Biomedical subjects

M J Daniels

Publications and source records attributed to M J Daniels.

At least 19 recordsLinked to original sources

PubMed2002

Risk factors for Johne's disease in Scotland--the results of a survey of farmers.

The reported incidence of Johne's disease has been increasing in the east of Scotland since 1993. A postal questionnaire survey was sent to 127 farms to identify potential risk factors for Johne's disease in relation to wildlife and farm management practices, and 86 returns were obtained. Of 22 farms which had been assumed to be free of the disease, on the basis of information held by local veterinary centres, seven (32 per cent) reported cases of Johne's disease in the 1990s, indicating that the disease is under-reported. Logistic regression analyses showed that eight of 63 potentially explanatory variables were significant at the 5 per cent level in affecting the likelihood of farms reporting Johne's disease. Of these, large numbers of livestock and rabbits, and access of wildlife to feed stores were the clearest and most consistent risk factors associated with the disease. The application of manure to grazing pasture, the type of water supply for the cattle and the numbers of crows were also related to the presence of Johne's disease but the nature of these relationships was less clear. Only 38 per cent of the farms reported taking any control measures to combat Johne's disease, but three of the control measures were relevant to risk factors identified as significant by the survey, namely maintaining a clean water supply, controlling rabbits and not spreading manure on to grazing pasture.

Animals↗

PubMed2002

Dynamic conditionally linear mixed models for longitudinal data.

We develop a new class of models, dynamic conditionally linear mixed models, for longitudinal data by decomposing the within-subject covariance matrix using a special Cholesky decomposition. Here 'dynamic' means using past responses as covariates and 'conditional linearity' means that parameters entering the model linearly may be random, but nonlinear parameters are nonrandom. This setup offers several advantages and is surprisingly similar to models obtained from the first-order linearization method applied to nonlinear mixed models. First, it allows for flexible and computationally tractable models that include a wide array of covariance structures; these structures may depend on covariates and hence may differ across subjects. This class of models includes, e.g., all standard linear mixed models, antedependence models, and Vonesh-Carter models. Second, it guarantees the fitted marginal covariance matrix of the data is positive definite. We develop methods for Bayesian inference and motivate the usefulness of these models using a series of longitudinal depression studies for which the features of these new models are well suited.

Antidepressive Agents↗

PubMed2001

Monarch larvae sensitivity to Bacillus thuringiensis- purified proteins and pollen.

Laboratory tests were conducted to establish the relative toxicity of Bacillus thuringiensis (Bt) toxins and pollen from Bt corn to monarch larvae. Toxins tested included Cry1Ab, Cry1Ac, Cry9C, and Cry1F. Three methods were used: (i) purified toxins incorporated into artificial diet, (ii) pollen collected from Bt corn hybrids applied directly to milkweed leaf discs, and (iii) Bt pollen contaminated with corn tassel material applied directly to milkweed leaf discs. Bioassays of purified Bt toxins indicate that Cry9C and Cry1F proteins are relatively nontoxic to monarch first instars, whereas first instars are sensitive to Cry1Ab and Cry1Ac proteins. Older instars were 12 to 23 times less susceptible to Cry1Ab toxin compared with first instars. Pollen bioassays suggest that pollen contaminants, an artifact of pollen processing, can dramatically influence larval survival and weight gains and produce spurious results. The only transgenic corn pollen that consistently affected monarch larvae was from Cry1Ab event 176 hybrids, currently <2% corn planted and for which re-registration has not been applied. Results from the other types of Bt corn suggest that pollen from the Cry1Ab (events Bt11 and Mon810) and Cry1F, and experimental Cry9C hybrids, will have no acute effects on monarch butterfly larvae in field settings.

Animals↗

PubMed2001

Regulation of the synthesis of cyclic glucan in Xanthomonas campestris by a diffusible signal molecule.

