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Search Results: 1 - 10 of 230474 matches for " Stephen C Bishop "
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On the Genetic Interpretation of Disease Data
Stephen C. Bishop,John A. Woolliams
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0008940
Abstract: The understanding of host genetic variation in disease resistance increasingly requires the use of field data to obtain sufficient numbers of phenotypes. We introduce concepts necessary for a genetic interpretation of field disease data, for diseases caused by microparasites such as bacteria or viruses. Our focus is on variance component estimation and we introduce epidemiological concepts to quantitative genetics.
A genetic epidemiological model to describe resistance to an endemic bacterial disease in livestock: application to footrot in sheep
Gert Nieuwhof, Joanne Conington, Stephen C Bishop
Genetics Selection Evolution , 2009, DOI: 10.1186/1297-9686-41-19
Abstract: Preventive measures and lost production due to endemic disease form an important component of the costs of production in many livestock production systems [1], and they also affect animal welfare and marketability of breeding stock. It is well known that, for many diseases, resistance has a genetic component [2] and selection for disease resistance has long been considered a promising way to reduce disease prevalence e.g. [3].Selection for resistance to an infectious disease has the added benefit that it may reduce the pathogen burden, especially when the population under selection is the main reservoir of pathogens. This will lead to an additional reduction in prevalence, in addition to the direct genetic effect, as a result of reduced contamination from infectious animals, e.g. [4].The phenotype used in selection for disease resistance is often a score, which includes a class of healthy animals, and one or more classes of affected animals. In the case of endemic diseases the vast majority of animals at any one time may be classified as healthy, and this limits the opportunity for intense selection. In a threshold model, that is appropriate for this type of data, prevalences that are much lower than 50% also lead to low heritabilities on the observed scale. A successful selection programme can therefore be expected to decrease the subsequent response to selection through increased resistance and decreased pathogen burden.Anderson and May [5] describe the spread of a microparasitic (viral or bacterial) infection through a population of animals using a so-called SIR model, based on the rates at which susceptible (S) animals are infected (I) and then recover or are removed (R). A key parameter is R0, which is the number of secondary infections caused by the first infected animal. One or more of these rates can be under genetic control and hence affect R0. This model can be extended in various ways; for instance Bishop and MacKenzie [6] have described how a disease tha
Genetic management strategies for controlling infectious diseases in livestock populations
Bishop Stephen C,MacKenzie Katrin M
Genetics Selection Evolution , 2003, DOI: 10.1186/1297-9686-35-s1-s3
Abstract: This paper considers the use of disease resistance genes to control the transmission of infection through an animal population. Transmission is summarised by R0, the basic reproductive ratio of a pathogen. If R0 > 1.0 a major epidemic can occur, thus a disease control strategy should aim to reduce R0 below 1.0, e.g. by mixing resistant with susceptible wild-type animals. Suppose there is a resistance allele, such that transmission of infection through a population homozygous for this allele will be R02 < R01, where R01 describes transmission in the wildtype population. For an otherwise homogeneous population comprising animals of these two groups, R0 is the weighted average of the two sub-populations: R0 = R01ρ + R02 (1 - ρ), where ρ is the proportion of wildtype animals. If R01 > 1 and R02 < 1, the proportions of the two genotypes should be such that R0 ≤ 1, i.e. ρ ≤ (R0 - R02)/(R01 - R02). If R02 = 0, the proportion of resistant animals must be at least 1 - 1/R01. For an n genotype model the requirement is still to have R0 ≤ 1.0. Probabilities of epidemics in genetically mixed populations conditional upon the presence of a single infected animal were derived. The probability of no epidemic is always 1/(R0 + 1). When R0 ≤ 1 the probability of a minor epidemic, which dies out without intervention, is R0/(R0 + 1). When R0 > 1 the probability of a minor and major epidemics are 1/(R0 + 1) and (R0 - 1)/(R0 + 1). Wherever possible a combination of genotypes should be used to minimise the invasion possibilities of pathogens that have mutated to overcome the effects of specific resistance alleles.
