Bayesian latent class estimation of sensitivity and specificity parameters of diagnostic tests for bovine tuberculosis in chronically infected herds in Northern Ireland.

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-γ) test as an ancillary test. The SICCT test has a moderate sensitivity (Se) and high specificity (Sp), while the IFN-γ 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-γ(bovine-avian) using a NI optical density (OD) cut-off difference of 0.05: IFN-γ(B-A)NI: Se 85.8-93.0%, Sp 75.6-96.2%; (4) IFN-γ(bovine-avian) using a standard 'commercial' OD cut-off difference of 0.1: IFN-γ(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.

An analysis of effects of heterozygosity in dairy cattle for bovine tuberculosis resistance.

Genetic 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.

Modelling the variation in skin-test tuberculin reactions, post-mortem lesion counts and case pathology in tuberculosis-exposed cattle: Effects of animal characteristics, histories and co-infection.

Correctly identifying bovine tuberculosis (bTB) in cattle remains a significant problem in endemic countries. We hypothesized that animal characteristics (sex, age, breed), histories (herd effects, testing, movement) and potential exposure to other pathogens (co-infection; BVDV, liver fluke and Mycobacterium avium reactors) could significantly impact the immune responsiveness detected at skin testing and the variation in post-mortem pathology (confirmation) in bTB-exposed cattle. Three model suites were developed using a retrospective observational data set of 5,698 cattle culled during herd breakdowns in Northern Ireland. A linear regression model suggested that antemortem tuberculin reaction size (difference in purified protein derivative avium [PPDa] and bovine [PPDb] reactions) was significantly positively associated with post-mortem maximum lesion size and the number of lesions found. This indicated that reaction size could be considered a predictor of both the extent (number of lesions/tissues) and the pathological progression of infection (maximum lesion size). Tuberculin reaction size was related to age class, and younger animals (<2.85 years) displayed larger reaction sizes than older animals. Tuberculin reaction size was also associated with breed and animal movement and increased with the time between the penultimate and disclosing tests. A negative binomial random-effects model indicated a significant increase in lesion counts for animals with M. avium reactions (PPDb-PPDa < 0) relative to non-reactors (PPDb-PPDa = 0). Lesion counts were significantly increased in animals with previous positive severe interpretation skin-test results. Animals with increased movement histories, young animals and non-dairy breed animals also had significantly increased lesion counts. Animals from herds that had BVDV-positive cattle had significantly lower lesion counts than animals from herds without evidence of BVDV infection. Restricting the data set to only animals with a bTB visible lesion at slaughter (n = 2471), an ordinal regression model indicated that liver fluke-infected animals disclosed smaller lesions, relative to liver fluke-negative animals, and larger lesions were disclosed in animals with increased movement histories.

Assessment of concurrent infection with bovine viral diarrhoea virus (BVDV) and Mycobacterium bovis: A herd-level risk factor analysis from Northern Ireland.

Bovine viral diarrhoea virus (BVDV) is a significant pathogen of cattle, leading to severe economic and animal-welfare impacts. Furthermore, the pathogen has been associated with impacting the progression or spread of other pathogens (e.g. Mycobacterium bovis, the causative agent of bovine tuberculosis (bTB)). During this study we investigated (i) risk factors for BVDV at a herd-level and (ii) whether there was any association between BVDV and herd-level bTB risk. The data for this study were gathered from a voluntary BVDV control programme in Northern Ireland (2013-2015) based on the identification of virus positive animals through tissue tag testing of calves. We assigned a herd-level BVDV status to 2827 participating herds, where a herd was assumed "infected" if one or more animals tested positive for BVDV. Two model suites were developed. Firstly, we assessed risk factors for BVDV herd status using multivariable logit random-effects modelling, aggregating to the calendar year level (2013-2015; n=4828; model 1). Secondly, we aggregated data across the three years of the study to give an overall status for the whole study period (n=2827; logistic model 2). Risk factors included year, herd-type, herd size, number of births, inward trade moves, calf mortality, and region. Furthermore, the herd-level bovine tuberculosis status (based on the single intradermal comparative cervical tuberculin (SICCT) test outcomes, or confirmation at post-mortem), or the size of bTB breakdowns (number of SICCT test positive animals), of herds was also investigated to assess whether there was an association (co-infection) with herd BVDV status. The final models suggested that BVDV herd status was positively associated with increased levels of calf mortality, herd size, number of births, the number of BVDV tests undertaken and the number of animals introduced to the herd. There was a significant univariable positive association between BVDV status, and SICCT breakdown risk, breakdown size and confirmed bTB status in model 2. However, there was no evidence of significant associations between bTB status (using SICTT status, confirmed status or herd breakdown size) and BVDV status in final multivariable models when controlling for other significant confounders. These results provide information for action for the future control and eradication of BVDV in Northern Ireland, though these data provide little support for the hypothesised association between BVDV and bTB status at herd-level. Further animal-level analyses are necessary to investigate whether there is support for a BVD-bTB co-infection association, including the impact of co-infection on the severity of infection.

