Surfactant-free purification of membrane proteins with intact native membrane environment

In order to study the structure and function of a protein, it is generally required that the protein in question is purified away from all others. For soluble proteins, this process is greatly aided by the lack of any restriction on the free and independent diffusion of individual protein particles in three dimensions. This is not the case for membrane proteins, as the membrane itself forms a continuum that joins the proteins within the membrane with one another. It is therefore essential that the membrane is disrupted in order to allow separation and hence purification of membrane proteins. In the present review, we examine recent advances in the methods employed to separate membrane proteins before purification. These approaches move away from solubilization methods based on the use of small surfactants, which have been shown to suffer from significant practical problems. Instead, the present review focuses on methods that stem from the field of nanotechnology and use a range of reagents that fragment the membrane into nanometre-scale particles containing the protein complete with the local membrane environment. In particular, we examine a method employing the amphipathic polymer poly(styrene-co-maleic acid), which is able to reversibly encapsulate the membrane protein in a 10 nm disc-like structure ideally suited to purification and further biochemical study.

Issues in learning an ontology from text

Ontology construction for any domain is a labour intensive and complex process. Any methodology that can reduce the cost and increase efficiency has the potential to make a major impact in the life sciences. This paper describes an experiment in ontology construction from text for the animal behaviour domain. Our objective was to see how much could be done in a simple and relatively rapid manner using a corpus of journal papers. We used a sequence of pre-existing text processing steps, and here describe the different choices made to clean the input, to derive a set of terms and to structure those terms in a number of hierarchies. We describe some of the challenges, especially that of focusing the ontology appropriately given a starting point of a heterogeneous corpus. Results - Using mainly automated techniques, we were able to construct an 18055 term ontology-like structure with 73% recall of animal behaviour terms, but a precision of only 26%. We were able to clean unwanted terms from the nascent ontology using lexico-syntactic patterns that tested the validity of term inclusion within the ontology. We used the same technique to test for subsumption relationships between the remaining terms to add structure to the initially broad and shallow structure we generated. All outputs are available at http://thirlmere.aston.ac.uk/~kiffer/animalbehaviour/ webcite. Conclusion - We present a systematic method for the initial steps of ontology or structured vocabulary construction for scientific domains that requires limited human effort and can make a contribution both to ontology learning and maintenance. The method is useful both for the exploration of a scientific domain and as a stepping stone towards formally rigourous ontologies. The filtering of recognised terms from a heterogeneous corpus to focus upon those that are the topic of the ontology is identified to be one of the main challenges for research in ontology learning.

AFM and SPR studies of protein adsorption at solid/liquid interface

Membrane-like structure formed by surfactant molecules of didodecyldimethylammonium bromide (DDAB) on both HOPG and gold electrodes were studied with AFM and SPR techniques. The study shows that the thickness of the adsorbed layer of DDAB is strongly dependent on the concentration of the vesicle solution. We have also investigated the adsorption of redox protein, Cytochrome c, on graphite electrode with in situ tapping mode AFM. The protein adsorbs spontaneously onto the electrode covered with an adsorbed phosphate layer and forms a uniform monolayer. The adsorbed protein exhibits a reversible electron transfer at 0.17 V (Ag/AgCI) once the electrode potential has been increased to 0.75V. Using surface plasmon resonance spectroscopy we have measured subtle conformational change in protein, Cyt c, due to electron transfer of a single electron on MPA-coated gold electrode. The electron transfer induced change in the resonant angle is about 0.006 deg., which corresponds to ~ 0.2 A decreases in the thickness. This is consistent with that reduced state is more compact than the oxidized state.

