 to 46.86% that was higher than other two methods. In table 6 the three methods compared by the number of detected QTLs, number of false positive QTLs, number of stable QTLs and the number of detected QTLs with MAF≤0.1. We found that QTLs with MAF≤0.1 were more frequently detected in RHM than the other two methods. These results confirmed that the RHM method was able to identifying more of QTLs affecting the trait variance
Behavioural Traits in Bos taurus Cattle, Their Heritability, Potential Genetic Markers, and Associations with Production Traits.
Get PDFPublication history: Accepted - 26 September 2022; Published online - 29 September 2022Simple Summary
Cattle have the potential to seriously injure humans and cause damage to property. The risk of cattle reacting in a dangerous manner can be reduced through genetic selection for cattle which have a better temperament. A literature search was undertaken which returned papers which met the criteria of “Bovine”, “Genetics” and “Behaviour” or terms therein. Behavioural traits were grouped and their heritability, genomic associations and correlations with production traits examined. It was found that heritability estimates were more accurate in studies with large populations (n > 1000). Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible, suggesting that genetic improvement can be undertaken without negatively affecting production. There was variation between the results of the studies examined, and this underlines that any genetic study is population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be required.
Abstract
People who work with cattle are at severe risk of serious injury due to the size and strength of the cattle. This risk can be minimised by breeding less dangerous cattle, which have a more favourable reaction to humans. This study provides a systematic review of literature pertaining to cattle genetics relating to behaviour. The review protocol was developed using the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) framework, with Population, Exposure and Outcome components identified as Bovine, Genetics and Behaviour respectively. Forty-nine studies were identified in the sifting and assigned non-exclusively to groups of heritability (22), genomic associations (13) and production traits related to behaviour (24). Behavioural traits were clustered into the following groups: “temperament, disposition and/ or docility”, “aggression”, “chute score”, “flight speed”, “milking temperament”, “non-restrained methods” and “restrained methods”. Fourteen papers reported high accuracy (Standard Error ≤ 0.05) estimates of heritability, the majority (n = 12) of these studies measured over 1000 animals. The heritability estimates were found to vary between studies. Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible. These studies suggest that additive improvement of behavioural traits in cattle is possible and would not negatively impact performance. However, the variation between studies demonstrates that the genetic relationships are population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be requiredThis research was funded by the Department of Agriculture, Environment and Rural Affairs
(DAERA), Northern Ireland as part of the “TemperGene” project, grant number 19 1 03 (48283
In-river behaviour and freshwater return rates of sea trout, Salmo trutta L., from two coastal river populations
No full textPublication history: Accepted - 9 July 2022; Published online - 14 July 2022.The effective management of anadromous Salmo trutta resources is challenging
because long-term data on life history, phenology and survival are sparse and most
stocks across the range are highly diverse and data-limited. The current study
employed acoustic telemetry to tag 448 sea trout across three life stages, to describe
the phenology, spawning behaviour and return rates of smolts, finnock (0+ sea age)
and adult (≥1+ sea age) sea trout in two Irish river systems during 2018–2021.
Tagged smolts (n = 206) exhibited river to sea transition rates of 78%–92% and a
number of surviving smolts returned to their natal river as 0+ sea age finnock, exhibiting overall smolt to finnock return rates of between 6% and 17%. Short-term
vagrancy occurred among smolts, and 14 individuals were detected in adjacent nonnatal rivers. Finnock tagged during the late summer (n = 205) exhibited a range of
behaviours with a minority (<30%) ascending upstream to spawning areas. Tagged
adult sea trout (n = 37) ascended upstream to the spawning grounds and between
50% and 80% successfully returned to sea as kelts after spawning. Subsequent return
rates of kelts back to the river in the following year ranged from 9% to 40%. The
current study indicated that body size was an influential predictor of behaviour and
survival across all three life stages. Increased body size was positively associated with
marine transition success in smolts, long-term marine survival in kelts and spawning
behaviour in finnock. This work further demonstrates the complexity of sea trout
life-history dynamics and provides a comparative perspective across different age
classes. An understanding of life-history variation, behaviour and survival is fThis work was conducted under the COMPASS project which has been supported by the EU's INTERREG VA Programme, managed by the Special EU Programmes Body. The views and opinions expressed in this document do not necessarily reflect those of the European Commission or the Special EU Programmes Body (SEUPB). Thanks to J. O'Callaghan (IFI), A. Kane and A. Moore (AFBI) and G. Marshall for practical assistance. Thanks to Inland Fisheries Ireland and DAERA field staff and to the Shimna Angling Club and the Dundalk and District Brown Trout and Salmon Anglers Association for support and assistance
The Effect of Transportation on Puppy Welfare from Commercial Breeding Kennels to a Distributor.