Farmers' beliefs about bovine tuberculosis control in Northern Ireland.

Beliefs can play an important role in farmer behaviour and willingness to adopt new policies. In Northern Ireland, bovine tuberculosis (bTB) is one of the most important endemic diseases facing the cattle industry. An observational study was conducted on 192 farms in a high bTB incidence area during 2010-2011 in order to obtain a better understanding of farmers' beliefs in relation to bTB control. The views of farmers who had experienced a recent confirmed or multiple reactor bTB breakdowns (cases) were compared to those of farmers who had no recent reactors or restricted herd tests (controls). Data were obtained from a face-to-face questionnaire assessing farmers' agreement to 22 statements. All participating farmers found bTB control important and most were keen to learn more about bTB biosecurity measures and were in favour of the cattle-related bTB control measures as presented in the questionnaire (isolation of skin test inconclusive animals, use of the gamma-interferon test and pre-movement testing). The majority of farmers would allow badger vaccination and culling on their own land with an overall preference for vaccination. Highest disagreement was shown for the statements querying a willingness to pay for bTB control measures. There was agreement on most issues between case and control farmers and between different age groups of farmers although case farmers showed more support for additional advice on bTB biosecurity measures (P = 0.042). Case farmers were also more in favour of allowing badger vaccination (P = 0.008) and culling (P = 0.043) on their land and showed less concern for public opposition (P = 0.048).

Herd-level risk factors for bovine tuberculosis and adoption of related biosecurity measures in Northern Ireland: A case-control study.

Bovine tuberculosis (bTB) is a zoonotic disease which is endemic in Northern Ireland. As it has proven difficult to eradicate this disease, partly due to a wildlife reservoir being present in the European badger (Meles meles), a case-control study was conducted in a high incidence area in 2010-2011. The aim was to identify risk factors for bTB breakdown relating to cattle and badgers, and to assess the adoption of bTB related biosecurity measures on farms. Face-to-face questionnaires with farmers and surveys of badger setts and farm boundaries were conducted on 117 farms with a recent bTB breakdown (cases) and 75 farms without a recent breakdown (controls). On logistic regression at univariable and multivariable levels, significant risk factors associated with being a case herd included having an accessible badger sett within the farm boundaries in a field grazed in the last year (odds ratio, OR, 4.14; 95% confidence interval, CI, 1.79, 9.55), observation of live badgers (OR 4.14; 95% CI 1.79, 9.55), purchase of beef cattle (OR 4.60; 95% CI 1.61, 13.13), use of contractors to spread slurry (OR 2.83; 95% CI 1.24, 6.49), feeding meal on top of silage (OR 3.55; 95% CI 1.53, 8.23) and feeding magnesium supplement (OR = 3.77; 95% CI 1.39, 10.17). The majority of setts within the farm boundary were stated to be accessible by cattle (77.1%; 95% CI 71.2, 83.0%) and 66.8% (95% CI 63.8, 69.7%) of farm boundaries provided opportunities for nose-to-nose contact between cattle. Adoption of bTB related biosecurity measures, especially with regards to purchasing cattle and badger-related measures, was lower than measures related to disinfection and washing.

Antegrade continence enema (ACE): predictors of outcome in 111 patients.

