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Item Metadata only 100 top consultations in small animal general practice(Blackwell Publishers Inc, 2011) Hill, P.; Warman, S.; Shawcross, G.Focusing on 'day one competencies', this book offers essential guidance to the most common problems encountered in small animal general practice. Addressing 100 core scenarios, it is ideal for the undergraduate or newly qualified vet, and for those seeking an up-to-date refresher. Organized by presenting sign (diarrhoea, itching) or disease (diabetes mellitus, pancreatitis), and with colour illustration throughout, each chapter explains: how to make a diagnosis, which interventions are most appropriate in general practice, what the vet should say to the client before and after examination .The authors also offer invaluable advice on other key topics such as annual health checks, neutering and euthanasia, and they tackle the tough questions: What if it doesn't get better? What is the low cost option? When should I refer? Never before has so much practical information been brought together in a single volume. Like having an experienced or specialist clinician standing by your side in the consulting room, 100 Top Consultations will become a trusted companion for students and practitioners alike.Item Metadata only A comparative system-level analysis of the neurodegenerative diseases(Wiley, 2019) Godini, R.; Fallahi, H.; Ebrahimie, E.Neurodegenerative diseases are disorders in the central nervous system with consequent progressive neurological symptoms including behavioral and cognitive disabilities. Alzheimer’s disease, amyotrophic lateral sclerosis, Huntington’s disease, Parkinson’s disease, multiple sclerosis, and schizophrenia are the most important and abundant neurodegenerative diseases that affect different parts of the brain. Detailed studies unveiled the molecular mechanisms and pathways affected in each of these disorders. The role of many genes has been documented in the onset and progression of each disease. Although many system‐level approaches have been used to understand the exact cause of these diseases, there is no comparative analysis in this regard. Despite all differences in the molecular basis of these diseases, overlapping symptoms might indicate the involvement of the similar pathways and processes. Here, we have applied a system biology approach to uncover many aspects of main neurodegenerative diseases using microarray data obtained from 118 cases of postmortem brain samples. Our analysis has identified key genes that might contribute to the status of diseases. We have also compared the involved biological process and pathway between different disease to find possible similar mechanisms that exist in all of them. We also predicted potentially important transcription factors in each disease and predicted the core gene regulatory networks. We have provided a list of possible new key regulators that could be further explored and also discussed the role of these hub genes. The results of this study would be useful to develop new diagnostic strategies and also to find new drug targets.Item Metadata only A comparison of antiserum and protein A as secondary reagents to assess Toxoplasma gondii antibody titers in cats and spotted hyenas(American Society of Parasitologists, 2015) Wait, L.; Srour, A.; Smith, I.; Cassey, P.; Sims, S.; McAllister, M.Toxoplasma gondii is a protozoal parasite with worldwide distribution that is able to infect a wide variety of mammals and birds. Our main goal was to screen for T. gondii antibody titers in a previously untested species, the spotted hyena ( Crocuta crocuta); however, this goal first required us to investigate serological procedures that could be suitable for hyenas. Cats are the closest domestic relations of hyenas, so T. gondii antibody titers were first compared in 26 feral cats with specific or nonspecific fluorophore-labeled secondary reagents, i.e., anti-cat IgG or protein A. Substitution of anti-cat IgG with protein A caused a statistically significant drop in titer measurements in cats (P = 0.01) with a reduction of the geometric mean titer equivalent to 1 doubling-dilution. The same procedures were then applied to captive spotted hyenas. Titers measured in 9 of 10 hyenas were identical whether anti-cat IgG or protein A was used as the secondary reagent: 5 had titers <1:16, 2 had titers of 1:16, and 2 had titers of 1:32. One hyena had maximum titers of 1:64 or 1:32 when anti-cat IgG or protein A was used, respectively. The use of protein A as the secondary reagent in serologic assays can be applied to a range of mammalian species and seems unlikely to affect test specificity; however, the use of protein A may reduce test sensitivity, as suggested in the present study using cats. Despite a control program, some exposure to T. gondii had