Sequence analysis and distribution of an IS3-like insertion element isolated from Salmonella enteritidis

The nucleotide sequence of a 3 kb region immediately upstream of the sef operon of Salmonella enteritidis was determined. A 1230 base pair insertion sequence which shared sequence identity (> 75%) with members of the IS3 family was revealed. This element, designated IS1230, had almost identical (90% identity) terminal inverted repeats to Escherichia coli IS3 but unlike other IS3-like sequences lacked the two characteristic open reading frames which encode the putative transposase. S. enteritidis possessed only one copy of this insertion sequence although Southern hybridisation analysis of restriction digests of genomic DNA revealed another fragment located in a region different from the sef operon which hybridised weakly which suggested the presence of an IS1230 homologue. The distribution of IS1230 and IS1230-like elements was shown to be widespread amongst salmonellas and the patterns of restriction fragments which hybridised differed significantly between Salmonella serotypes and it is suggested that IS1230 has potential for development as a differential diagnostic tool.

Oral uptake and distribution of microspheres

There is a growing body of experimental evidence suggesting that the gastrointestinal tract (GIT) may be penetrated by sub-micron sized polymeric particles which have the capacity to deliver therapeutic compounds. We investigated this, initially with Fluoresbrite™ carboxylate latex microspheres (0.87 m diameter) which were administered orally to rats. Microsphere numbers within blood samples were then quantified using fluorescence microscopy or FACS technology. These studies were prone to quantitative error, but indicated that increased microsphere translocation occurred if particles were administered in conjunction with large volumes of hypotonic liquid, and that uptake was very rapid. Test particles were detected in blood, only a few minutes after dosing. To improve quantification, GPC technology was adopted. 0.22 m latex particles were found to accumulate in greatest numbers within the Mononuclear phagocyte system tissues after gavage. Again translocation was rapid. The ability of test particles to leave the intestinal lumen and access systemic compartments was found to be highly dependent on their size and hydrophobicity, determined by hydrophobic interaction chromatography. Considerably lower numbers of 0.97 m diameter latex microspheres were detectable within extra-intestinal tissue locations after gavage. Histological studies showed that Fluoresbrite™ microspheres accumulate within the liver, spleen, Mesenteric lymph node and vasculature of rats after oral administration. Fluorescent particles were observed in both the Peyer's patches (PPs), and non lymphoid regions of rat intestinal mucosa after gavage, conductive to the acceptance that more than one mechanism of particle absorption may operate.

The application of artificial neural networks to the interpretation and classification of freshwater benthic invertebrate communities

This thesis presents a thorough and principled investigation into the application of artificial neural networks to the biological monitoring of freshwater. It contains original ideas on the classification and interpretation of benthic macroinvertebrates, and aims to demonstrate their superiority over the biotic systems currently used in the UK to report river water quality. The conceptual basis of a new biological classification system is described, and a full review and analysis of a number of river data sets is presented. The biological classification is compared to the common biotic systems using data from the Upper Trent catchment. This data contained 292 expertly classified invertebrate samples identified to mixed taxonomic levels. The neural network experimental work concentrates on the classification of the invertebrate samples into biological class, where only a subset of the sample is used to form the classification. Other experimentation is conducted into the identification of novel input samples, the classification of samples from different biotopes and the use of prior information in the neural network models. The biological classification is shown to provide an intuitive interpretation of a graphical representation, generated without reference to the class labels, of the Upper Trent data. The selection of key indicator taxa is considered using three different approaches; one novel, one from information theory and one from classical statistical methods. Good indicators of quality class based on these analyses are found to be in good agreement with those chosen by a domain expert. The change in information associated with different levels of identification and enumeration of taxa is quantified. The feasibility of using neural network classifiers and predictors to develop numeric criteria for the biological assessment of sediment contamination in the Great Lakes is also investigated.

Clustering and periodicity of neurofibrillary tangles in the upper and lower cortical laminae in Alzheimer's disease