Exploitation du potentiel sismique des étoiles naines blanches

Le but de cette thèse est d’explorer le potentiel sismique des étoiles naines blanches pulsantes, et en particulier celles à atmosphères riches en hydrogène, les étoiles ZZ Ceti. La technique d’astérosismologie exploite l’information contenue dans les modes normaux de vibration qui peuvent être excités lors de phases particulières de l’évolution d’une étoile. Ces modes modulent le flux émergent de l’étoile pulsante et se manifestent principalement en termes de variations lumineuses multi-périodiques. L’astérosismologie consiste donc à examiner la luminosité d’étoiles pulsantes en fonction du temps, afin d’en extraire les périodes, les amplitudes apparentes, ainsi que les phases relatives des modes de pulsation détectés, en utilisant des méthodes standards de traitement de signal, telles que des techniques de Fourier. L’étape suivante consiste à comparer les périodes de pulsation observées avec des périodes générées par un modèle stellaire en cherchant l’accord optimal avec un modèle physique reconstituant le plus fidèlement possible l’étoile pulsante. Afin d’assurer une recherche optimale dans l’espace des paramètres, il est nécessaire d’avoir de bons modèles physiques, un algorithme d’optimisation de comparaison de périodes efficace, et une puissance de calcul considérable. Les périodes des modes de pulsation de modèles stellaires de naines blanches peuvent être généralement calculées de manière précise et fiable sur la base de la théorie linéaire des pulsations stellaires dans sa version adiabatique. Afin de définir dans son ensemble un modèle statique de naine blanche propre à l’analyse astérosismologique, il est nécessaire de spécifier la gravité de surface, la température effective, ainsi que différents paramètres décrivant la disposition en couche de l’enveloppe. En utilisant parallèlement les informations obtenues de manière indépendante (température effective et gravité de surface) par la méthode spectroscopique, il devient possible de vérifier la validité de la solution obtenue et de restreindre de manière remarquable l’espace des paramètres. L’exercice astérosismologique, s’il est réussi, mène donc à la détermination précise des paramètres de la structure globale de l’étoile pulsante et fournit de l’information unique sur sa structure interne et l’état de sa phase évolutive. On présente dans cette thèse l’analyse complète réussie, de l’extraction des fréquences à la solution sismique, de quatre étoiles naines blanches pulsantes. Il a été possible de déterminer les paramètres structuraux de ces étoiles et de les comparer remarquablement à toutes les contraintes indépendantes disponibles dans la littérature, mais aussi d’inférer sur la dynamique interne et de reconstruire le profil de rotation interne. Dans un premier temps, on analyse le duo d’étoiles ZZ Ceti, GD 165 et Ross 548, afin de comprendre les différences entre leurs propriétés de pulsation, malgré le fait qu’elles soient des étoiles similaires en tout point, spectroscopiquement parlant. L’analyse sismique révèle des structures internes différentes, et dévoile la sensibilité de certains modes de pulsation à la composition interne du noyau de l’étoile. Afin de palier à cette sensibilité, nouvellement découverte, et de rivaliser avec les données de qualité exceptionnelle que nous fournissent les missions spatiales Kepler et Kepler2, on développe une nouvelle paramétrisation des profils chimiques dans le coeur, et on valide la robustesse de notre technique et de nos modèles par de nombreux tests. Avec en main la nouvelle paramétrisation du noyau, on décroche enfin le ”Saint Graal” de l’astérosismologie, en étant capable de reproduire pour la première fois les périodes observées à la précision des observations, dans le cas de l’étude sismique des étoiles KIC 08626021 et de GD 1212.

(Table 1) Radiocarbon ages of core AB01/94 obtained in the Tromper Wiek, western Baltic Sea

In the Tromper Wiek northeast of Rügen, acoustical investigations using Air Gun, Boomer, Chirp Sonar and Sediment-Echosounder were carried out. Together with sediment core information, it allowed the identification of five seismostratigraphic units (E1 to E5). Conventional and AMS-14C-datings supported their chronostratigraphical classification. The uppermost till (E1) was incised by late glacial channels filled with glaciolacustrine sediments (E2) of the early Baltic Ice Lake stages. These were regionally overlain with a sharp unconformity by a thick (locally >20 m) sedimentary complex (E3) of acoustically laminated silts of freshwater origin. This lower part of the E3-complex (E3a) is overlain by fluvial to coastal silty fine sands (E3b) deeper towards the Arkona Basin. Fine plant debris in the uppermost part of sub-unit E3a yielded ages of 10,100 and 10,500 14C-years B.P., representing the final phase of the Baltic Ice Lake. The fine sands of sub-unit E3b were deposited after the final drainage of the Baltic Ice Lake. In the shallower central part of the bay, the silts of sub-unit E3a were covered by a younger unit (E4) of fine sand with plant debris. A sedge peat occurring at the basis of unit E4 yielded an age of 9,590 14C-years B.P. The fine sands overlying the unit E3 in the central part of Tromper Wiek were deposited in the Ancylus Lake. Their position at about 20 m below present sea level (b.s.l.) reflects the maximum highstand in this area. The character and distribution of the Early Holocene deposits at greater depth suggest a lake water level at about 30 m b.s.l. after this highstand. Below 25 m b.s.l. muddy Littorina Sea sediments are observed. The thickness of these muds and sandy muds increases gradually towards the Arkona Basin. Locally, they are found in a channel-like structure immediately north of Jasmund.