occurred in the Zoo's spotted hyenas.Item Metadata only A comparison of pharmacokinetic methods for in vivo studies of non-mediated glucose absorption(Oxford University Press (OUP), 2012) Napier, K.; Mcwhorter, T.; Del Rio, M.; Fleming, P.; Annual Meeting of the Society for Integrative and Comparative Biology (SICB) (3 Jan 2012 - 7 Jan 2012 : Charleston, SC)Item Metadata only A comparison of pharmacokinetic methods for in vivo studies of nonmediated glucose absorption(Univ Chicago Press, 2012) Napier, K.; McWhorter, T.; Fleming, P.Two pharmacokinetic methods are used primarily to assess systematic bioavailability of orally dosed water-soluble compounds in vivo, but there have been no direct comparisons of the estimates obtained. The “area under the curve” (AUC) method employs a single oral dose of probe compound(s) followed by multiple blood sampling to obtain plasma concentration time curves. Separate injection of probe(s) followed by multiple blood sampling is used to calculate fractional elimination rate (Kel) and distribution pool space (S). The “steady state feeding” method relies on ad lib. feeding of a marked diet, with a single blood sample taken to measure steady state feeding concentration of probe(s); Kel is estimated from the decline in probe concentration in excreta after injection, with a single blood sample taken to estimate S. We compared these methods directly in the Australian red wattlebird (Anthochaera carnunculata), measuring absorption of 3H-l-glucose. The Kel values estimated using the steady state feeding protocol were significantly higher, and estimates of S and bioavailability consequently lower, compared with the AUC protocol. The AUC method relies on fewer assumptions and allows simultaneous comparisons of absorption by mediated and nonmediated (i.e., paracellular) mechanisms but cannot be easily applied to freely feeding animals. The steady state feeding method allows work with smaller species and exploration of the effects of feeding on nutrient uptake but requires careful attention to the validity of assumptions that increase error in the calculations.Item Open Access A comprehensive mapping of the structure and gene organisation in the sheep MHC class I region(BioMed Central, 2015) Siva Subramaniam, N.; Morgan, E.; Wetherall, J.; Stear, M.; Groth, D.Background: The major histocompatibility complex (MHC) is a chromosomal region that regulates immune responsiveness in vertebrates. This region is one of the most important for disease resistance because it has been associated with resistance or susceptibility to a wide variety of diseases and because the MHC often accounts for more of the variance than other loci. Selective breeding for disease resistance is becoming increasingly common in livestock industries, and it is important to determine how this will influence MHC polymorphism and resistance to diseases that are not targeted for selection. However, in sheep the order and sequence of the protein coding genes is controversial. Yet this information is needed to determine precisely how the MHC influences resistance and susceptibility to disease. Methods: CHORI bacterial artificial chromosomes (BACs) known to contain sequences from the sheep MHC class I region were sub-cloned, and the clones partially sequenced. The resulting sequences were analysed and re-assembled to identify gene content and organisation within each BAC. The low resolution MHC class I physical map was then compared to the cattle reference genome, the Chinese Merino sheep MHC map published by Gao, et al. (2010) and the recently available sheep reference genome. Results: Immune related class I genes are clustered into 3 blocks; beta, kappa and a novel block not previously identified in other organisms. The revised map is more similar to Bovidae maps than the previous sheep maps and also includes several genes previously not annotated in the Chinese Merino BAC assembly and others not currently annotated in the sheep reference chromosome 20. In particular, the organisation of nonclassical MHC class I genes is similar to that present in the cattle MHC. Sequence analysis and prediction of amino acid sequences of MHC class I classical and nonclassical genes was performed and it was observed that the map contained one classical and eight nonclassical genes together with three possible pseudogenes. Conclusions: The comprehensive physical map of the sheep MHC class I region enhances our understanding of the genetic architecture of the class I MHC region in sheep and will facilitate future studies of MHC function.Item Metadata only A consideration of the role of biology and test design as confounding factors in judgement bias tests(Elsevier BV, 2020) Whittaker, A.; Barker, T.The assessment of positive emotional states in animals has been advanced considerably through the use of judgement bias testing. JBT