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Using Coupled Hydrodynamic Biogeochemical Models to Predict the Effects of Tidal Turbine Arrays on Phytoplankton Dynamics
Get PDF17 May Publication history: Accepted - 17 May 2018; Published online - 22 May 2018The effects of large scale tidal energy device (TED) arrays on phytoplankton processes owing to the changes in hydrodynamic flows are unknown. Coupled two-dimensional biogeochemical and hydrodynamic models offer the opportunity to predict potential effects of large scale TED arrays on the local and regional phytoplankton dynamics in coastal and inshore environments. Using MIKE 21 Software by DHI (https://www.dhigroup.com), coupled two-dimensional biogeochemical and hydrodynamic models were developed with simulations including no turbines or an array of 55 turbines with four solar radiation scenarios to assess the temporal and spatial changes of phytoplankton dynamics in an idealised domain. Results suggest that the effect of TEDs on phytoplankton dynamics accounted for up to 25% of the variability in phytoplankton concentrations, most likely associated with an increased residence time in an inshore basin. However, natural variation, such as the intensity of photosynthetically active radiation, had a larger effect on phytoplankton dynamics than an array of TEDsThe research was financially supported by the EPSRC research grant EP/J010065/
The underlying microbial mechanism of epizootic rabbit enteropathy triggered by a low fiber diet
Get PDFPublication history: Accepted - 24 July 2018; Published online - 21 August 2018.Epizootic rabbit enteropathy (ERE) is reproduced successfully in the present study by feeding rabbits a
low-fibre diet, and high-throughput sequencing and quantitative real-time PCR (qPCR) analysis were
applied to examine the microbial variations in the stomach, small intestine and caecum. The evenness
was disturbed and the richness was decreased in the ERE groups. When the rabbits were suffering from
ERE, the abundance of the Firmicutes was decreased in three parts of the digestive tract, whereas the
Proteobacteria was increased in the stomach and caecum, the Bacteroidetes and Verrucomicrobia were
increased in the small intestine. Correlation analysis showed that the reduced concentrations of TVFA
and butyrate in the caeca of the ERE group were attributed to the decreased abundances of genera
such as Lactobacillus, Alistipes and other fibrolytic bacteria and butyrate- producing bacteria such as
Eubacterium and Faecalibacterium. It is concluded that, in terms of microorganisms, the overgrowth
of Bacteroides fragilis, Clostridium perfringen, Enterobacter sakazakii and Akkermansia muciniphila
and inhibition of Bifidobacterium spp. and Butyrivibrio fibrisolvens in the stomach, small intestine and
caecum resulted in a decrease in butyrate yield, leading to the incidence of ERE, and the probability of
developing ERE could be manipulated by adjusting the dietary fibre level.The financial support was provided by the International Cooperation Project of Ministry of Science and
Technology of China (2014DFA32860)
Ocean current connectivity propelling the secondary spread of a marine invasive comb jelly across western Eurasia
Get PDFPublication history: Accepted - 15 February 2018; Published - 16 May 2018.Aim: Invasive species are of increasing global concern. Nevertheless, the mechanisms driving further
distribution after the initial establishment of non-native species remain largely unresolved, especially
in marine systems. Ocean currents can be a major driver governing range occupancy, but this has
not been accounted for in most invasion ecology studies so far. We investigate how well initial
establishment areas are interconnected to later occupancy regions to test for the potential role of
ocean currents driving secondary spread dynamics in order to infer invasion corridors and the
source–sink dynamics of a non-native holoplanktonic biological probe species on a continental scale.
Location: Western Eurasia.
Time period: 1980s–2016.
Major taxa studied: ‘Comb jelly’ Mnemiopsis leidyi.
Methods: Based on 12,400 geo-referenced occurrence data, we reconstruct the invasion history
of M. leidyi in western Eurasia. We model ocean currents and calculate their stability to match the
temporal and spatial spread dynamics with large-scale connectivity patterns via ocean currents.
Additionally, genetic markers are used to test the predicted connectivity between subpopulations.
Results: Ocean currents can explain secondary spread dynamics, matching observed range expansions
and the timing of first occurrence of our holoplanktonic non-native biological probe species,
leading to invasion corridors in western Eurasia. In northern Europe, regional extinctions after cold winters were followed by rapid recolonizations at a speed of up to 2,000 km per season. Source areas hosting year-round populations in highly interconnected regions can re-seed genotypes over
large distances after local extinctions.