In Alzheimer's disease (AD), neurofibrillary tangles (NFT) occur within neurons in both the upper and lower cortical laminae. Using a statistical method that estimates the size and spacing of NFT clusters along the cortex parallel to the pia mater, two hypotheses were tested: 1) that the cluster size and distribution of the NFT in gyri of the temporal lobe reflect degeneration of the feedforward (FF) and feedback (FB) cortico-cortical pathways, and 2) that there is a spatial relationship between the clusters of NFT in the upper and lower laminae. In 16 temporal lobe gyri from 10 cases of sporadic AD, NFT were present in both the upper and lower laminae in 11/16 (69%) gyri and in either the upper or lower laminae in 5/16 (31%) gyri. Clustering of the NFT was observed in all gyri. A significant peak-to-peak distance was observed in the upper laminae in 13/15 (87%) gyri and in the lower laminae in 8/ 12 (67%) gyri, suggesting a regularly repeating pattern of NFT clusters along the cortex. The regularly distributed clusters of NFT were between 500 and 800 μm in size, the estimated size of the cells of origin of the FF and FB cortico-cortical projections, in the upper laminae of 6/13 (46%) gyri and in the lower laminae of 2/8 (25%) gyri. Clusters of NFT in the upper laminae were spatially correlated (in phase) with those in the lower laminae in 5/16 (31%) gyri. The clustering patterns of the NFT are consistent with their formation in relation to the FF and FB cortico-cortical pathways. In most gyri, NFT clusters appeared to develop independently in the upper and lower laminae.

Elasto-plastic impact of fine particles and fragmentation of small agglomerates

Surface deposition of dense aerosol particles is of major concern in the nuclear industry for safety assessment. This study presents theoretical investigations and computer simulations of single gas-born U3O8 particles impacting with the in-reactor surface and the fragmentation of small agglomerates. A theoretical model for elasto-plastic spheres has been developed and used to analyse the force-displacement and force-time relationships. The impulse equations, based on Newton's second law, are applied to govern the tangential bouncing behaviour. The theoretical model is then incorporated into the Distinct Element Method code TRUBAL in order to perform computer simulated tests of particle collisions. A comparison of simulated results with both theoretical predictions and experimental measurements is provided. For oblique impacts, the results in terms of the force-displacement relationship, coefficients of restitution, trajectory of the impacting particle, and distribution of kinetic energy and work done during the process of impact are presented. The effects of Poisson's ratio, friction, plastic deformation and initial particle rotation on the bouncing behaviour are also discussed. In the presence of adhesion an elasto-plastic collision model, which is an extension to the JKR theory, is developed. Based on an energy balance equation the critical sticking velocity is obtained. For oblique collisions computer simulated results are used to establish a set of criteria determining whether or not the particle bounces off the target plate. For impact velocities above the critical sticking value, computer simulated results for the coefficients of restitution and rebound angles of the particle are presented. Computer simulations of fracture/fragmentation resulting from agglomerate-wall impact have also been performed, where two randomly generated agglomerates (one monodisperse, the other polydisperse), each consisting of 50 primary particles are used. The effects of impact angle, local structural arrangements close to the impact point, and plastic deformation at the contacts on agglomerate damage are examined. The simulated results show a significant difference in agglomerate strength between the two assemblies. The computer data also shows that agglomerate damage resulting from an oblique impact is determined by the normal velocity component rather than the impact speed.

Ecological studies on:(a) the use of colonisation samplers in relation to biological surveillance of river water quality (b) the requirements of freshwater gastropoda

Some of the factors affecting colonisation of a colonisation sampler, the Standard Aufwuchs Unit (S. Auf. U.) were investigated, namely immersion period, whether anchored on the bottom or suspended, and the influence of riffles. It was concluded that a four-week immersion period was best. S. Auf. U. anchored on the bottom collected both more taxa and individuals than suspended ones. Fewer taxa but more individuals colonised S. Auf. U. in the potamon zone compared to the rhithron zone with a consequent reduction in the values of pollution indexes and diversity. It was concluded that a completely different scoring system was necessary for lowland rivers. Macroinvertebrates colonising S. Auf. U. in simulated streams, lowland rivers and the R. Churnet reflected water quality. A variety of pollution and diversity indexes were applied to results from lowland river sites. Instead of these, it was recommended that an abbreviated species - relative abundance list be used to summarise biological data for use in lowland river surveillance. An intensive study of gastropod populations was made in simulated streams. Lynnaea peregra increased in abundance whereas Potamopyrgas jenkinsi decreased with increasing sewage effluent concentration. No clear-cut differences in reproduction were observed. The presence/absence of eight gastropod taxa was compared with concentrations of various pollutants in lowland rivers. On the basis of all field work it appeared that ammonia, nitrite, copper and zinc were the toxicants most likely to be detrimental to gastropods and that P. jenkinsi and Theodoxus fluviatilis were the least tolerant taxa. 96h acute toxicity tests of P. jenkinsi using ammonia and copper were carried out in a flow-through system after a variety of static range finding tests. P. jenkinsi was intolerant to both toxicants compared to reports on other taxa and the results suggested that these toxicants would affect distribution of this species in the field.