methods have now been reported in a range of species. Generally, these tests show good validity as ascertained through use of corroborating methods of affective state determination. However, published reports of judgement bias task findings can be counter-intuitive and show high inter-individual variability. It is proposed that these outcomes may arise as a result of inherent inter- and intra-individual differences as a result of biology. This review discusses the potential impact of sex and reproductive cycles, social status, genetics, early life experience and personality on judgement bias test outcomes. We also discuss some aspects of test design that may interact with these factors to further confound test interpretation. There is some evidence that a range of biological factors affect judgement bias test outcomes, but in many cases this evidence is limited and needs further characterisation to reproduce the findings and confirm directions of effect. It is our proposition that researchers should consider dedicated study on these factors and their impact on judgement biasing. This is needed to confirm effect, and investigate mechanisms. Alternately, consideration and reporting of these factors in JBT studies through incorporation in statistical analyses will provide much needed additional data on their impact. These actions will enhance the validity and practical applicability of the JBT for welfare assessment.Item Metadata only A decade of discoveries in veterinary protozoology changes our concept of "subclinical" toxoplasmosis(Elsevier Science BV, 2005) McAllister, M.One of the most compelling topics to emerge from the last decade of veterinary protozoology is disease caused by a zoonotic pathogen, Toxoplasma gondii, in otherwise healthy people. These findings may catch the health professions by surprise, because veterinary and medical courses and textbooks typically emphasize that T. gondii infections are subclinical, unless acquired in utero or the patient has a serious immunosuppressive condition. Nevertheless, numerous reports in the last decade associate toxoplasmosis with lymphadenopathy, fever, weakness and debilitation, ophthalmitis, and severe multisystemic infections in people who do not have immunosuppressive conditions. Toxoplasmosis in rodents causes altered behavior, and similar mental aberrations are coming to light in humans; recent studies associate T. gondii infection with personality shifts and increased likelihood of reduced intelligence or schizophrenia. These conditions reduce the quality of life of individuals, and may exact a significant economic burden upon society. Of course, toxoplasmosis continues to cause serious conditions in AIDS patients and congenitally infected people, as well as abortions and encephalitis in domestic and wild animals. Environmental contamination is heavy enough to extend into marine wildlife. It is time for the health professions to amend teaching curricula regarding T. gondii. Veterinary parasitologists should lead the way in developing methods to reduce the prevalence of T. gondii in food animals. Public health policies should prohibit the practice of allowing pet cats to roam. Organizations and individuals that feed feral cats are unwittingly contributing to the dissemination of T. gondii, by sustaining artificially dense populations of a definitive host of this protozoal parasite.Item Metadata only A descriptive analysis of the antimicrobial susceptibility of mastitis-causing bacteria isolated from samples submitted to commercial diagnostic laboratories in New Zealand (2003-2006)(New Zealand Veterinary Assoc Inc, 2011) Petrovski, K.; Laven, R.; Lopez-Villalobos, N.AIM: To describe the antimicrobial susceptibility of mastitis-causing bacteria isolated from milk samples submitted to commercial laboratories over a period of 40 months. METHODS: The records of reported results of milk samples submitted by veterinary practitioners to five commercial veterinary laboratories in the North and South Islands of New Zealand, between August 2003 and December 2006 were reviewed. Logistic regression was used to analyse the effect of year, island, and the interaction of year and antimicrobial on the probability of antimicrobial susceptibility for each pathogen and antimicrobial combination, where the causative bacteria had >1,000 susceptibility tests in total and the antimicrobials was tested on >500 isolates. A total of 9,262 isolates were included in this study, with an average of nearly seven susceptibility tests per isolate, totalling 62,918 tests. RESULTS: Streptococcus uberis isolates demonstrated high overall susceptibility (>90.0%) to the majority of antimicrobial agents except ampicillin (81.7%), lincomycin (85.3%), trimethoprim/sulphonamide combination (88.6%), and, as expected, aminoglycosides (<4%). The susceptibility of