Genetic parameters for somatic cell score according to udder infection status in Valle del Belice dairy sheep and impact of imperfect diagnosis of infection
Valentina Riggio, Baldassare Portolano, Henk Bovenhuis, Stephen C Bishop
Genetics Selection Evolution , 2010, DOI: 10.1186/1297-9686-42-30
Abstract: Data on SCS and udder infection status for 1,120 ewes were collected from four Valle del Belice flocks. The pedigree file included 1,603 animals. The SCS dataset was split according to whether animals were infected or not at the time of sampling. A repeatability test-day animal model was used to estimate genetic parameters for SCS traits and the heritability of infection status. The genetic correlation between bacteria negative SCS and infection status was estimated using an MCMC threshold model, implemented by Gibbs Sampling.The heritability was 0.10 for bacteria negative SCS, 0.03 for bacteria positive SCS, and 0.09 for infection status, on the liability scale. The genetic correlation between bacteria negative and bacteria positive SCS was 0.62, suggesting that they may be genetically different traits. The genetic correlation between bacteria negative SCS and infection status was 0.51. We demonstrate that imperfect diagnosis of infection leads to underestimation of differences between bacteria negative and bacteria positive SCS, and we derive formulae to predict impacts on estimated genetic parameters.The results suggest that bacteria negative and bacteria positive SCS are genetically different traits. A positive genetic correlation between bacteria negative SCS and liability to infection was found, suggesting that the approach of selecting animals for decreased SCS should help to reduce mastitis prevalence. However, the results show that imperfect diagnosis of infection has an impact on estimated genetic parameters, which may reduce the efficiency of selection strategies aiming at distinguishing between bacteria negative and bacteria positive SCS.Somatic cell count (SCC), and therefore somatic cell score (SCS) have been widely promoted as an indirect method of predicting mammary infections [1] and as a selection criterion to improve mastitis resistance [2]. It has been demonstrated that mastitis is associated with an increase in SCC in small ruminants [3,4] and c
Uses and Implications of Field Disease Data for Livestock Genomic and Genetics Studies
Stephen C. Bishop,Andrea B. Doeschl-Wilson
Frontiers in Genetics , 2012, DOI: 10.3389/fgene.2012.00114
Abstract: This paper identifies issues associated with field disease data and their implications on the interpretation of estimated genetic parameters and experimental designs. The main focus is on concepts relating to the impacts of diagnostic test properties and exposure to infection, and how exposure to infection is intricately related to within-herd epidemic dynamics. The following are raised challenges: (i) to more fully understand and describe the dynamic impacts of disease epidemics on genetic interpretations; (ii) to develop statistical methods to jointly estimate epidemiological and genetic parameters from complex epidemiological data; (iii) to develop and explore optimal experimental designs for case-control studies, exploiting field disease data. Solving these problems would add insight to both disease genetic and epidemiological studies, as well as enabling us to better select animals for increased disease resistance.
Association of selected SNP with carcass and taste panel assessed meat quality traits in a commercial population of Aberdeen Angus-sired beef cattle
Jennifer L Gill, Stephen C Bishop, Caroline McCorquodale, John L Williams, Pamela Wiener
Genetics Selection Evolution , 2009, DOI: 10.1186/1297-9686-41-36
Abstract: A total of 27 traits were examined, 19 relating to carcass quality, such as carcass weight and fatness, one mechanical measure of tenderness, and the remaining seven were sensory traits, such as flavour and tenderness, assessed by a taste panel.An SNP in the CAPN1 gene, CAPN316, was significantly associated with tenderness measured by both the tenderometer and the taste panel as well as the weight of the hindquarter, where animals inheriting the CC genotype had more tender meat and heavier hindquarters. An SNP in the leptin gene, UASMS2, significantly affected overall liking, where animals with the TT genotype were assigned higher scores by the panellists. The SNP in the GHR gene was significantly associated with odour, where animals inheriting the AA genotype produced steaks with an intense odour when compared with the other genotypes. Finally, the SNP in the DGAT1 gene was associated with sirloin weight after maturation and fat depth surrounding the sirloin, with animals inheriting the AA genotype having heavier sirloins and more fat.The results of this study confirm some previously documented associations. Furthermore, novel associations have been identified which, following validation in other