Main conclusions: Although the release of ballast water from container ships may contribute to
the dispersal of non-native species, our results highlight the importance of ocean currents driving
secondary spread dynamics. Highly interconnected areas hosting invasive species are crucial for
secondary spread dynamics on a continental scale. Invasion risk assessments should consider
large-scale connectivity patterns and the potential source regions of non-native marine species.Danish Council for Independent Research;
Grant/Award Number: DFF-1325-00102B;
FP7 People: Marie-Curie Actions,
Grant/Award Number: MOBILEX, DFF -
1325-00025; EU, BONUS, BMBF, Grant/
Award Number: 03F0682; Excellence
Cluster “Future Ocean”, Grant/Award
Number: CP153
An analysis of effects of heterozygosity in dairy cattle for bovine tuberculosis resistance
Get PDFPublication history: Accepted - 23 November 2017; Published online - 24 January 2018Genetic selection of cattle more resistant to bovine tuberculosis (bTB) may offer a complementary control strategy. Hypothesising underlying non-additive genetic variation, we present an approach using genome-wide high density markers to identify genomic loci with dominance effects on bTB resistance and to test previously published regions with heterozygote advantage in bTB. Our data comprised 1151 Holstein–Friesian cows from Northern Ireland, confirmed bTB cases and controls, genotyped with the 700K Illumina BeadChip. Genome-wide markers were tested for associations between heterozygosity and bTB status using marker-based relationships. Results were tested for robustness against genetic structure, and the genotypic frequencies of a significant locus were tested for departures from Hardy-Weinberg equilibrium. Genomic regions identified in our study and in previous publications were tested for dominance effects. Genotypic effects were estimated through ASReml mixed models. A SNP (rs43032684) on chromosome 6 was significant at the chromosome-wide level, explaining 1.7% of the phenotypic variance. In the controls, there were fewer heterozygotes for rs43032684 (P < 0.01) with the genotypic values suggesting that heterozygosity confers a heterozygote disadvantage. The region surrounding rs43032684 had a significant dominance effect (P < 0.01). SNP rs43032684 resides within a pseudogene with a parental gene involved in macrophage response to infection and within a copy-number-variation region previously associated with nematode resistance. No dominance effect was found for the region on chromosome 11, as indicated by a previous candidate region bTB study. These findings require further validation with large-scale data.We are grateful for the financial support from the University of Edinburgh and the Roslin Institute, through the Principal's Career Development Scholarship (ST), and the Biotechnology and Biological Sciences Research Council institute strategic project ISP3: BB/P013759/1 (JAW). We would also like to thank BBSRC for their support through CEDFAS initiative grants BB/E018386/1 (RS); EJG; SCB; JAW also received support through CEDFAS grants: BB/E018335/1 and 2; Animal Health Research Club grant BB/L004054/1; Institute Strategic Programme Grants (ISP3 Innate Immunity & Endemic Disease, BB/J004227/1; ISP1 Analysis and Prediction in Complex Animal Systems, BB/J004235/1; and ISP2 Control of Infectious Diseases, BB/P013740/1)
Can We Breed Cattle for Lower Bovine TB Infectivity?
Get PDFPublication history: Accepted - 22 November 2018; Published - 7 December 2018.Host resistance and infectivity are genetic traits affecting infectious disease transmission.
This Perspective discusses the potential exploitation of genetic variation in cattle
infectivity, in addition to resistance, to reduce the risk, and prevalence of bovine
tuberculosis (bTB). In bTB, variability in M. bovis shedding has been previously reported
in cattle and wildlife hosts (badgers and wild boars), but the observed differences
were attributed to dose and route of infection, rather than host genetics. This article
addresses the extent to which cattle infectivity may play a role in bTB transmission,
and discusses the feasibility, and potential benefits from incorporating infectivity into
breeding programmes. The underlying hypothesis is that bTB infectivity, like resistance,
is partly controlled by genetics. Identifying and reducing the number of cattle with
high genetic infectivity, could reduce further a major risk factor for herds exposed to
bTB. We outline evidence in support of this hypothesis and describe methodologies for
detecting and estimating genetic parameters for infectivity. Using genetic-epidemiological
predictionmodels we discuss the potential benefits of selection for reduced infectivity and
increased resistance in terms of practical field measures of epidemic risk and severity.
Simulations predict that adding infectivity to the breeding programme could enhance and
accelerate the reduction in breakdown risk compared to selection on resistance alone.