PURPOSE: The antegrade continence enema (ACE) is used as a means of managing faecal incontinence and constipation with varying outcomes. We aim to evaluate our outcomes of ACEs and identify predictors of outcome. METHODS: A retrospective case-note review of patients ≤16 years of age undergoing an ACE (March 2000-September 2013) was carried out. Data collected included: patient demographics, functional outcomes and complications. Data are quoted as median (range) and compared using Mann-Whitney and Fisher's exact test. Univariate analysis was performed to identify predictors of successful outcomes. P < 0.05 is significant. Successful outcome = total continence/occasional leakage and failed outcome = regular soiling and/or constipation. RESULTS: 111 patients with complete data sets underwent an ACE [59% male, median age = 9.5 years (3.4-16 years)] and median follow-up = 48 months (4 months-11 years 4 months). Underlying diagnoses were idiopathic constipation (n = 68), anorectal malformation (n = 27), neuropathic bowel (n = 7), Hirschsprung disease (n = 5) and gastrointestinal dysmotility (n = 4). Social continence was achieved in 87/111 (78%). Fifteen percent of patients underwent reversal of ACE due to resolution of symptoms. There was no difference in outcomes related to diagnosis, gender, age or follow-up duration. Complication rate was 20.7% (23/111). CONCLUSIONS: The ACE is safe and effective in the management of intractable constipation and soiling. No predictors of outcome were identified.

Genome-wide association study identifies novel loci associated with resistance to bovine tuberculosis.

Tuberculosis (TB) caused by Mycobacterium bovis is a re-emerging disease of livestock that is of major economic importance worldwide, as well as being a zoonotic risk. There is significant heritability for host resistance to bovine TB (bTB) in dairy cattle. To identify resistance loci for bTB, we undertook a genome-wide association study in female Holstein-Friesian cattle with 592 cases and 559 age-matched controls from case herds. Cases and controls were categorised into distinct phenotypes: skin test and lesion positive vs skin test negative on multiple occasions, respectively. These animals were genotyped with the Illumina BovineHD 700K BeadChip. Genome-wide rapid association using linear and logistic mixed models and regression (GRAMMAR), regional heritability mapping (RHM) and haplotype-sharing analysis identified two novel resistance loci that attained chromosome-wise significance, protein tyrosine phosphatase receptor T (PTPRT; P=4.8 × 10(-7)) and myosin IIIB (MYO3B; P=5.4 × 10(-6)). We estimated that 21% of the phenotypic variance in TB resistance could be explained by all of the informative single-nucleotide polymorphisms, of which the region encompassing the PTPRT gene accounted for 6.2% of the variance and a further 3.6% was associated with a putative copy number variant in MYO3B. The results from this study add to our understanding of variation in host control of infection and suggest that genetic marker-based selection for resistance to bTB has the potential to make a significant contribution to bTB control.

Dietary management of urea cycle disorders: European practice.

BACKGROUND: There is no published data comparing dietary management of urea cycle disorders (UCD) in different countries. METHODS: Cross-sectional data from 41 European Inherited Metabolic Disorder (IMD) centres (17 UK, 6 France, 5 Germany, 4 Belgium, 4 Portugal, 2 Netherlands, 1 Denmark, 1 Italy, 1 Sweden) was collected by questionnaire describing management of patients with UCD on prescribed protein restricted diets. RESULTS: Data for 464 patients: N-acetylglutamate synthase (NAGS) deficiency, n=10; carbamoyl phosphate synthetase (CPS1) deficiency, n=29; ornithine transcarbamoylase (OTC) deficiency, n=214; citrullinaemia, n=108; argininosuccinic aciduria (ASA), n=80; arginase deficiency, n=23 was reported. The majority of patients (70%; n=327) were aged 0-16y and 30% (n=137) >16y. Prescribed median protein intake/kg body weight decreased with age with little variation between disorders. The UK tended to give more total protein than other European countries particularly in infancy. Supplements of essential amino acids (EAA) were prescribed for 38% [n=174] of the patients overall, but were given more commonly in arginase deficiency (74%), CPS (48%) and citrullinaemia (46%). Patients in Germany (64%), Portugal (67%) and Sweden (100%) were the most frequent users of EAA. Only 18% [n=84] of patients were prescribed tube feeds, most commonly for CPS (41%); and 21% [n=97] were prescribed oral energy supplements. CONCLUSIONS: Dietary treatment for UCD varies significantly between different conditions, and between and within European IMD centres. Further studies examining the outcome of treatment compared with the type of dietary therapy and nutritional support received are required.

Field trial of six serological tests for bovine brucellosis.