Strep. dysgalactiae was similar to that of Strep. uberis, except for greater susceptibility to oxacillin (98.1%) and much lower susceptibility to tetracyclines (11.2%). The susceptibility of Staphylococcus aureus isolates was markedly different from that of Strep. uberis for the majority of antimicrobials tested. Susceptibility of Staph. aureus was lower than 90% to ampicillin (73.4%), erythromycin (74.7%), lincomycin (66.1%), penicillin (73.1%), and streptomycin (71.7%). No antimicrobial was effective against all Staph. aureus isolates. Minor changes were found in the overall susceptibility of the main mastitis-causing bacteria between 2003 and 2006. CONCLUSIONS: The antimicrobial agents intended for treatment of bovine mastitis currently available in New Zealand generally demonstrated good in-vitro efficacy against streptococci and staphylococci, with the exception of aminoglycosides. CLINICAL RELEVANCE: Analysis of the results of antimicrobial susceptibility of bacterial isolates from milk samples from dairy cows in New Zealand provides useful data for surveillance purposes, and a baseline for identifying changes in antimicrobial sensitivity in this population. However, the variation in antimicrobial susceptibility between individual isolates means that these data are of limited value when determining treatment of mastitis at the farm level.Item Metadata only A gene expression atlas of the domestic water buffalo (Bubalus bubalis)(Frontiers Media, 2019) Young, R.; Lefevre, L.; Bush, S.J.; Joshi, A.; Singh, S.H.; Jadhav, S.K.; Lisowski, Z.M.; Iamartino, D.; Summers, K.M.; Williams, J.L.; Archibald, A.L.; Gokhale, S.; Kumar, S.; Hume, D.A.The domestic water buffalo (Bubalus bubalis) makes a major contribution to the global agricultural economy in the form of milk, meat, hides, and draught power. The global water buffalo population is predominantly found in Asia, and per head of population more people depend upon the buffalo than on any other livestock species. Despite its agricultural importance, there are comparatively fewer genomic and transcriptomic resources available for buffalo than for other livestock species. We have generated a large-scale gene expression atlas covering multiple tissue and cell types from all major organ systems collected from three breeds of riverine water buffalo (Mediterranean, Pandharpuri and Bhadawari) and used the network analysis tool Graphia Professional to identify clusters of genes with similar expression profiles. Alongside similar data, we and others have generated for ruminants as part of the Functional Annotation of Animal Genomes Consortium; this comprehensive transcriptome supports functional annotation and comparative analysis of the water buffalo genome.Item Open Access A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions(American Association for the Advancement of Science, 2019) John Wallace, R.; Sasson, G.; Garnsworthy, P.C.; Tapio, I.; Gregson, E.; Bani, P.; Huhtanen, P.; Bayat, A.R.; Strozzi, F.; Biscarini, F.; Snelling, T.J.; Saunders, N.; Potterton, S.L.; Craigon, J.; Minuti, A.; Trevisi, E.; Callegari, M.L.; Cappelli, F.P.; Cabezas-Garcia, E.H.; Vilkki, J.; et al.A 1000-cow study across four European countries was undertaken to understand to what extent ruminant microbiomes can be controlled by the host animal and to identify characteristics of the host rumen microbiome axis that determine productivity and methane emissions. A core rumen microbiome, phylogenetically linked and with a preserved hierarchical structure, was identified. A 39-member subset of the core formed hubs in co-occurrence networks linking microbiome structure to host genetics and phenotype (methane emissions, rumen and blood metabolites, and milk production efficiency). These phenotypes can be predicted from the core microbiome using machine learning algorithms. The heritable core microbes, therefore, present primary targets for rumen manipulation toward sustainable and environmentally friendly agriculture.Item Metadata only A high-fat high-sugar diet in adolescent rats impairs social memory and alters chemical markers characteristic of atypical neuroplasticity and parvalbumin interneuron depletion in the medial prefrontal cortex(Royal Society of Chemistry, 2019) Reichelt, A.C.; Gibson, G.D.; Abbott, K.N.; Hare, D.J.Brain plasticity is a multifaceted process that is dependent on both neurons and extracellular matrix (ECM) structures, including perineuronal nets (PNNs). In the medial prefrontal cortex (mPFC) PNNs primarily surround fast-spiking parvalbumin (PV)-containing GABAergic interneurons and are central to regulation of neuroplasticity. In addition to the development of obesity, high-fat and high-sugar (HFHS) diets are also associated with alterations in brain plasticity and emotional behaviours in humans. To examine the underlying involvement of PNNs and cortical