Studies presented in this thesis looked at developing new methods for the diagnosis of virulent footrot (VFR) in sheep and identification of serogroups of Dichelobacter nodosus, the principal causative agent of footrot. Earlier studies had shown that immunological memory response in sheep recovered from VFR can be aroused by natural or recurrent infection or by injection of outer membrane protein (OMP) antigens to be used as a retrospective diagnostic test for VFR. But OMP antigen was found to be non-specific in older animals. To overcome this non-specificity of OMP antigen in anamnestic response, pilus antigen was evaluated in a trial at Camden. The results of this trial indicated that antibodies to pilus antigen can be detected over time in a manner similar to OMP antibodies so a retrospective assessment of VFR status can be made by anamnestic test with pilus antigens. The anamnestic response to pilus was similar in character to OMP antigen but unlike OMP was highly specific. The response to anamnestic challenge with pilus was determined by severity of the lesions they had expressed, with severe lesions triggering the greater responses. However, there was variation between individuals, with some (6 of 46 with severe lesions) failing to respond. This individual variation is probably mediated genetically as is response to vaccination. This anamnestic test was tested in flocks of sheep in Nepal that had a history of VFR which had apparently been eradicated. That assessment, based on clinical findings, was confirmed by the uniformly negative results in the pilus anamnestic test applied to a representative sample of the population. This allowed a conclusion that the virulent strains of D. nodosus involved had been eliminated from these flocks. As mentioned in the preceding study pilus antigen was found to be very specific and ideal for retrospective diagnosis of virulent footrot with an anamnestic challenge ELISA test. However, serogroup specificity was seen as a disadvantage of using pilus antigen for the anamnestic test. The possibility of using multivalent pilus antigens was tested in another trial. These animals had been involved in a clinical expression experiment conducted by another research group and had a clinical and bacteriological history extending over more than 12 months. After these initial trials all these animals were treated for footrot and managed for 5 months as a single flock at Camden. These were then challenged with multivalent pilus antigen (serogroup A - I) as a single injection. The results obtained indicate that multivalent pilus anamnestic ELISA is equally effective as monovalent pilus. This has the added advantage that prior knowledge of the serogroups present in the flock is not required. It has the possibility of being used as an indirect test to check the presence of serogroups in a flock without doing the bacterial cultures. This test can identify most animals with pre-existing underrunning lesions (Scores of 3 or higher). However, the sensitivity and specificity of this test need to be tested extensively in flocks of known clinical history before it could be adopted as a routine test. As a key component of a larger study to determine the role of fimbrial genes (fimA and fimB) of D. nodosus in the pathogenesis of footrot using allelic exchange to disrupt these genes of a strain (serogroup G), the study presented in this thesis contributed a detailed characterisation of the resultant mutant and the wild strains and tested these strains for virulence in sheep. The results presented provided the first definitive evidence that the fimA gene is essential for virulence of D.nodosus in sheep. In vivo virulence testing of two fimA mutants showed that they were not able to establish any footrot whereas the wild type of the same strain produced virulent footrot in the same trial conducted under similar conditions. These mutant bacteria were not re-isolated from interdigital skin after in vivo challenge. This indicated that fimA mutant strains could not colonise the ovine foot, and the simplest and most likely explanation for these results was that colonisation of the interdigital skin and subsequent penetration of the stratum corneum requires the adhesive activity of type IV fimbriae. However, since these mutants also had altered ability to secrete extracellular proteases, and perhaps other as yet unknown extracellular proteins, the possibility of the involvement of these factors as major determinants of host colonisation or invasion cannot be excluded. Current methods for the identification of the serogroup of D. nodosus present in the bacterial population requires isolation of the organism and after purification by subculture, antigenic analysis with agglutination tests. This usually takes at least 3 to 4 weeks. With the objective of developing a rapid serogroup specific PCR assay, the basis of serogroup variation in D. nodosus localised in the fimbrial gene region was exploited. A common forward primer and 9 serogroup specific reverse primers were selected from the fimbrial gene sequences of the prototype strains. Analytical sensitivity of the serogroup specific primers on chromosomal DNA was similar to PCR tests in other bacterial species reported before. Immuno-magnetic bead capture PCR method was able to detect 5 to 10 cells in cell lysates. Specificity within and between the serogroups of D. nodosus was tested with all the prototype strains. They were found to be very specific to each serogroup and specific only to D. nodosus when tested with 84 commonly found bacterial strains or strains related to D. nodosus. To overcome the time delay in conducting 9 different amplifications to find out the prevalence of