Get PDFPublication history: Accepted - 24 November 2022; Published online - 1 December 2022Many puppies from commercial breeding kennels (CBKs) are transported by ground from their kennels of origin to a distributor. This experience may elicit fear and stress during a sensitive developmental period, which may in turn negatively impact the puppies’ short- and long-term welfare. This study aimed to measure short-term effects of transportation on puppy welfare metrics. Eight-week-old puppies (n = 383) from 12 CBKs were tested at their kennels (pre-trans) and ~48 h after arriving at a distributor (post-trans). At each location, puppies underwent an isolation test, a stranger-approach test, and a physical health assessment. Behavioral responses to testing were scored from videos. Fecal glucocorticoid metabolites (FGM), fecal secretory immunoglobulin A (sIgA), and presence of intestinal parasites were also analyzed. Linear mixed-effects models identified decreased exploration (p < 0.001), and increased locomotion (p < 0.001) and escape attempts (p = 0.001) during the post-trans isolation test. Increased affiliative behavior (p < 0.001), FGM (p < 0.001) and sIgA (p = 0.014) were also observed post-trans. Findings support good physical health both pre- and post-trans, while behavioral and physiological changes suggest increased puppy distress post-trans. Higher post-transport affiliative behavior may indicate that puppies sought social support as a coping strategy after experiencing transport-related distress. Future studies should explore the efficacy of transportation-related interventions to mitigate puppy distress.The Endocrine Technologies Core (ETSC) at the Oregon National Primate Research Center (ONPRC) is supported by NIH grant P51 OD011092 awarded to ONPRC
Public perceptions and attitudes toward urban wildlife encounters – A decade of change
Get PDFPublication history: Accepted - 26 April 2022; Published online - 4 May 2022.Europe is currently undergoing dynamic land use changes causing the expansion of urban habitat, which is driving
wildlife species to colonise conurbations, resulting in an increased likelihood of human-wildlife conflict (HWC). Understanding
people's attitudes toward wildlife is essential to manage these conflicts. This study assessed people's attitudes
toward urban wildlife, the types of conflicts that existed, preferences for managing conflict situations, and
determined any changes in perceptions of urban wildlife over a decade. A questionnaire survey of residents of Krakow,
the second-largest city in Poland, was conducted in 2010 (n = 721) and repeated in 2020 (n =887). We found that
encounters with certain urban wildlife such as wild boars, red squirrels, roe deer, brown hares, and red foxes had increased
significantly in 2020 compared to 2010. Respondents reported that wild boar and beavers did not show fear
when encountering humans. Stone martens were considered the most nuisance wildlife species in 2010, while in
2020 wild boar were the most conflictual wildlife species. There were additional reports of conflicts with roe deer
and red foxes. The most frequent HWC responses were personal anxiety, intrusion into property and destruction of
crops, which increased significantly over the decade, independent of respondents' gender. Respondents preferred nonlethal
methods to mitigate conflicts. The study provides valuable information and knowledge on changes in people's attitudes toward urban wildlife that can help with wildlife management in urban areas. Incorporating perception and
attitude data fromthe public, along with a multi-stakeholder approach that includes wildlife professionals, in the planning
and design of future urban environments is critical to minimise HWC.The paper was supported by the project ATUT PhD Programme in
Biology. The project is co-financed by the European Union under the
European Social Fund – _Operational Programme Knowledge Education
Development Axis III Higher Education for Economy and Development,
Action 3.2 PhD Programme.