populations, could be incorporated into breeding programmes to improve meat quality.Meat quality is of great importance to the beef industry where the consumer is willing to pay more for superior products [1]. Traditional trait improvement has centred on quantitative genetics, using statistical analysis of phenotypic data to determine animals with the highest genetic merit [2]. This selection approach is most effectively implemented for highly heritable traits that are easily recorded before reproductive age. However, meat quality traits can usually only be measured post-slaughter and often have low heritabilities [3], therefore making progress using direct measurement is difficult for these traits. Marker-assisted selection has the potential to significantly increase the
Sequencing and Characterisation of an Extensive Atlantic Salmon (Salmo salar L.) MicroRNA Repertoire
Micha?l Bekaert, Natalie R. Lowe, Stephen C. Bishop, James E. Bron, John B. Taggart, Ross D. Houston
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0070136
Abstract: Atlantic salmon (Salmo salar L.), a member of the family Salmonidae, is a totemic species of ecological and cultural significance that is also economically important in terms of both sports fisheries and aquaculture. These factors have promoted the continuous development of genomic resources for this species, furthering both fundamental and applied research. MicroRNAs (miRNA) are small endogenous non-coding RNA molecules that control spatial and temporal expression of targeted genes through post-transcriptional regulation. While miRNA have been characterised in detail for many other species, this is not yet the case for Atlantic salmon. To identify miRNAs from Atlantic salmon, we constructed whole fish miRNA libraries for 18 individual juveniles (fry, four months post hatch) and characterised them by Illumina high-throughput sequencing (total of 354,505,167 paired-ended reads). We report an extensive and partly novel repertoire of miRNA sequences, comprising 888 miRNA genes (547 unique mature miRNA sequences), quantify their expression levels in basal conditions, examine their homology to miRNAs from other species and identify their predicted target genes. We also identify the location and putative copy number of the miRNA genes in the draft Atlantic salmon reference genome sequence. The Atlantic salmon miRNAs experimentally identified in this study provide a robust large-scale resource for functional genome research in salmonids. There is an opportunity to explore the evolution of salmonid miRNAs following the relatively recent whole genome duplication event in salmonid species and to investigate the role of miRNAs in the regulation of gene expression in particular their contribution to variation in economically and ecologically important traits.
Traits associated with innate and adaptive immunity in pigs: heritability and associations with performance under different health status conditions
Mary Clapperton, Abigail B Diack, Oswald Matika, Elizabeth J Glass, Christy D Gladney, Martha A Mellencamp, Annabelle Hoste, Stephen C Bishop
Genetics Selection Evolution , 2009, DOI: 10.1186/1297-9686-41-54
Abstract: The control of infection represents a major challenge to the pig industry. Over the last decade, this challenge has become greater due to the spread of viral infections such as PMWS (post-weaning multi-systemic wasting syndrome), PRRS (porcine reproductive and respiratory syndrome) and enzootic pneumonia. In addition to the impact of these infections or diseases upon pig morbidity and mortality, they can also affect pig health by increasing susceptibility to secondary bacterial infections [1-3].Since antibiotics and bio-security control measures can only partially control infection, and effective vaccines are not always available, it would be advantageous to find a method of selecting pigs with increased resistance to a wide range of infectious diseases or an increased ability to maintain high performance levels in the face of disease pressure. In pig breeding companies, pigs are generally selected for improved performance within the high health status environment of a nucleus farm, but often their progeny are reared within a lower health status environment and, as a result, their performance may be compromised. Hence there is a need to find a way of selecting boars that can produce progeny with an increased resistance to a wide range of infectious diseases so that they are able to perform well under a range of health conditions.In pig production systems it is difficult to select animals directly for disease resistance since the major challenges often differ in different environments and most husbandry practices attempt to minimise exposure to infection. Therefore, an alternative approach is needed. One such approach would be to use measures of innate and adaptive immunity which are heritable and associated with parameters related to health and/or performance. In order to predict progeny that will perform equally well in a range of environments, these immune markers would have to be heritable regardless of health status.Previously, we have shown peripheral blood mon