Therefore, given the recent launch of genetic evaluations for bTB resistance and the UK
government’s goal to eradicate bTB, it is timely to consider the potential of integrating
infectivity into breeding schemes.This work was carried out with funding from the Biotechnology
and Biological Sciences Research Council Institute Strategic
Programme grants BB/J004235/1 (ISP1) and BB/P013740/1
(ISP2) (OA, AD-W, GB and JW), and the European Union
FP7 project FISHBOOST (KBBE - 7-613611) (ST). GB was also
supported by the Rural and Environment Science and Analytical
Services Division of the Scottish Government
The contribution of cattle urine and dung to nitrous oxide emissions: Quantification of country specific emission factors and implications for national inventories
Get PDFPublication history: Accepted - 10 April 2018; Published online - 24 April 2018.Urine patches and dung pats from grazing livestock create hotspots for production and emission of the greenhouse
gas, nitrous oxide (N2O), and represent a large proportion of total N2O emissions in many national agricultural
greenhouse gas inventories. As such, there is much interest in developing country specific N2O emission
factors (EFs) for excretal nitrogen (EF3, pasture, range and paddock) deposited during gazing. The aims of this
study were to generate separate N2O emissions data for cattle derived urine and dung, to provide an evidence
base for the generation of a country specific EF for the UK from this nitrogen source. The experiments were
also designed to determine the effects of site and timing of application on emissions, and the efficacy of the nitrification
inhibitor, dicyandiamide (DCD) on N2O losses. This co-ordinated set of 15 plot-scale, year-long field experiments
using static chambers was conducted at five grassland sites, typical of the soil and climatic zones of
grazed grassland in the UK. We show that the average urine and dung N2O EFs were 0.69% and 0.19%, respectively,
resulting in a combined excretal N2O EF (EF3), of 0.49%, which is b25% of the IPCC default EF3 for excretal
returns from grazing cattle. Regression analysis suggests that urineN2O EFs were controlledmore by composition
than was the case for dung, whilst dung N2O EFs were more related to soil and environmental factors. The urine
N2O EF was significantly greater from the site in SW England, and significantly greater from the early grazing season urine application than later applications. Dycandiamide reduced the N2O EF fromurine patches by an average
of 46%. The significantly lower excretal EF3 than the IPCC default has implications for the UK's national inventory
and for subsequent carbon footprinting of UK ruminant livestock productsThe authors are grateful to the UK Department for Environment,
Food and Rural Affairs (Defra), the Department of Agriculture and Rural
Development (now the Department of Agriculture, Environment and
Rural Affairs) in Northern Ireland, and the Scottish Government and
the Welsh Government for financial support via the InveN2Ory project
(AC0116). The work by Rothamsted Research was additionally supported
by the Biotechnology and Biological Sciences Research Council
(BBS/E/C/000I0320). We would also like to thank Jon Moorby (IBERS,
Wales, UK), Reading University, SRUC (Scotland, UK) and Conrad Ferris
(AFBI, Northern Ireland, UK), for provision of cattle urine and dung
The population and landscape genetics of the European badger (Meles meles) in Ireland
Get PDFPublication history: Accepted - 27 July 2018; Published - 12 September 2018.The population genetic structure of free-ranging
species is expected to reflect
landscape-level
effects. Quantifying the role of these factors and their relative contribution
often has important implications for wildlife management. The population
genetics of the European badger (Meles meles) have received considerable attention,
not least because the species acts as a potential wildlife reservoir for bovine tuberculosis
(bTB) in Britain and Ireland. Herein, we detail the most comprehensive population
and landscape genetic study of the badger in Ireland to date—comprised of 454
Irish badger samples, genotyped at 14 microsatellite loci. Bayesian and multivariate
clustering methods demonstrated continuous clinal variation across the island, with
potentially distinct differentiation observed in Northern Ireland. Landscape genetic
analyses identified geographic distance and elevation as the primary drivers of genetic
differentiation, in keeping with badgers exhibiting high levels of philopatry.