Creating Structured PDF Files Using XML Templates

This paper describes a tool for recombining the logical structure from an XML document with the typeset appearance of the corresponding PDF document. The tool uses the XML representation as a template for the insertion of the logical structure into the existing PDF document, thereby creating a Structured/Tagged PDF. The addition of logical structure adds value to the PDF in three ways: the accessibility is improved (PDF screen readers for visually impaired users perform better), media options are enhanced (the ability to reflow PDF documents, using structure as a guide, makes PDF viable for use on hand-held devices) and the re-usability of the PDF documents benefits greatly from the presence of an XML-like structure tree to guide the process of text retrieval in reading order (e.g. when interfacing to XML applications and databases).

Gewebeansatz-Strukturen auf pyritisierten Steinkernen von Ammonoideen

3400 pyritized internal moulds of Upper Devonian, Triassic, Jurassic and Lower Cretaceous ammonoids show various soft tissue attachment structures. They are preserved as regularly distributed black patterns on the moulds. All structures can be interpreted as attachment areas of muscles, ligaments and intracameral membranes. Paired structures are developed along the umbilicus and on the flanks of the moulds, unpaired ones appear on the middle of their dorsal and ventral sides. Strong lateral muscles cause paired twin lines on the flanks of the phragmocone and of the body chamber. A ventral muscle is deduced from small rounded or crescent shaped spots in front of each septum on the ventral side. These spots are often connected, forming a band-like structure. Broad dark external bands on the ventral side of the phragmocone, ventral preseptal areas in the posterior part of the living chamber, small twin lines or oval shaped areas on the ventral side of the living chamber represent paired or unpaired attachment areas of the hyponome muscle. A middorsal muscle is documented by small roughened areas in front of each dorsal lobe. Dark spots along the umbilicus, often connected and thus forming a band-like structure (tracking band), are remains of a pair of small dorsolateral muscles at the posterior end of the soft body. Dark bands, lines and rows of small crescent shaped structures behind the tips of sutural lobes are due to spotlike fixation places of the posterior part of the mantle and their translocation before subsequent septal secretion. Devonian goniatites had a paired system of lateral and ventrolateral muscles preserved on the moulds as black or incised lines on the flanks of the living chamber and as dark preseptal areas, ventrally indented. These structures represent the attachment areas of paired lateral cephalic and paired ventral hyponome retractors. Fine black lines on the phragmocone situated parallel to the sutures (pseudosutures) represent a rhythmical secretion of camera! membranes during softbody translocation. Goniatites had a paired system of lateral and ventrolateral muscles, whilst Neoammonoids have a paired lateral and dorsolateral system, and, additionally, an unpaired system on the ventral and on the dorsal side. Mesoammonoids show only a paired lateral and an unpaired dorsal one. Fine black lines situated parallel to the saddles and behind the lobes of the suture line can be interpreted as structures left during softbody translocation and a temporary attachment of rhythmical secreted cameral membranes. Cameral membranes had supported the efficiency of the phragmocone. Only some of the observed structures are also present in recent Nautilus. Differences in the form and position of attachment sites between ammonoids and recent Nautilus indicate different soft body organizations between ammonoids and nautiloids. The attachment structures of goniatites especially of tornoceratids can be compared with those of Nautilus which indicates Richter - Gewebeansatz-Strukturen bei Ammonoideen 3 a comparable mode of life. Differences in the form and position of attachment structures between goniatites and ammonites may indicate an increasing differentiation of the muscular system in the phylogeny of this group. Different soft body organization may depend on shell morphology and on a different mode of life. On the modification or reduction of distinct muscle systems ammonoids can be assigned to different ecotypes. Based on shell morphology and the attachment areas of cephalic and hyponome retractor muscles two groups can be subdivided: - Depressed, evolute morphotypes with longidome body-chambers show only small ventral hyponome retractor muscles. Lateral cephalic retractors are not developed. These morphotypes are adapted to a demersal mode of life. Without strong cephalic retractor muscles no efficient jet propulsion can be produced. These groups represent vertical migrants with efficient phragmocone properties (multilobate sutures, cameral membranes, narrow septal spacing). - Compressed, involute moiphotypes with brevidome body-chambers show strong cephalic and hyponome retractor muscles and represent a group of active swimmers. These morphotypes were able to live at different depths, in the free water column or/and near the seafloor. They are not confined only to one habitat. Most of the examined genera and species belong to this group. Changes of the attachment structures in the course of ontogeny confirm that juveniles of Amaltheus and Quenstedtoceras lived as passive planche drifters in upper and intermediate parts of the free water column after hatching. At the end of the juvenile stage with a shell diameter of 0,3 - 0,5 cm cephalic retractor muscles developed. With the beginning of an active swimming mode of life (neanic stage) the subadult animals left the free water column and moved into shallow water habitats. Fuciniceras showed no marked changes in the attachment structures during ontogeny. This indicates that there occur no differences in the mode of life between juvenile and adult growth stages. Based on attachment structures and shell morphology of Devonian goniatites their relation to the systematic position permits statements about probable phylogenetic relationships between the Cheiloceratidae and Tornoceratidae. In some cases attachment structures of ammonites permit statements about phylogenetic relationships on family and genus level.