Associations between lamb survival and prion protein genotype: analysis of data for ten sheep breeds in Great Britain
Simon Gubbins, Charlotte J Cook, Kieran Hyder, Kay Boulton, Carol Davis, Eurion Thomas, Will Haresign, Stephen C Bishop, Beatriz Villanueva, Rachel D Eglin
BMC Veterinary Research , 2009, DOI: 10.1186/1746-6148-5-3
Abstract: Survival times from birth to weaning were analysed for over 38000 lambs (2427 dead and 36096 live lambs) from 128 flocks using Cox proportional hazard models for each breed, including additive animal genetic effects. No significant associations between PrP genotype and lamb survival were identified, except in the Charollais breed for which there was a higher risk of mortality in lambs of the ARR/VRQ genotype compared with those of the ARR/ARR genotype. Significant effects of birth weight, litter size, sex, age of dam and year of birth on survival were also identified. For all breeds the reasons for death changed significantly with age; however, no significant associations between reason for death and PrP genotype were found for any of the breeds.This study found no evidence to suggest that a selective breeding programme based on PrP genotype will have a detrimental effect on lamb survival. The only significant effect of PrP genotype identified was likely to be of little consequence because an increased risk of mortality was associated with a genotype that is selected against in current breeding strategies.Large-scale selective breeding programmes have been introduced throughout the European Union to reduce the risk of sheep transmissible spongiform encephalopathies (TSEs) and, in particular, the risk to human health posed by the possible presence of bovine spongiform encephalopathy (BSE) in sheep [1]. These programmes exploit a strong host genetic component at the ovine prion protein (PrP) gene, which influences both the risk of infection and the incubation period for scrapie [2-4]. They aim to decrease the frequency of high risk alleles (ARQ and VRQ) and increase the frequency of the major low risk allele (ARR).Concerns have been expressed, however, that such large-scale breeding programmes based on one specific factor (in this case, PrP genotype) could have detrimental side-effects on sheep performance. These concerns stem from farmers' assertions that sheep carry
MAVIDOS Maternal Vitamin D Osteoporosis Study: study protocol for a randomized controlled trial. The MAVIDOS Study Group
Nicholas C Harvey, Kassim Javaid, Nicholas Bishop, Stephen Kennedy, Aris T Papageorghiou, Robert Fraser, Saurabh V Gandhi, Inez Schoenmakers, Ann Prentice, Cyrus Cooper
Trials , 2012, DOI: 10.1186/1745-6215-13-13
Abstract: Osteoporosis is a major public health problem as a result of associated fragility fractures. Skeletal strength increases from birth to a peak in early adulthood. This peak predicts osteoporosis risk in later life. Vitamin D insufficiency in pregnancy is common (31% in a recent Southampton cohort) and predicts reduced bone mass in the offspring. In this study we aim to test whether offspring of mothers supplemented with vitamin D in pregnancy have higher bone mass at birth than those whose mothers were not supplemented.Women have their vitamin D status assessed after ultrasound scanning in the twelfth week of pregnancy at 3 trial centres (Southampton, Sheffield, Oxford). Women with circulating 25(OH)-vitamin D levels 25-100 nmol/l are randomised in a double-blind design to either oral vitamin D supplement (1000 IU cholecalciferol/day, n = 477) or placebo at 14 weeks (n = 477). Questionnaire data include parity, sunlight exposure, dietary information, and cigarette and alcohol consumption. At 19 and 34 weeks maternal anthropometry is assessed and blood samples taken to measure 25(OH)-vitamin D, PTH and biochemistry. At delivery venous umbilical cord blood is collected, together with umbilical cord and placental tissue. The babies undergo DXA assessment of bone mass within the first 14 days after birth, with the primary outcome being whole body bone mineral content adjusted for gestational age and age. Children are then followed up with yearly assessment of health, diet, physical activity and anthropometric measures, with repeat assessment of bone mass by DXA at age 4 years.As far as we are aware, this randomised trial is one of the first ever tests of the early life origins hypothesis in human participants and has the potential to inform public health policy regarding vitamin D supplementation in pregnancy. It will also provide a valuable resource in which to study the influence of maternal vitamin D status on other childhood outcomes such as glucose tolerance, blood
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