plasticity in the mPFC in diet-evoked social behaviour deficits (in this case social recognition), we exposed adolescent (postnatal days P28-P56) rats to a HFHS-supplemented diet. At P56 HFHS-fed animals and age-matched controls fed standard chow were euthanized and co-localization of PNNs with PV neurons in the prelimbic (PrL) and infralimbic (IL) and anterior cingulate (ACC) sub regions of the PFC were examined by dual fluorescence immunohistochemistry. ΔFosB expression was also assessed as a measure of chronic activity and behavioural addiction marker. Consumption of the HFHS diet reduced the number of PV+ neurons and PNNs in the infralimbic (IL) region of the mPFC by -21.9% and -16.5%, respectively. While PV+ neurons and PNNs were not significantly decreased in the ACC or PrL, the percentage of PV+ and PNN co-expressing neurons was increased in all assessed regions of the mPFC in HFHS-fed rats (+33.7% to +41.3%). This shows that the population of PV neurons remaining are those surrounded by PNNs, which may afford some protection against HFHS diet-induced mPFC-dysregulation. ΔFosB expression showed a 5-10-fold increase (p < 0.001) in each mPFC region, supporting the hypothesis that a HFHS diet induces mPFC dysfunction and subsequent behavioural deficits. The data presented shows a potential neurophysiological mechanism and response to specific diet-evoked social recognition deficits as a result of hypercaloric intake in adolescence.Item Open Access A large proportion of genetic variation in cow and ewe body composition is independent of yearling composition(CSIRO Publishing, 2023) Pitchford, W.S.; Hatcher, S.Commercial beef and sheep producers have adopted using condition score for management of cows and ewes to maximise productivity. Significant premiums are being paid for bulls and rams with higher-fat breeding values based on young animal measurements, with the aim of increased resilience in adult female progeny. Aims. The aim of this study was to quantify the relationship between adult body condition score and young muscle and fat and also the genetic variation in condition that is independent of yearling traits. Methods. Published genetic parameters for four large data sets from Angus and tropically adapted cattle, and composite and Merino sheep were used to partition genetic variation in adult condition that is associated with, or independent of, young composition measures. Key results. One genetic standard deviation in young muscle or fat was associated with approximately just 0.1 adult body condition scores. Approximately ¾ of the genetic variation in adult body condition score (BCS) is independent of genetic variation in young weight and composition traits. Conclusions and implications. Producers need to be careful with premiums paid for bulls and rams with superior yearling composition traits with the aim of changing adult BCS. The best way to achieve this is for seedstock breeders to record and report breeding values for cow and ewe BCS.Item Metadata only A large-scale study of indicators of sub-clinical mastitis in dairy cattle by attribute weighting analysis of milk composition features: highlighting the predictive power of lactose and electrical conductivity(Hannah Dairy Research Foundation, 2018) Ebrahimie, E.; Ebrahimi, F.; Ebrahimi, M.; Tomlinson, S.; Petrovski, K.R.Sub-clinical mastitis (SCM) affects milk composition. In this study, we hypothesise that large-scale mining of milk composition features by pattern recognition models can identify the best predictors of SCM within the milk composition features. To this end, using data mining algorithms, we conducted a large-scale and longitudinal study to evaluate the ability of various milk production parameters as indicators of SCM. SCM is the most prevalent disease of dairy cattle, causing substantial economic loss for the dairy industry. Developing new techniques to diagnose SCM in its early stages improves herd health and is of great importance. Test-day Somatic Cell Count (SCC) is the most common indicator of SCM and the primary mastitis surveillance approach worldwide. However, test-day SCC fluctuates widely between days, causing major concerns for its reliability. Consequently, there would be great benefit to identifying additional efficient indicators from large-scale and longitudinal studies. With this intent, data was collected at every milking (twice per day) for a period of 2 months from a single farm using in-line electronic equipment (346 248 records in total). The following data were analysed: milk volume, protein concentration, lactose concentration, electrical conductivity (EC), milking time and peak flow. Three SCC cut-offs were used to estimate the prevalence of SCM: Australian ≥ 250 000 cells/ml, European ≥200 000 cells/ml and New Zealand ≥ 150 000 cells/ml. At first, 10 different Attribute Weighting