Serum agglutination (SAT), complement fixation (CFT), indirect ELISA (iELISA), competitive ELISA (cELISA), Rose Bengal (RBT) and EDTA-modified agglutination (EDTA) tests were used in parallel on serological samples from 19,935 cattle in 301 herds. The study herds were selected according to putative exposure to Brucellaabortus with cases defined by bacteriological culture or test agreement. No single test identified all infected cattle and, at diagnostic thresholds, relative sensitivity was highest in the iELISA (67.9%) or RBT (78.1%), using bacteriological culture or test agreement, respectively, to define cases. As screening tests, the relative sensitivity of the SAT was highest (75.9% by culture or 84.9% by test agreement), with an optimal threshold of 31 IU. The relative specificity of the diagnostic tests ranged from 99.6% (SAT 31IU) to 100% (iELISA, RBT and CFT). The trial confirmed the value of the SAT as a screening test and the value of parallel testing.

Epidemiology and management of a bovine brucellosis cluster in Northern Ireland.

An epidemiological investigation was undertaken of 41 bovine brucellosis outbreaks that occurred within a 10-month period, in a region where eradication measures appeared to be succeeding. The primary outbreak comprised three herds with significant within-herd spread and a high probability of multiple abortions. Direct contact between cattle at pasture was the most likely means of between-herd transmission for most (71%) outbreaks, with an attack rate of 28.1% in herds immediately neighbouring the primary outbreak herds and 11.3% in the next concentric ring of farms. Resolution of the incident was attributed to a rapid response by the veterinary authorities, detailed epidemiological investigations, repeated, prolonged testing of contact herds and employment of parallel testing.

Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations.

Enzymes generally are thought to derive their functional activity from conformational motions. The limited chemical variation in RNA suggests that such structural dynamics may play a particularly important role in RNA function. Minimal hammerhead ribozymes are known to cleave efficiently only in ∼ 10-fold higher than physiologic concentrations of Mg(2+) ions. Extended versions containing native loop-loop interactions, however, show greatly enhanced catalytic activity at physiologically relevant Mg(2+) concentrations, for reasons that are still ill-understood. Here, we use Mg(2+) titrations, activity assays, ensemble, and single molecule fluorescence resonance energy transfer (FRET) approaches, combined with molecular dynamics (MD) simulations, to ask what influence the spatially distant tertiary loop-loop interactions of an extended hammerhead ribozyme have on its structural dynamics. By comparing hammerhead variants with wild-type, partially disrupted, and fully disrupted loop-loop interaction sequences we find that the tertiary interactions lead to a dynamic motional sampling that increasingly populates catalytically active conformations. At the global level the wild-type tertiary interactions lead to more frequent, if transient, encounters of the loop-carrying stems, whereas at the local level they lead to an enrichment in favorable in-line attack angles at the cleavage site. These results invoke a linkage between RNA structural dynamics and function and suggest that loop-loop interactions in extended hammerhead ribozymes-and Mg(2+) ions that bind to minimal ribozymes-may generally allow more frequent access to a catalytically relevant conformation(s), rather than simply locking the ribozyme into a single active state.

Bovine tuberculosis: the genetic basis of host susceptibility.

The prevalence of bovine tuberculosis (BTB) in the UK remains a significant economic burden and problem for the agri-food industry. Much effort has been directed towards improving diagnostics, finding vaccine candidates and assessing the usefulness of badger culling. The contribution that host genotype makes to disease outcome has, until recently, been overlooked; yet, it is biologically untenable that genetic variation does not play a role. In this review, we highlight the evidence, past and present, for a role of host genetics in determining susceptibility to BTB in livestock. We then address some of the major issues surrounding the design of future studies tasked with finding the exact causative genetic variation underpinning the TB susceptibility phenotype. Finally, we discuss some of the potential future benefits, and problems, that a knowledge of the genetic component to BTB resistance/susceptibility may bring to the agricultural industries and the wider scientific community.

Initial incursion of pandemic (H1N1) 2009 influenza A virus into European pigs.

The initial incursion of pandemic (H1N1) 2009 influenza A virus (pH1N1) into a European pig population is reported. Diagnosis of swine influenza caused by pandemic virus was made during September 2009 following routine submission of samples for differential diagnosis of causative agents of respiratory disease, including influenza A virus. All four pigs (aged six weeks) submitted for investigation from a pig herd of approximately 5000 animals in Northern Ireland, experiencing acute-onset respiratory signs in finishing and growing pigs, were positive by immunofluorescence for influenza A. Follow-up analysis of lung tissue homogenates by real-time RT-PCR confirmed the presence of pH1N1. The virus was subsequently detected on two other premises in Northern Ireland; on one premises, detection followed the pre-export health certification testing of samples from pigs presumed to be subclinically infected as no clinical signs were apparent. None of the premises was linked to another epidemiologically. Sequencing of the haemagglutinin and neuraminidase genes revealed high nucleotide identity (>99.4 per cent) with other pH1N1s isolated from human beings. Genotypic analyses revealed all gene segments to be most closely related to those of contemporary pH1N1 viruses in human beings. It is concluded that all three outbreaks occurred independently, potentially as a result of transmission of the virus from human beings to pigs.