'An Artificial Immune System as a Recommender System for Web Sites'

Artificial Immune Systems have been used successfully to build recommender systems for film databases. In this research, an attempt is made to extend this idea to web site recommendation. A collection of more than 1000 individuals' web profiles (alternatively called preferences / favourites / bookmarks file) will be used. URLs will be classified using the DMOZ (Directory Mozilla) database of the Open Directory Project as our ontology. This will then be used as the data for the Artificial Immune Systems rather than the actual addresses. The first attempt will involve using a simple classification code number coupled with the number of pages within that classification code. However, this implementation does not make use of the hierarchical tree-like structure of DMOZ. Consideration will then be given to the construction of a similarity measure for web profiles that makes use of this hierarchical information to build a better-informed Artificial Immune System.

Étude de la réparation des lésions induites par les UVs dans les extrémités chromosomiques de la levure Saccharomyces cerevisiae

Résumé : Les télomères sont des structures nucléoprotéiques spécialisées qui assurent la stabilité du génome en protégeant les extrémités chromosomiques. Afin d’empêcher des activités indésirables, la réparation des dommages à l’ADN doit être convenablement régulée au niveau des télomères. Pourtant, il existe peu d’études de la réparation des dommages induits par les ultraviolets (UVs) dans un contexte télomérique. Le mécanisme de réparation par excision de nucléotides (NER pour « Nucleotide Excision Repair ») permet d’éliminer les photoproduits. La NER est un mécanisme très bien conservé de la levure à l’humain. Elle est divisée en deux sous voies : une réparation globale du génome (GG-NER) et une réparation couplée à la transcription (TC-NER) plus rapide et plus efficace. Dans notre modèle d’étude, la levure Saccharomyces cerevisiae, une forme compactée de la chromatine nommée plus fréquemment « hétérochromatine » a été décrite. Cette structure particulière est présente entre autres, au niveau des régions sous-télomériques des extrémités chromosomiques. La formation de cette chromatine particulière implique quatre protéines nommées Sir (« Silent Information Regulator »). Elle présente différentes marques épigénétiques dont l’effet est de réprimer la transcription. L’accès aux dommages par la machinerie de réparation est-il limité par cette chromatine compacte ? Nous avons donc étudié la réparation des lésions induites par les UVs dans différentes régions associées aux télomères, en absence ou en présence de protéines Sir. Nos données ont démontré une modulation de la NER par la chromatine, dépendante des nucléosomes stabilisés par les Sir, dans les régions sous-télomériques. La NER était moins efficace dans les extrémités chromosomiques que dans les régions plus proches du centromère. Cet effet était dépendant du complexe YKu de la coiffe télomérique, mais pas dépendant des protéines Sir. La transcription télomériques pourrait aider la réparation des photoproduits, par l’intermédiaire de la sous-voie de TC-NER, prévenant ainsi la formation de mutations dans les extrémités chromosomiques. Des ARN non codants nommés TERRA sont produits mais leur rôle n’est pas encore clair. Par nos analyses, nous avons confirmé que la transcription des TERRA faciliterait la NER dans les différentes régions sous-télomériques.