Algorithms (AWM) were applied to the data. In the absence of SCC, lactose concentration featured as the most important variable, followed by EC. For the first time, using attribute weighted modelling, we showed that the concentration of lactose in milk can be used as a strong indicator of SCM. The development of machine-learning expert systems using two or more milk variables (such as lactose concentration and EC) may produce a predictive pattern for early SCM detection.Item Metadata only A lipoglycopeptide antibiotic for Gram-positive biofilm-related infections(American Association for the Advancement of Science, 2022) Blaskovich, M.A.T.; Hansford, K.A.; Butler, M.S.; Ramu, S.; Kavanagh, A.M.; Jarrad, A.M.; Prasetyoputri, A.; Pitt, M.E.; Huang, J.X.; Lindahl, F.; Ziora, Z.M.; Bradford, T.; Muldoon, C.; Rajaratnam, P.; Pelingon, R.; Edwards, D.J.; Zhang, B.; Amado, M.; Elliott, A.G.; Zuegg, J.; et al.Drug-resistant Gram-positive bacterial infections are still a substantial burden on the public health system, with two bacteria (Staphylococcus aureus and Streptococcus pneumoniae) accounting for over 1.5 million drug-resistant infections in the United States alone in 2017. In 2019, 250,000 deaths were attributed to these pathogens globally. We have developed a preclinical glycopeptide antibiotic, MCC5145, that has excellent potency (MIC90 ≤0.06 g/ml) against hundreds of isolates of methicillin-resistant S. aureus (MRSA) and other Gram-positive bacteria, with a greater than 1000-fold margin over mammalian cell cytotoxicity values. The antibiotic has therapeutic in vivo efficacy when dosed subcutaneously in multiple murine models of established bacterial infections, including thigh infection with MRSA and blood septicemia with S. pneumoniae, as well as when dosed orally in an antibioticinduced Clostridioides difficile infection model. MCC5145 exhibited reduced nephrotoxicity at microbiologically active doses in mice compared to vancomycin. MCC5145 also showed improved activity against biofilms compared to vancomycin, both in vitro and in vivo, and a low propensity to select for drug resistance. Characterization of drug action using a transposon library bioinformatic platform showed a mechanistic distinction from other glycopeptide antibiotics.Item Metadata only A live vaccine against Neospora caninum abortions in cattle(Elsevier, 2015) Reichel, M.P.; Moore, D.P.; Hemphill, A.; Ortega-Mora, L.M.; Dubey, J.P.; Ellis, J.T.Item Open Access A long-term efficacy trial of a live, attenuated Salmonella Typhimurium vaccine in layer hens(Frontiers Media, 2018) McWhorter, A.; Chousalkar, K.Salmonella remains one of the most common causes of bacterial foodborne gastrointestinal disease in humans. Raw eggs or food items containing undercooked eggs are frequently identified as the source of Salmonella. Salmonella Typhimurium contamination of table eggs most commonly occurs when they are laid in a contaminated environment. Several control strategies, including vaccination, are widely used to mitigate the total Salmonella load. It is unclear, however, whether live attenuated Salmonella vaccines are efficacious over the life span of a layer hen. Live attenuated Salmonella vaccines have been favored due to their ability to illicit a strong humoral immune response. The lifespan of a layer hen ranges between 60 and 80 weeks and the long term efficacy of attenuated vaccine strains has not been investigated. In this study, commercial brown layer chicks were vaccinated at day old, 6 weeks of age, and again at 10 weeks of age with the Bioproperties VaxsafeTM STM1 aroA mutant vaccine. Birds were challenged at 18 weeks of age with Salmonella Typhimurium DT9 (MLVA 03 15 08 11 550). Feces and eggs were monitored for S. Typhimurium for 40 weeks post-infection. Birds produced a strong immune response following the final dose which was administered intramuscularly. The serum antibody response to S. Typhimurium DT9 infection did not differ between challenged groups. Fecal shedding and egg contamination was highly variable and did not differ significantly between vaccinated and unvaccinated birds that had been challenged with S. Typhimurium DT9. Total bacterial load in feces was quantified using qPCR. No significant difference was detected between unvaccinated and vaccinated birds after challenge.Item Metadata only A longitudinal study of mastitis on an experimental farm with two herds, one managed organically, the other conventionally(Organic eprints, 2008) Thatcher, A.; Petrovski, K.; Holmes, C.; Dowson, K.; Kelly, T.; McLeod, K.; International Society of Organic Agriculture Research Scientific Conference (2nd : 2008 : Modena, Italy)Mastitis in two herds managed as a comparison between organic and conventional dairy farming systems was monitored for 4 years utilising regular bacterial culture of milk samples, individual and bulk