Mycobacterium bovis genotypes in Northern Ireland: herd-level surveillance (2003 to 2008).

Surveillance genotyping (variable number tandem repeat profiling and spoligotyping) of Mycobacterium bovis isolates from culture-confirmed bovine tuberculosis (TB)-affected herds in Northern Ireland is presented for the years 2003 to 2008 inclusive. A total of 175 M bovis genotypes were identified in 8630 isolates from 6609 herds. On average, 73 genotypes were identified each year, with 29 genotypes present in all six years. Highly significant differences (P<0.0001) were observed between the relative frequency of some genotypes in the years 2003 to 2008. The spatial distribution of M bovis genotypes was not random (P<0.0001). Significant geographical localisation of M bovis genotypes was evident, suggesting that sources tended to be local. Despite regions being dominated by geographically localised genotypes, substantial and exploitable local diversity was still evident. Genotypes were also translocated significant distances from their normal geographical location.

Using the Spinal Cord Independence Measure III to measure functional recovery in a post-acute spinal cord injury program.

STUDY DESIGN: A prospective design was conducted using admission and discharge Spinal Cord Independence Measure III (SCIM-III) data for persons discharged from a post-acute rehabilitation program. OBJECTIVE: The purpose of this study is to analyze the functional gains as measured by the SCIM-III that occur during a post-acute rehabilitation program. SETTING: Shepherd Center, Atlanta, GA, USA. METHODS: Participants were included if they had a motor complete spinal cord injury (SCI), were within 12 months from the date of injury and completed the recommended length of stay. Median SCIM-III changes between admission and discharge were calculated by subgroups (C1-4, C5, C6, C7-8, T1-6 and T7-12) based on the American Spinal Injury Association motor injury levels. Ceiling and floor effects were examined by item and the percentage of participants showing change between admission and discharge were calculated. RESULTS: In all, 114 participants were included in the analysis. The median total SCIM-III score at admission was 42 (range 13-68), whereas the median total SCIM-III score at discharge was 50 (range 16-72). The median improvement of 5 points in total SCIM-III score between admission and discharge was statistically significant. Significant improvements were also observed between admission and discharge across all subgroups except C1-4. Ceiling and floor effects were noted in some subgroups. CONCLUSIONS: The SCIM-III seems to be an effective measure for functional assessment of persons with SCI in a post-acute rehabilitation program. There are some ceiling and floor effects noted; however, the SCIM-III seems to be sensitive enough to capture functional changes during a post-acute rehabilitation program.

Campylobacter spp. in conventional broiler flocks in Northern Ireland: epidemiology and risk factors.

Risk factors for Campylobacter infection in conventional broiler flocks in the time period up to the first removal of birds to slaughter were investigated over a maximum of five consecutive production cycles in a cohort of 88 broiler farms in Northern Ireland. Samples for Campylobacter culture, which consisted of 14 cloacal swabs per flock, were collected from one house on each farm prior to the first depopulation of birds. In total 388 flocks were sampled, of which 163 tested positive for Campylobacter spp. (42.0%; 95% CI 35.1-48.9%). Data on farm and flock variables were obtained from questionnaires and random-effects logistic regression modelling used to investigate the association between these and the Campylobacter status of flocks. Six variables, all of which were significant at p<0.05, were included in the final multivariable model. These included a combined variable on the presence of rodents on farms, which showed an increased odds of infection in flocks where the farmer reported having observed rodents during the production cycle (OR=2.1) and/or where rodent droppings were observed at the sampling visit (OR=2.9). Other variables that were significantly associated with an increased odds of infection included the age of the birds at sampling (odds ratio for its linear effect=1.16 for each day of increase in age), season (summer versus other seasons OR=2.0), farms with three or more broiler houses (OR=2.9 compared to those with one house), the frequency of footbath disinfectant changes (OR=2.5 for once weekly and OR=4.0 for less than once weekly compared to twice weekly changes) and a categorical variable on the standard of tidiness and cleanliness of the broiler house ante-room (OR=2.0 and OR=4.9 for flocks from houses with poorer standards). There was no significant evidence of direct carry-over of infection from one production cycle to the next, neither was there evidence of other farm species acting as a source of infection.