all possible serogroups in a flock multiplex PCR reactions with common forward primer and groups of 3, 4 and 5 reverse primers were successful in reducing the number of reactions to 2 (with groups of 4 and 5) or 3 (with groups of 3) primers. A drawback of the multiplex reaction was that if a template was 1000 times less concentrated that the others in the mixture it was not amplified but the margin for difference is very high. The main aim of developing rapid serogroup specific PCR was to apply these tests directly on footrot lesion samples to make it a rapid diagnostic test for field samples. The sensitivity of the test on lesion samples was found to be very low. To try and improve the sensitivity an overnight or four days old pre-enrichment culture in broth was tested but was found to be no better than direct PCR. The immuno-magnetic capture method which improved the sensitivity of pure culture samples by 10 -100 fold also had very low sensitivity with lesion samples. However, this drawback can be overcome by picking up colonies from 4 days old lesion cultures on hoof agar (HA) plates for serogroup specific multiplex PCR. If the colonies are too small/ too few on the lesion cultures these can be sub cultured onto a quarter of 4 percent HA plates and then used for the PCR test which also reduces the time taken for serogrouping at least by 2 weeks. The other advantage is that individual colonies do not need to be isolated. A PCR test can be done on pooled colonies just as well and can be used to identify all serogroups present in the sample. Serogroup specific PCR is much faster and is more sensitive and accurate than slide agglutination tests which take 3 to 4 weeks to complete. Multiplex PCR makes it easier to detect different serogroups in a sample with a maximum of 3 PCR tests. Serogroup specific multiplex PCR will be a useful tool for footrot control based on specific vaccination. The difficulty in using the test on direct lesion swabs needs to be further looked into. There may be future advances in the application of PCR tests to clinical samples.

Studies presented in this thesis looked at developing new methods for the diagnosis of virulent footrot (VFR) in sheep and identification of serogroups of Dichelobacter nodosus, the principal causative agent of footrot. Earlier studies had shown that immunological memory response in sheep recovered from VFR can be aroused by natural or recurrent infection or by injection of outer membrane protein (OMP) antigens to be used as a retrospective diagnostic test for VFR. But OMP antigen was found to be non-specific in older animals. To overcome this non-specificity of OMP antigen in anamnestic response, pilus antigen was evaluated in a trial at Camden. The results of this trial indicated that antibodies to pilus antigen can be detected over time in a manner similar to OMP antibodies so a retrospective assessment of VFR status can be made by anamnestic test with pilus antigens. The anamnestic response to pilus was similar in character to OMP antigen but unlike OMP was highly specific. The response to anamnestic challenge with pilus was determined by severity of the lesions they had expressed, with severe lesions triggering the greater responses. However, there was variation between individuals, with some (6 of 46 with severe lesions) failing to respond. This individual variation is probably mediated genetically as is response to vaccination. This anamnestic test was tested in flocks of sheep in Nepal that had a history of VFR which had apparently been eradicated. That assessment, based on clinical findings, was confirmed by the uniformly negative results in the pilus anamnestic test applied to a representative sample of the population. This allowed a conclusion that the virulent strains of D. nodosus involved had been eliminated from these flocks. As mentioned in the preceding study pilus antigen was found to be very specific and ideal for retrospective diagnosis of virulent footrot with an anamnestic challenge ELISA test. However, serogroup specificity was seen as a disadvantage of using pilus antigen for the anamnestic test. The possibility of using multivalent pilus antigens was tested in another trial. These animals had been involved in a clinical expression experiment conducted by another research group and had a clinical and bacteriological history extending over more than 12 months. After these initial trials all these animals were treated for footrot and managed for 5 months as a single flock at Camden. These were then challenged with multivalent pilus antigen (serogroup A - I) as a single injection. The results obtained indicate that multivalent pilus anamnestic ELISA is equally effective as monovalent pilus. This has the added advantage that prior knowledge of the serogroups present in the flock is not required. It has the possibility of being used as an indirect test to check the presence of serogroups in a flock without doing the bacterial cultures. This test can identify most animals with pre-existing underrunning lesions (Scores of 3 or higher). However, the sensitivity and specificity of this test need to be tested extensively in flocks of known clinical history before it could be adopted as a routine test. As a key component of a larger study to determine the role of fimbrial genes (fimA and fimB) of D. nodosus in the pathogenesis of footrot using allelic exchange to disrupt these genes of a strain (serogroup G), the study presented in this thesis contributed a detailed characterisation of the resultant mutant and the wild strains and tested these strains for virulence in sheep. The results presented provided the first definitive evidence that the fimA gene is essential for