somatic cell counts and observation by farm staff. The objective was to develop strategies for the control of mastitis in organic cows without the use of antibiotics. The herds showed differences in clinical mastitis incidence, subclinical mastitis prevalence and bulk milk somatic cell count. Despite these differences, the level of mastitis in the organic herd remained manageable.Item Open Access A Microbiological map of the healthy equine gastrointestinal tract(Public Library of Science (PLoS), 2016) Ericsson, A.; Johnson, P.; Lopes, M.; Perry, S.; Lanter, H.; Smidt, H.Horses are exquisitely sensitive to non-specific gastrointestinal disturbances as well as systemic and extraintestinal conditions related to gut health, yet minimal data are available regarding the composition of the microbiota present in the equine stomach, small intestine, and cecum and their relation to fecal microbiota. Moreover, there is minimal information regarding the concordance of the luminal and mucosal microbial communities throughout the equine gut. Illumina-based 16S rRNA gene amplicon sequencing of the luminal and mucosal microbiota present in seven regions of the gastrointestinal tract of nine healthy adult horses revealed a distinct compositional divide between the small and large intestines. This disparity in composition was more pronounced within the luminal contents, but was also detected within mucosal populations. Moreover, the uniformity of the gut microbiota was much higher in the cecum and colon relative to that in the stomach, jejunum and ileum, despite a significantly higher number of unique sequences detected in the colon. Collectively, the current data suggest that while colonic samples (a proxy for feces) may provide a reasonable profile of the luminal contents of the healthy equine large intestine, they are not informative with regard to the contents of the stomach or small intestine. In contrast to the distinct difference between the highly variable upper gastrointestinal tract microbiota and relatively uniform large bowel microbiota present within the lumen, these data also demonstrate a regional continuity present in mucosal microbial communities throughout the length of the equine gut.Item Metadata only A modelling approach to predict the variation of repeatability and reproducibility of a RT-PCR assay for infectious salmon anaemia virus across infection prevalences and infection stages(Elsevier Science BV, 2012) Caraguel, C.; Stryhn, H.; Gagne, N.; Dohoo, I.; Hammell, L.Conventional studies on the precision of diagnostic tests with binary outcomes report single descriptive estimates of agreement for a particular pool of samples. However, agreement for binary tests is intrinsically associated with the assay operating characteristics that are influenced by population and laboratory covariate factors. Therefore, reporting agreement estimates under various conditions may be more appropriate for diagnostic test comprehension. In this study, the influence of various submission factors (tissue sample homogenization, prevalence of infection and pathogen level) on agreement was further analyzed using test result information from a previous descriptive report of within and between laboratories agreement (repeatability and reproducibility, respectively) of a Reverse-Transcription Polymerase Chain Reaction (RT-PCR) assay for infectious salmon anaemia virus (ISAV). Multilevel logistic regression models were constructed separately for non-, low- or high-infected salmon (classified using a study pseudogold standard) to predict probabilities of testing positive under different testing conditions. For each of the 3 infection categories, agreement and kappa values within and between laboratories were computed from the models' predicted values using probability formulae. Thereafter, overall estimates were predicted using simple category weighting for various proportions of infection stages. Agreement varied substantially among infection categories and, consequently, overall repeatability and reproducibility varied greatly with prevalence. This confirmed that the report of a single descriptive estimate (corresponding to a set prevalence) may not be appropriate. Low-infected fish had the lowest agreement estimate which was improved by sample homogenization. This supported a heterogeneous distribution of ISAV in early infected salmon kidney. However, tissue homogenization increased the probability to obtain a false-positive test result (cross-contamination suspected) and decreased agreement in non-infected fish. Compared to conventional report of test agreement estimation, the modelling approach identified influencing submission factors and provided predictive intervals of agreement that give a better expectation and understanding of assay repeatability and reproducibility under different circumstances of use.