Salmonella in slaughter pigs in Northern Ireland: prevalence and use of statistical modelling to investigate sample and abattoir effects.

A cross-sectional survey of pigs at slaughter in Northern Ireland was undertaken to determine the overall prevalence of Salmonella infection. In total 513 pigs were sampled across four abattoirs, with Salmonella spp. isolated from the caecal contents of 31.4% (95% confidence interval [CI] 27.4%-35.4%) and from 40.0% (95% CI 35.8%-44.3%) of swabs taken from the surface of carcasses post-evisceration. Two serovars, S. Typhimurium and S. Derby, were predominant and accounted for 52% and 35% respectively, of isolates from caecal contents. Antimicrobial resistance was most common amongst isolates of S. Typhimurium with 63.9% multiresistant compared to 10.8% of S. Derby isolates and 8.0% of other Salmonella spp. The proportion of pigs showing serological evidence of infection was significantly lower, with 11.5% (95% CI 8.9%-14.6%) and 10.1% (95% CI 7.7%-13.1%) of meat-juice samples giving positive and suspect reactions, respectively. The ratio of caecal positive to serologically positive animals is higher than in a number of other studies and may suggest recent infection, such as infection occurring during transport or lairage, in a proportion of animals. Statistical (logistic regression) modelling was used to investigate the association between the risk of Salmonella on carcasses and the isolation of Salmonella from caecal contents, and/or the serological status of the animal, while adjusting for other possible explanatory and confounding variables such as abattoir, season, day and time of sampling. The occurrence of Salmonella in caecal contents (odds ratio [OR] 2.39; 95% CI 1.52-3.77) or a suspect/positive serological reaction (OR 2.15; 95% CI 1.28-3.61) were both independently associated with the occurrence of Salmonella on carcasses in homebred, but interestingly not in imported animals. In most multivariable models there were also significant differences in carcass contamination between seasons with the highest odds of carcass contamination occurring in the April to June quarter and the lowest in the October to December quarter. Differences between sampling days were also evident with the highest odds of carcass contamination at the end of the week (Fridays) and the lowest at the start of the week (Mondays). These associations, after adjusting for the caecal or serological result, would suggest the occurrence of abattoir effects, such varying residual levels of abattoir contamination, which are independent of the individual pig status.

Molecular dynamics simulations of RNA: an in silico single molecule approach.

RNA molecules are now known to be involved in the processing of genetic information at all levels, taking on a wide variety of central roles in the cell. Understanding how RNA molecules carry out their biological functions will require an understanding of structure and dynamics at the atomistic level, which can be significantly improved by combining computational simulation with experiment. This review provides a critical survey of the state of molecular dynamics (MD) simulations of RNA, including a discussion of important current limitations of the technique and examples of its successful application. Several types of simulations are discussed in detail, including those of structured RNA molecules and their interactions with the surrounding solvent and ions, catalytic RNAs, and RNA-small molecule and RNA-protein complexes. Increased cooperation between theorists and experimentalists will allow expanded judicious use of MD simulations to complement conceptually related single molecule experiments. Such cooperation will open the door to a fundamental understanding of the structure-function relationships in diverse and complex RNA molecules. .

Salmonella surveillance in raw and cooked meat and meat products in the Republic of Ireland from 2002 to 2004.

The food industry, under the regulation of the Department of Agriculture and Food (DAF) in the Republic of Ireland, is required to undertake all microbiological testing in relation to zoonoses control, in laboratories approved by DAF. These laboratories submit a monthly report of all tests undertaken, together with all presumptive Salmonella isolates for confirmation, typing and storage to the Central Veterinary Research Laboratory (CVRL). Details of Salmonella tests on 110,229 raw and 25,189 cooked meat samples from 25 laboratories were recorded over the 3-year period 2002-2004. Salmonella spp. were isolated from 1.0% of the 110,229 raw meat samples and 0.1% of the 25,189 cooked meat samples tested. The percentage of raw meat samples contaminated with Salmonella decreased over the three-year period from 1.2% to 0.9%. There was no seasonal trend in the isolation of Salmonella from any of the meats or meat products. Recoveries of the organism were highest for turkey and chicken meats at 3.1% and 2.8%, respectively, followed by porcine meats at 2.1%. The recoveries were much lower for ovine meats and meat products at 0.2% and bovine meat and meat products at 0.16%.