The open-access publication of this article was funded
by the programme “Excellence Initiative – Research University” at the
Faculty of Biology of the Jagiellonian University in Kraków, Poland
Performance and milk quality parameters of Jersey crossbreds in low-input dairy systems
Get PDFPublication history: Accepted - 6 April 2022; Published online - 9 May 2022Previous work has demonstrated some benefit from alternative breeds in low-input dairying, although there has been no systematic analysis of the simultaneous effect of Jersey crossbreeding on productivity, health, fertility parameters or milk nutritional quality. This work aimed to understand the effects of, and interactions/interrelations between, dairy cow genotypes (Holstein-Friesian (HF), Holstein-Friesian × Jersey crossbreds (HF × J)) and season (spring, summer, autumn) on milk yield; basic composition; feed efficiency, health, and fertility parameters; and milk fatty acid (FA) profiles. Milk samples (n = 219) and breed/diet data were collected from 74 cows in four UK low-input dairy farms between March and October 2012. HF × J cows produced milk with more fat (+ 3.2 g/kg milk), protein (+ 2.9 g/kg milk) and casein (+ 2.7 g/kg milk); and showed higher feed, fat, and protein efficiency (expressed as milk, fat and protein outputs per kg DMI) than HF cows. Milk from HF × J cows contained more C4:0 (+ 2.6 g/kg FA), C6:0 (+ 1.9 g/kg FA), C8:0 (+ 1.3 g/kg FA), C10:0 (+ 3.0 g/kg FA), C12:0 (+ 3.7 g/kg FA), C14:0 (+ 4.6 g/kg FA) and saturated FA (SFA; + 27.3 g/kg milk) and less monounsaturated FA (MUFA; -23.7 g/kg milk) and polyunsaturated FA (− 22.3 g/kg milk). There was no significant difference for most health and fertility parameters, but HF × J cows had shorter calving interval (by 39 days). The superior feed, fat and protein efficiency of HF × J cows, as well as shorter calving interval can be considered beneficial for the financial sustainability of low-input dairy farms; and using such alternative breeds in crossbreeding schemes may be recommended. Although statistically significant, it is difficult to determine if differences observed between HF and HF × J cows in fat composition are likely to impact human health, considering average population dairy fat intakes and the relatively small difference. Thus, the HF × J cow could be used in low-input dairying to improve efficiency and productivity without impacting milk nutritional properties.Tis work was supported by (i) the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities as part of LowInputBreeds (http://www.lowinputbreeds.org/
home.html; grant no: 222623), and (ii) the Biotechnology and Biological Sciences Research Council (BBSRC) [grant
number BB/T008776/1] as part of the Doctoral Training Partnership FoodBioSystems: biological processes across the
Agri-Food system from pre-farm to post-fork. Te APC was funded by the University of Reading
A new direction for tackling phosphorus inefficiency in the UK food system
Get PDFPublication history: Accepted - 3 April 2022; Published online - 25 April 2022The UK food system is reliant on imported phosphorus (P) to meet food production demand, though inefficient use and poor stewardship means P is currently accumulating in agricultural soils, wasted or lost with detrimental impacts on aquatic environments. This study presents the results of a detailed P Substance Flow Analysis for the UK food system in 2018, developed in collaboration with industry and government, with the key objective of highlighting priority areas for system interventions to improve the sustainability and resilience of P use in the UK food system. In 2018 the UK food system imported 174.6 Gg P, producing food and exportable commodities containing 74.3 Gg P, a P efficiency of only 43%. Three key system hotspots for P inefficiency were identified: Agricultural soil surplus and accumulation (89.2 Gg P), loss to aquatic environments (26.2 Gg P), and waste disposal to landfill and construction (21.8 Gg P). Greatest soil P accumulation occurred in grassland agriculture (85% of total accumulation), driven by loadings of livestock manures. Waste water treatment (12.5 Gg P) and agriculture (8.38 Gg P) account for most P lost to water, and incineration ashes from food system waste (20.3 Gg P) accounted for nearly all P lost to landfill and construction. New strategies and policy to improve the handling and recovery of P from manures, biosolids and food system waste are therefore necessary to improve system P efficiency and reduce P accumulation and losses, though critically, only if they effectively replace imported mineral P fertilisers.This paper was produced as part of the RePhoKUs project (The role of phosphorus in the sustainability and resilience of the UK food system) funded by BBSRC, ESRC, NERC, and the Scottish Government under the UK Global Food Security research programme (Grant No. BB/R005842/1)
Farm fatalities in Northern Ireland agriculture: What fifty years of data tell us
Get PDFPublication history: Accepted - 8 March 2022; Published online - 10 March 2022.Agriculture is one of the most hazardous sectors in terms of fatal and non-fatal accidents. This paper utilises an
administrative dataset that recorded farm fatalities in Northern Ireland over a 50 year timeframe (1968–2017) to
undertake an age-period analysis of accident related mortality rates by sex, cause of death, season, and day of the
week. Public policies aimed to improve farm safety should consider that fatalities due to animals have increased
while the incidence of deaths due to vehicles and equipment has substantially decreased over the years although
it is still the primary cause of death. With respect to age, elderly still actively involved in farming and children in
the spring and at week-ends are most exposed to the risk of a fatal accident. Overall, men die on farms five times
more than women.This research was supported by the Department of Agriculture,
Environment, and Rural Affairs of Northern Ireland, grant number E-I
18-01-19