The rpf gene cluster of Xanthomonas campestris pv. campestris is involved in the co-ordinate positive regulation of the production of extracellular enzymes and the extracellular polysaccharide xanthan. Several of the rpf genes are involved in a regulatory system involving the small diffusible molecule DSF (for diffusible signal factor). Synthesis of DSF requires RpfF, and a two-component sensory transduction system involving RpfC has been implicated in the perception of the signal and signal transduction. Here we show that mutations in both rpfF and rpfC lead to reductions in the levels of cyclic glucan. The levels of cyclic glucan synthetase in membrane preparations from rpfF and rpfC mutants were, however, unaltered from the wild-type. Similar alterations in the level of cyclic glucan without changes in cyclic glucan synthetase activity were seen when wild-type bacteria were exposed to osmotic stress. These results extend the range of cellular functions subject to regulation by the rpf genes and DSF system.

Bacterial Proteins↗

PubMed2001

Investigation of avenacin-deficient mutants of Avena strigosa.

The biosynthesis of cyclic triterpenoids in ten saponin-deficient (sad) mutant varieties of the diploid oat Avena strigosa is reported. Two mutants were found to be deficient in 2,3-oxidosqualene:beta-amyrin cyclase (OSbetaAC) (EC 5.4.99) and thus unable to produce the beta-amyrin necessary for the production of avenacins. The other mutants studied had post beta-amyrin lesions. 2,3-Oxidosqualene:cycloartenol cyclase (OSCC) (EC 5.4.99.8) needed for sterol formation was present in all ten mutants.

Avena↗

PubMed2001

Genetic diversity and introgression in the Scottish wildcat.

This paper describes a genetic analysis of wild-living cats in Scotland. Samples from 230 wild-living Scottish cats (including 13 museum skins) and 74 house cats from England and Scotland were surveyed for nine microsatellite loci. Pelage characteristics of the wild-living cats were recorded, and the cats were then grouped into five separate categories depending on the degree to which they conformed to the characteristics attributed to Felis silvestris Schreber, 1775. Allele frequency differences between the morphological groups are greater than those among the three house cat samples. Analysis of genetic distances suggests that more of the differences between individuals can be explained by pelage than geographical proximity, and that pelage and geographical location are not confounded. Ordination of the genetic distances suggests two main groups of wild-living cats, with intermediates, and one group is genetically very similar to the house cats, while the other group contains all cats taxonomically identified as wildcat based on morphology. A genetic mixture analysis gives similar results to the ordination, but also suggests that the genotypes of a substantial number of cats in the wildcat group are drawn from a gene pool with genotypes in approximately equilibrium proportions. We argue that this is evidence that these cats do not have very recent domestic ancestry. However, from the morphological data it is highly likely that this gene pool also contains a contribution from earlier introgression of domestic cat genes.

Animals↗

PubMed2001

Natural paratuberculosis infection in rabbits in Scotland.

Natural paratuberculosis infection of rabbits (Oryctolagus cuniculus) was recently diagnosed in Scotland, and an investigation into the pathology of the disease in wild rabbits is reported in this paper. Evidence of Mycobacterium avium subsp. paratuberculosis (M.a. paratuberculosis) infection was detected in 22% of 110 rabbits; the organism was cultured from 17 of 110 rabbits, and histopathological lesions consistent with M.a. paratuberculosis infection were noted in 18 of 98 rabbits examined. No macroscopical lesions suggestive of M.a. paratuberculosis infection were observed. The histopathological lesions were either severe or mild. Severe lesions consisted of extensive macrophage granulomata and numerous giant cells, with many intracellular acid-fast bacteria in the small intestine. For the examination of formalin-fixed, paraffin wax-embedded tissues, neither immunohistochemistry nor the polymerase chain reaction was as sensitive a method of diagnosis as histopathology.

Animals↗

PubMed2001

The grazing response of cattle to pasture contaminated with rabbit faeces and the implications for the transmission of paratuberculosis.

Transmission of Mycobacterium avium subspecies paratuberculosis, the organism responsible for paratuberculosis (or Johne's disease) in ruminants, occurs through the faecal-oral route. As M. a. paratuberculosis has been isolated from rabbit faeces, cattle grazing rabbit faecal contaminated pasture may thus be at risk.A herd of 57 beef cattle was monitored on a farm in Perthshire, throughout the 1999 'grazing year', to investigate whether the cattle avoided rabbit faecal contaminated pasture and thus the potential for disease transmission. Grazing was measured every two days over eight rotations by sward heights on 40 marked treatment plots (0.5 m x 0.5 m) to which 0, 10, 50 and 250 rabbit faecal pellets were added. Cattle were also monitored by an active transponder system which enabled individual animals contacting two plots per field rotation (one control and one contaminated) to be recorded. During the monitored grazing year, grazing pressure was low with a net mean sward offtake of 18% of sward height per rotation. There were no significant differences between rabbit faecal treatments (0, 10, 50 and 250 pellets) with respect to the height or proportion of sward removed, or between the numbers of contacts made by cattle on contaminated and uncontaminated plots. Over 90% of all the cattle contacted contaminated plots, indicating that the potential for disease transmission was widespread among the herd. To our knowledge, this is the first reported instance of a lack of avoidance by grazing cattle towards swards contaminated with faeces, and implies that the potential for transmission of paratuberculosis from rabbit contaminated pasture is high.