'An Artificial Immune System as a Recommender System for Web Sites'

Artificial Immune Systems have been used successfully to build recommender systems for film databases. In this research, an attempt is made to extend this idea to web site recommendation. A collection of more than 1000 individuals' web profiles (alternatively called preferences / favourites / bookmarks file) will be used. URLs will be classified using the DMOZ (Directory Mozilla) database of the Open Directory Project as our ontology. This will then be used as the data for the Artificial Immune Systems rather than the actual addresses. The first attempt will involve using a simple classification code number coupled with the number of pages within that classification code. However, this implementation does not make use of the hierarchical tree-like structure of DMOZ. Consideration will then be given to the construction of a similarity measure for web profiles that makes use of this hierarchical information to build a better-informed Artificial Immune System.

Exploitation du potentiel sismique des étoiles naines blanches

Le but de cette thèse est d’explorer le potentiel sismique des étoiles naines blanches pulsantes, et en particulier celles à atmosphères riches en hydrogène, les étoiles ZZ Ceti. La technique d’astérosismologie exploite l’information contenue dans les modes normaux de vibration qui peuvent être excités lors de phases particulières de l’évolution d’une étoile. Ces modes modulent le flux émergent de l’étoile pulsante et se manifestent principalement en termes de variations lumineuses multi-périodiques. L’astérosismologie consiste donc à examiner la luminosité d’étoiles pulsantes en fonction du temps, afin d’en extraire les périodes, les amplitudes apparentes, ainsi que les phases relatives des modes de pulsation détectés, en utilisant des méthodes standards de traitement de signal, telles que des techniques de Fourier. L’étape suivante consiste à comparer les périodes de pulsation observées avec des périodes générées par un modèle stellaire en cherchant l’accord optimal avec un modèle physique reconstituant le plus fidèlement possible l’étoile pulsante. Afin d’assurer une recherche optimale dans l’espace des paramètres, il est nécessaire d’avoir de bons modèles physiques, un algorithme d’optimisation de comparaison de périodes efficace, et une puissance de calcul considérable. Les périodes des modes de pulsation de modèles stellaires de naines blanches peuvent être généralement calculées de manière précise et fiable sur la base de la théorie linéaire des pulsations stellaires dans sa version adiabatique. Afin de définir dans son ensemble un modèle statique de naine blanche propre à l’analyse astérosismologique, il est nécessaire de spécifier la gravité de surface, la température effective, ainsi que différents paramètres décrivant la disposition en couche de l’enveloppe. En utilisant parallèlement les informations obtenues de manière indépendante (température effective et gravité de surface) par la méthode spectroscopique, il devient possible de vérifier la validité de la solution obtenue et de restreindre de manière remarquable l’espace des paramètres. L’exercice astérosismologique, s’il est réussi, mène donc à la détermination précise des paramètres de la structure globale de l’étoile pulsante et fournit de l’information unique sur sa structure interne et l’état de sa phase évolutive. On présente dans cette thèse l’analyse complète réussie, de l’extraction des fréquences à la solution sismique, de quatre étoiles naines blanches pulsantes. Il a été possible de déterminer les paramètres structuraux de ces étoiles et de les comparer remarquablement à toutes les contraintes indépendantes disponibles dans la littérature, mais aussi d’inférer sur la dynamique interne et de reconstruire le profil de rotation interne. Dans un premier temps, on analyse le duo d’étoiles ZZ Ceti, GD 165 et Ross 548, afin de comprendre les différences entre leurs propriétés de pulsation, malgré le fait qu’elles soient des étoiles similaires en tout point, spectroscopiquement parlant. L’analyse sismique révèle des structures internes différentes, et dévoile la sensibilité de certains modes de pulsation à la composition interne du noyau de l’étoile. Afin de palier à cette sensibilité, nouvellement découverte, et de rivaliser avec les données de qualité exceptionnelle que nous fournissent les missions spatiales Kepler et Kepler2, on développe une nouvelle paramétrisation des profils chimiques dans le coeur, et on valide la robustesse de notre technique et de nos modèles par de nombreux tests. Avec en main la nouvelle paramétrisation du noyau, on décroche enfin le ”Saint Graal” de l’astérosismologie, en étant capable de reproduire pour la première fois les périodes observées à la précision des observations, dans le cas de l’étude sismique des étoiles KIC 08626021 et de GD 1212.