Other factors hypothesized to affect gene flow, including earth worm habitat suitability,
land cover type, and the River Shannon, had little to no detectable effect. By
providing a more accurate picture of badger population structure and the factors
effecting it, these data can guide current efforts to manage the species in Ireland and
to better understand its role in bTB.DAFM - Department of Food Agriculture
and the Marine, Republic of Ireland;
Department of Agriculture Environment
and Rural Affairs for Northern Ireland
(DAERA-NI
Effect of passive transfer status on response to a glycoprotein E (gE)-negative bovine herpesvirus type 1 (BoHV-1) and bovine respiratory syncytial virus (BRSV) vaccine and weaning stress in pre-weaned dairy calves
Get PDFPublication history: Accepted - 20 December 2017; Published online - 9 January 2018The study objectives were to: 1) examine how calves of divergent immune status respond to BRSV vaccination at 3 weeks of age; 2) trace glycoprotein E negative BoHV-1 antibodies from vaccinated dams to calf sera and to investigate how passive transfer affects response to live BoHV-1 vaccine at 6 weeks of age; 3) explore the impact of passive transfer status on blood metabolites around weaning. Thirty seven Holstein cows and their calves were included in the study. All cows were immunised with a commercial marker vaccine against BoHV-1(gE-) administered intra-muscularly at 4 month prior to the start of calving. Calves were assigned to 1 of 2 colostrum treatment groups: 1) 5% of BW in colostrum fed at birth, or 2) 10% of BW in colostrum fed at birth. Calves were also immunised at 3 weeks of age with a respiratory commercial vaccine, and a booster administered 4 weeks later. Calves were also immunised against BoHV-1 at 6 weeks of age, using one dose of a live commercial vaccine. The results demonstrated that level of passive immunity had no effect on immune response to vaccination and the importance of feeding colostrum from vaccinated BoHV-1 gE- dams to provide calves with passive protection against IBRV.This work was supported by Department of Agriculture, Food and the Marine; Department of Agriculture and Rural Development in Northern Ireland; AgriSearch (farmer levy)
Bayesian latent class estimation of sensitivity and specificity parameters of diagnostic tests for bovine tuberculosis in chronically infected herds in Northern Ireland
Get PDFPublication history: Accepted - 26 April 2018; Published online - 1 May 2018.In the European Union, the recommended ante-mortem diagnostic methods for bovine tuberculosis (bTB)
include the single intradermal cervical comparative tuberculin (SICCT) test and the interferon-gamma (IFN-
g) test as an ancillary test. The SICCT test has a moderate sensitivity (Se) and high specificity (Sp), while the
IFN-g test has good Se, but a lower Sp than the SICCT test. A retrospective Bayesian latent class analysis was
conducted on 71,185 cattle from 806 herds chronically infected with bTB distributed across Northern Ireland
(NI) to estimate the Se and Sp of the common ante-mortem tests and meat inspection. Analyses were also
performed on data stratified by farming type and herd location to explore possible differences in test
performance given the heterogeneity in the population. The mean estimates in chronically infected herds
were: (1) ‘standard’ SICCT: Se 40.5–57.7%, Sp 96.3–99.7%; (2) ‘severe’ SICCT: Se 49.0%–60.6%, Sp 94.4–99.4%;
(3) IFN-g(bovine–avian) using a NI optical density (OD) cut-off difference of 0.05: IFN-g(B–A)NI: Se 85.8–
93.0%, Sp 75.6–96.2%; (4) IFN-g(bovine–avian) using a standard ‘commercial’ OD cut-off difference of 0.1:
IFN-g(B–A)0.1: Se 83.1–92.1%, Sp 83.1–97.3%; and (5) meat inspection: Se 49.0–57.1% Se, Sp 99.1–100%. Se
estimates were lower in cattle from dairy farms than from beef farms. There were no notable differences in
estimates by location of herds. Certain population characteristics, such as production type, might influence
the ability of bTB tests to disclose truly infected cases.This study is part of a larger project on the evaluation of the
performance characteristics of the test in chronic bTB herds in NI
from 2004 to 2010. It was
financed by DAERA (E&I grant code 11/
03/10)
Effect of substituting fresh-cut perennial ryegrass with fresh-cut white clover on bovine milk fatty acid profile
Get PDFPublication history: Accepted - 6 March 2018; Published online - 15 April 2018BACKGROUND
Including forage legumes in dairy systems can help address increasing environmental/economic concerns about perennial ryegrass monoculture pastures. This work investigated the effect of substituting fresh-cut grass with increasing quantities of fresh-cut white clover (WC) on milk fatty acid (FA) profile and transfer efficiency of dietary linoleic (LA) and α-linolenic (ALNA) acids to milk fat. Three groups of three crossbred dairy cows were used in a 3 × 3 crossover design. Dietary treatments were 0 g kg−1 WC + 600 g kg−1 grass, 200 g kg−1 WC + 400 g kg−1 grass, and 400 g kg−1 WC + 200 g kg−1 grass. All treatments were supplemented with 400 g kg−1 concentrates on a dry matter basis. Cows had a 19-day adaptation period to the experimental diet before a 6-day measurement period in individual tie stalls.
RESULTS
Increasing dietary WC did not affect dry matter intake, milk yield or milk concentrations of fat, protein or lactose. Milk polyunsaturated FA concentrations (total n-3, total n-6, LA and ALNA) and transfer efficiency of LA and ALNA were increased with increasing dietary WC supply.
CONCLUSION
Inclusion of WC in pastures may increase concentrations of nutritionally beneficial FA, without influencing milk yield and basic composition, but any implications on human health cannot be drawn.We gratefully acknowledge financial support from the Department of Agriculture, Food and the Marine of Republic of Ireland as part of a Stimulus-funded project (11-S-105)