Animal Husbandry↗

PubMed2001

The response of cattle and sheep to feed contaminated with rodent faeces.

On farms where rats and mice are present, unprotected livestock feed may become contaminated with rodent faeces, thereby creating a possible source of infection for cattle and sheep. Livestock unable to avoid contaminated feed may choose to eat it entirely, reject it completely or attempt to reject faeces selectively while consuming some of the feed. Two experiments were conducted to investigate which of these three responses were demonstrated by livestock. Ten cattle and ten sheep were presented individually with three repeats of ten feed treatments. Treatments were based on two feed types (meal and pelleted compound), with three levels of contamination (none, 'low' and 'high'), from one of two rodent species (rat and mouse). Avoidance behaviour was greater for feed contaminated with rat faeces compared to feed contaminated with mouse faeces. At low levels of rat contamination there was evidence that livestock actively rejected faeces whilst consuming feed. At higher levels of contamination animals rejected faeces and feed. Livestock could not actively discriminate against mouse faeces and thus rejection of feed was used to avoid faeces ingestion. Despite rejection of contaminated feed and some discrimination against faeces, significant numbers of rodent faeces were ingested illustrating that livestock feeding behaviour cannot prevent ingestion of rodent faeces. Feed contaminated with rodent faeces therefore poses a significant risk of disease infection to livestock.

Animal Feed↗

PubMed2001

Expression of the gum operon directing xanthan biosynthesis in Xanthomonas campestris and its regulation in planta.

The gum gene cluster of Xanthomonas campestris pv. campestris comprises 12 genes whose products are involved in the biosynthesis of the extracellular polysaccharide xanthan. These genes are expressed primarily as an operon from a promoter upstream of the first gene, gumB. Although the regulation of xanthan synthesis in vitro has been well studied, nothing is known of its regulation in planta. A reporter plasmid was constructed in which the promoter region of the gum operon was fused to gusA. In liquid cultures, the expression of the gumgusA reporter was correlated closely with the production of xanthan, although a low basal level of beta-glucuronidase activity was seen in the absence of added carbon sources when xanthan production was very low. The expression of the gumgusA fusion also was subject to positive regulation by rpfF, which is responsible for the synthesis of the diffusible signal factor (DSF). The expression of the gumgusA fusion in bacteria recovered from inoculated turnip leaves was maximal at the later phases of growth and was subject to regulation by rpfF. These results provide indirect support for the operation of the DSF regulatory system in bacteria in planta.

Bacterial Proteins↗

PubMed2001

Induction of hydroxycinnamoyl-tyramine conjugates in pepper by Xanthomonas campestris, a plant defense response activated by hrp gene-dependent and hrp gene-independent mechanisms.

Inoculation of pepper leaves, Capsicum annuum cv. Early Calwonder ECW 10R, with strains of Xanthomonas campestris led to an accumulation of the phenolic conjugates feruloyltyramine (FT) and p-coumaroyltyramine (CT) 24 h postinoculation in nonhost- and gene-for-gene-determined incompatible interactions with X. campestris pv. campestris and X. campestris pv. vesicatoria, respectively. In contrast, neither compound was detected in compatible interactions with X. campestris pv. vesicatoria. The accumulation of FT and CT was preceded by an increase in the extractable activity of tyrosine decarboxylase as well as increases in the transcription of genes encoding phenylalanine ammonia-lyase and tyramine hydroxycinnamoyl transferase. No such changes were detected in compatible interactions. Very rapid accumulation of FT and CT occurred (4 h postinoculation) in pepper in response to a X. campestris pv. campestris mutant carrying a deletion of the hrp gene cluster. In contrast, hrp mutants of X. campestris pv. vesicatoria failed to elicit the production of FT and CT. These observations suggest the existence of hrp gene-dependent and -independent activation mechanisms of a defense response involving hydroxycinnamoyltyramines.