Anatomical, histochemical and immunohistochemical characterization of the outflow tract of ray hearts (Rajiformes; Chondrichthyes)

Recent work has shown that the cardiac outflow tract of sharks and chimaeras does not consist of a single myocardial component, the conus arteriosus, as classically accepted, but two, namely, the myocardial conus arteriosus and the non-myocardial bulbus arteriosus. However, the anatomical composition of the outflow tract of the batoid hearts remains unknown. The present study was designed to fill this gap. The material examined consisted of hearts of two species of rays, namely, the Mediterranean starry ray (Raja asterias) and sandy ray (Leucoraja circularis). They were studied using scanning electron microscopy, and histochemical and inmunohistochemical techniques. In both species, the outflow tract consists of two components, proximal and distal with regard to the ventricle. The proximal component is the conus arteriosus; it is characterized by the presence of compact myocardium in its wall and several transverse rows of pocket-shaped valves at its luminal side. Each valve consists of a leaflet and its supporting sinus. Histologically, the leaflet has two fibrosas, inner and outer, and a middle coat, the spongiosa. The distal component lacks myocardium. Its wall consists of smooth muscle cells, elastic fibers and collagen. Thus, it shows an arterial-like structure. However, it differs from the aorta because it is covered by the epicardium and crossed by coronary arteries. These findings indicate that the distal component is morphologically equivalent to the bulbus arteriosus of sharks and chimaeras. In contrast to foregoing descriptions, the valves of the first transverse row are distally anchored to the bulbus arteriosus and not to the ventral aorta. Our findings give added support to the notion that presence of a bulbus arteriosus at the arterial pole of the heart is common to all chondrichtyans, and not an apomorphy of actinopterygians as classically thought.

Produção de fibras de alumina biomórfica a partir do sisal

Sisal is a renewable agricultural resource adapted to the hostile climatic and soil conditions particularly encountered in the semi-arid areas of the state of Rio Grande do Norte. Consequently, sisal has played a strategic role in the economy of the region, as one of few options of income available in the semi-arid. Find new options and adding value to products manufactured from sisal are goals that contribute not only to the scientific and technological development of the Northeastern region, but also to the increase of the family income for people that live in the semi-arid areas where sisal is grown. Lignocellulosic fibers are extracted from sisal and commonly used to produce both handcrafted and industrial goods including ropes, mats and carpets. Alternatively, addedvalue products can be made using sisal to produce alumina fibers (Al2O3) by biotemplating, which consists in the reproduction of the natural fiber-like structure of the starting material. The objective of this study was to evaluate the conditions necessary to convert sisal into alumina fibers by biotemplating. Alumina fibers were obtaining after pretreating sisal fibers and infiltrating them with a Al2Cl6 saturated solution, alumina sol from aluminum isopropoxide or aluminum gas. Heat-treating temperatures varied from 1200 ºC to 1650 °C. The resulting fibers were then characterized by X-ray diffraction and scanning electronic microscopy. Fibers obtained by liquid infiltration revealed conversion only of the surface of the fiber into α-Al2O3, which yielded limited resistance to handling. Gas infiltration resulted in stronger fibers with better reproduction of the inner structure of the original fiber. All converted fibers consisted of 100% α-Al2O3 suggesting a wide range of technological applications especially those that require thermal isolation

ArmA methyltransferase in a monophasic Salmonella enterica isolate from food

The 16S rRNA methyltransferase ArmA is a worldwide emerging determinant that confers high-level resistance to most clinically relevant aminoglycosides. We report here the identification and characterization of a multidrug-resistant Salmonella enterica subspecies I.4,12:i:- isolate recovered from chicken meat sampled in a supermarket on February 2009 in La Reunion, a French island in the Indian Ocean. Susceptibility testing showed an unusually high-level resistance to gentamicin, as well as to ampicillin, expanded-spectrum cephalosporins and amoxicillin-clavulanate. Molecular analysis of the 16S rRNA methyltransferases revealed presence of the armA gene, together with bla(TEM-1), bla(CMY-2), and bla(CTX-M-3). All of these genes could be transferred en bloc through conjugation into Escherichia coli at a frequency of 10(-5) CFU/donor. Replicon typing and S1 pulsed-field gel electrophoresis revealed that the armA gene was borne on an ~150-kb broad-host-range IncP plasmid, pB1010. To elucidate how armA had integrated in pB1010, a PCR mapping strategy was developed for Tn1548, the genetic platform for armA. The gene was embedded in a Tn1548-like structure, albeit with a deletion of the macrolide resistance genes, and an IS26 was inserted within the mel gene. To our knowledge, this is the first report of ArmA methyltransferase in food, showing a novel route of transmission for this resistance determinant. Further surveillance in food-borne bacteria will be crucial to determine the role of food in the spread of 16S rRNA methyltransferase genes worldwide.