Anti-Bacterial Agents↗

PubMed2001

Shrinkage estimators for covariance matrices.

Estimation of covariance matrices in small samples has been studied by many authors. Standard estimators, like the unstructured maximum likelihood estimator (ML) or restricted maximum likelihood (REML) estimator, can be very unstable with the smallest estimated eigenvalues being too small and the largest too big. A standard approach to more stably estimating the matrix in small samples is to compute the ML or REML estimator under some simple structure that involves estimation of fewer parameters, such as compound symmetry or independence. However, these estimators will not be consistent unless the hypothesized structure is correct. If interest focuses on estimation of regression coefficients with correlated (or longitudinal) data, a sandwich estimator of the covariance matrix may be used to provide standard errors for the estimated coefficients that are robust in the sense that they remain consistent under misspecification of the covariance structure. With large matrices, however, the inefficiency of the sandwich estimator becomes worrisome. We consider here two general shrinkage approaches to estimating the covariance matrix and regression coefficients. The first involves shrinking the eigenvalues of the unstructured ML or REML estimator. The second involves shrinking an unstructured estimator toward a structured estimator. For both cases, the data determine the amount of shrinkage. These estimators are consistent and give consistent and asymptotically efficient estimates for regression coefficients. Simulations show the improved operating characteristics of the shrinkage estimators of the covariance matrix and the regression coefficients in finite samples. The final estimator chosen includes a combination of both shrinkage approaches, i.e., shrinking the eigenvalues and then shrinking toward structure. We illustrate our approach on a sleep EEG study that requires estimation of a 24 x 24 covariance matrix and for which inferences on mean parameters critically depend on the covariance estimator chosen. We recommend making inference using a particular shrinkage estimator that provides a reasonable compromise between structured and unstructured estimators.

Analysis of Variance↗

PubMed2001

Paratuberculosis infection of nonruminant wildlife in Scotland.

Recent reports of natural paratuberculosis (or Johne's disease) in rabbits, foxes, and stoats has focused debate on the presence and importance of wildlife reservoirs in the epidemiology of this disease. This paper describes an extensive study investigating 18 nonruminant wildlife species for evidence of paratuberculosis. Using both culture and histopathological analysis, fox, stoat, weasel, crow, rook, jackdaw, rat, wood mouse, hare, and badger were found to harbor Mycobacterium avium subsp. paratuberculosis, the causative organism of paratuberculosis, suggesting that the epidemiology of this disease is more complex than previously realized.

Animals↗

PubMed2000

Estimating particulate matter-mortality dose-response curves and threshold levels: an analysis of daily time-series for the 20 largest US cities.

Numerous studies have shown a positive association between daily mortality and particulate air pollution, even at concentrations below regulatory limits. These findings have motivated interest in the shape of the exposure-response relation. The authors have developed flexible modeling strategies for time-series data that include spline and threshold exposure-response models; they apply these models to daily time-series data for the 20 largest US cities for 1987-1994, using the concentration of particulate matter <10 microm in aerodynamic diameter (PM10) as the exposure measure. The spline model showed a linear relation without indication of threshold for PM10 and relative risk of death for all causes and cardiorespiratory causes; by contrast, for other causes, the risk did not increase until approximately 50 microg/m3 PM10. For all-cause mortality, a linear model without threshold was preferred to the threshold model and to the spline model, using the Akaike information criterion (AIC). The findings were similar for cardiovascular and respiratory deaths combined. By contrast, for causes other than cardiovascular and respiratory, a threshold model was more competitive with a threshold value estimated at 65 microg/m3. These findings indicate that linear models without a threshold are appropriate for assessing the effect of particulate air pollution on daily mortality even at current levels.

Air Pollutants↗

PubMed2000

Biosynthesis of avenacins and phytosterols in roots of Avena sativa cv. Image.