New prophylactic and therapeutic treatments to combat pathogenic Enterohaemorrhagic Escherichia coli

Bacterial diarrhoeal diseases have significant influence on global human health, and are a leading cause of preventable death in the developing world. Enterohaemorrhagic Escherichia coli (EHEC), pathogenic strains of E. coli that carry potent toxins, have been associated with a high number of large-scale outbreaks caused by contaminated food and water sources. This pathotype produces diarrhoea and haemorrhagic colitis in infected humans, and in some patients leads to the development of haemolytic uremic syndrome (HUS), which can result in mortality and chronic kidney disease. A major obstacle to the treatment of EHEC infections is the increased risk of HUS development that is associated with antibiotic treatment, and rehydration and renal support are often the only options available. New treatments designed to prevent or clear E. coli infections and reduce symptoms of illness would therefore have large public health and economic impacts. The three main aims of this thesis were: to explore mouse models for pre-clinical evaluation in vivo of small compounds that inhibit a major EHEC colonisation factor, to assess the production and role of two proteins considered promising candidates for a broad-spectrum vaccine against pathogenic E. coli, and to investigate a novel compound that has recently been identified as a potential inhibitor of EHEC toxin production. As EHEC cannot be safely tested in humans due to the risk of HUS development, appropriate small animal models are required for in vivo testing of new drugs. A number of different mouse models have been developed to replicate different features of EHEC pathogenesis, several of which we investigated with a focus on colonisation mediated by the Type III Secretion System (T3SS), a needle-like structure that translocates bacterial proteins into host cells, resulting in a tight, intimate attachment between pathogen and host, aiding colonisation of the gastrointestinal tract. As E. coli models were found not to depend significantly on the T3SS for colonisation, the Citrobacter rodentium model, a natural mouse pathogen closely related to E. coli, was deemed the most suitable mouse model currently available for in vivo testing of T3SS-targeting compounds. Two bacterial proteins, EaeH (an outer membrane adhesin) and YghJ (a putative secreted lipoprotein), highly conserved surface-associated proteins recently identified as III protective antigens against E. coli infection of mice, were explored in order to determine their suitability as candidates for a human vaccine against pathogenic E. coli. We focused on the expression and function of these proteins in the EHEC O157:H7 EDL933 strain and the adherent-invasive E. coli (AIEC) LF82 strain. Although expression of EaeH by other E. coli pathotypes has recently been shown to be upregulated upon contact with host intestinal cells, no evidence of this upregulation could be demonstrated in our strains. Additionally, while YghJ was produced by the AIEC strain, it was not secreted by bacteria under conditions that other YghJ-expressing E. coli pathotypes do, despite the AIEC strain carrying all the genes required to encode the secretion system it is associated with. While our findings indicate that a vaccine that raises antibodies against EaeH and YghJ may have limited effect on the EHEC and AIEC strains we used, recent studies into these proteins in different E. coli pathogens have suggested they are still excellent candidates for a broadly effective vaccine against E. coli. Finally, we characterised a small lead compound, identified by high-throughput screening as a possible inhibitor of Shiga toxin expression. Shiga toxin production causes both the symptoms of illness and development of HUS, and thus reduction of toxin production, release, or binding to host receptors could therefore be an effective way to treat infections and decrease the risk of HUS. Inhibition of Shiga toxin production by this compound was confirmed, and was shown to be caused by an inhibitory effect on activation of the bacterial SOS response rather than on the Shiga toxin genes themselves. The bacterial target of this compound was identified as RecA, a major regulator of the SOS response, and we hypothesise that the compound binds covalently to its target, preventing oligomerisation of RecA into an activated filament. Altogether, the results presented here provide an improved understanding of these different approaches to combating EHEC infection, which will aid the development of safe and effective vaccines and anti-virulence treatments against EHEC.