In keeping with the proposal that avenacin biosynthesis is restricted to the tips of primary roots of oat seedlings, the incorporation of radioactivity from R-[2-(14)C]mevalonic acid (MVA) into avenacins and beta-amyrin by serial sections of primary roots was found to be more-or-less restricted to root tip sections. Squalene synthase (SQS) (EC 2.5.1.21) and 2,3-oxidosqualene:beta-amyrin cyclase (OS beta AC) (EC 5.4.99) were also most active in these sections. The incorporation of radiolabel from R-[2-(14)C]MVA into cycloartenol and 24-methylene cycloartanol by, and the 2,3-oxidosqualene:cycloartenol cyclase (OSCC) (EC 5.4.99) activity in, the various serial sections were consistent with phytosterol biosynthesis occurring in all the sections of the root with some tailing-off in the rate of synthesis in the more distal sections.

Avena↗

PubMed2000

A two-component system involving an HD-GYP domain protein links cell-cell signalling to pathogenicity gene expression in Xanthomonas campestris.

The synthesis of extracellular enzymes and extracellular polysaccharide (EPS) in Xanthomonas campestris pv. campestris (Xcc) is regulated by a cluster of genes called rpf (for regulation of pathogenicity factors). Two of the genes, rpfF and rpfB, have previously been implicated in the synthesis of a diffusible regulatory molecule, DSF. Here, we describe a screen of transposon insertion mutants of Xcc that identified two DSF-overproducing strains. In each mutant, the gene disrupted is rpfC, which encodes a hybrid two-component regulatory protein in which the sensor and regulator domains are fused and which contains an additional C-terminal phosphorelay (HPt) domain. We show that rpfC is in an operon with rpfH and rpfG. The predicted protein RpfG has a regulatory input domain attached to a specialized version of an HD domain, previously suggested to function in signal transduction. The predicted protein RpfH is structurally related to the sensory input domain of RpfC. We show that RpfC and RpfG act positively to regulate the synthesis of extracellular enzymes and EPS, but that RpfC acts negatively to regulate the synthesis of DSF. We propose that RpfGHC is a signal transduction system that couples the synthesis of pathogenicity factors to sensing of environmental signals that may include DSF itself.

Amino Acid Sequence↗

PubMed2000

Genetic polymorphism in Xanthomonas albilineans strains originating from 11 geographical locations, revealed by two DNA probes.

Two DNA fragments from Xanthomonas albilineans were used as probes to study the molecular diversity among strains of this pathogen. Two serologically distinct groups, serovars I and II, could be differentiated by hybridization to the probes. These probes, designated 830 and 838, were cloned after subtractive DNA hybridization of common sequences of Xanthomonas campestris pv. vasculorum from a serovar I strain of X. albilineans. They did not hybridize to the DNA of several other xanthomonads or to sugarcane DNA under the conditions of hybridization used. Faint bands were observed upon hybridization of probe 830 with one strain of X. campestris pv. phaseoli. The same banding patterns were obtained with a strain of X. albilineans from Burkina Faso and the serovar II strains of Mauritius. The serovar I strains from Mauritius and two other strains each from Reunion and South Africa had similar pattern.

Africa↗

PubMed2000

Reparameterizing the pattern mixture model for sensitivity analyses under informative dropout.

Pattern mixture models are frequently used to analyze longitudinal data where missingness is induced by dropout. For measured responses, it is typical to model the complete data as a mixture of multivariate normal distributions, where mixing is done over the dropout distribution. Fully parameterized pattern mixture models are not identified by incomplete data; Little (1993, Journal of the American Statistical Association 88, 125-134) has characterized several identifying restrictions that can be used for model fitting. We propose a reparameterization of the pattern mixture model that allows investigation of sensitivity to assumptions about nonidentified parameters in both the mean and variance, allows consideration of a wide range of nonignorable missing-data mechanisms, and has intuitive appeal for eliciting plausible missing-data mechanisms. The parameterization makes clear an advantage of pattern mixture models over parametric selection models, namely that the missing-data mechanism can be varied without affecting the marginal distribution of the observed data. To illustrate the utility of the new parameterization, we analyze data from a recent clinical trial of growth hormone for maintaining muscle strength in the elderly. Dropout occurs at a high rate and is potentially informative. We undertake a detailed sensitivity analysis to understand the impact of missing-data assumptions on the inference about the effects of growth hormone on muscle strength.

Aged↗