virulence of D.nodosus in sheep. In vivo virulence testing of two fimA mutants showed that they were not able to establish any footrot whereas the wild type of the same strain produced virulent footrot in the same trial conducted under similar conditions. These mutant bacteria were not re-isolated from interdigital skin after in vivo challenge. This indicated that fimA mutant strains could not colonise the ovine foot, and the simplest and most likely explanation for these results was that colonisation of the interdigital skin and subsequent penetration of the stratum corneum requires the adhesive activity of type IV fimbriae. However, since these mutants also had altered ability to secrete extracellular proteases, and perhaps other as yet unknown extracellular proteins, the possibility of the involvement of these factors as major determinants of host colonisation or invasion cannot be excluded. Current methods for the identification of the serogroup of D. nodosus present in the bacterial population requires isolation of the organism and after purification by subculture, antigenic analysis with agglutination tests. This usually takes at least 3 to 4 weeks. With the objective of developing a rapid serogroup specific PCR assay, the basis of serogroup variation in D. nodosus localised in the fimbrial gene region was exploited. A common forward primer and 9 serogroup specific reverse primers were selected from the fimbrial gene sequences of the prototype strains. Analytical sensitivity of the serogroup specific primers on chromosomal DNA was similar to PCR tests in other bacterial species reported before. Immuno-magnetic bead capture PCR method was able to detect 5 to 10 cells in cell lysates. Specificity within and between the serogroups of D. nodosus was tested with all the prototype strains. They were found to be very specific to each serogroup and specific only to D. nodosus when tested with 84 commonly found bacterial strains or strains related to D. nodosus. To overcome the time delay in conducting 9 different amplifications to find out the prevalence of all possible serogroups in a flock multiplex PCR reactions with common forward primer and groups of 3, 4 and 5 reverse primers were successful in reducing the number of reactions to 2 (with groups of 4 and 5) or 3 (with groups of 3) primers. A drawback of the multiplex reaction was that if a template was 1000 times less concentrated that the others in the mixture it was not amplified but the margin for difference is very high. The main aim of developing rapid serogroup specific PCR was to apply these tests directly on footrot lesion samples to make it a rapid diagnostic test for field samples. The sensitivity of the test on lesion samples was found to be very low. To try and improve the sensitivity an overnight or four days old pre-enrichment culture in broth was tested but was found to be no better than direct PCR. The immuno-magnetic capture method which improved the sensitivity of pure culture samples by 10 -100 fold also had very low sensitivity with lesion samples. However, this drawback can be overcome by picking up colonies from 4 days old lesion cultures on hoof agar (HA) plates for serogroup specific multiplex PCR. If the colonies are too small/ too few on the lesion cultures these can be sub cultured onto a quarter of 4 percent HA plates and then used for the PCR test which also reduces the time taken for serogrouping at least by 2 weeks. The other advantage is that individual colonies do not need to be isolated. A PCR test can be done on pooled colonies just as well and can be used to identify all serogroups present in the sample. Serogroup specific PCR is much faster and is more sensitive and accurate than slide agglutination tests which take 3 to 4 weeks to complete. Multiplex PCR makes it easier to detect different serogroups in a sample with a maximum of 3 PCR tests. Serogroup specific multiplex PCR will be a useful tool for footrot control based on specific vaccination. The difficulty in using the test on direct lesion swabs needs to be further looked into. There may be future advances in the application of PCR tests to clinical samples.

Orientador: Alessandra Alves de Souza / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-12T18:36:53Z (GMT). No. of bitstreams: 1 Caserta_Raquel_M.pdf: 8932792 bytes, checksum: 642a7e654340f17e79b37b6fa4a560cc (MD5) Previous issue date: 2008 / Resumo: É inquestionável a importância da participação da citricultura na economia brasileira. O Brasil é o maior exportador de suco concentrado do mundo. Em 2007 as exportações brasileiras quase alcançaram 400 milhões de caixas de laranja, retrato de uma cultura que gera uma diversidade enorme de empregos diretos e indiretos, movimentando também a indústria de insumos. O estado de São Paulo tem maior destaque nessa produção e no final dos anos 80 foi severamente prejudicado pela Clorose Variegada dos Citros (CVC), uma doença que acarreta danos da ordem de milhões de dólares por diminuir o tamanho dos frutos e, por conseqüência, a quantidade de suco produzido. Foi comprovado que a bactéria causadora da CVC é a Xylella fastidiosa, um fitopatógeno de crescimento limitado ao xilema. Devido a importância da citricultura para o estado de São Paulo, a X. fastidiosa teve seu genoma completo seqüenciado e foram encontrados diversos genes relacionados a adesão, muitos deles similares a patógenos de humanos e animais. Isso sugeriu que a adesão e a formação do biofilme fossem fatores essenciais para a sobrevivência da bactéria na planta. Essa hipótese é reforçada pelo fato de plantas sintomáticas apresentarem colônias de bactérias aderidas nas paredes dos vasos do xilema. Trabalhos posteriores comprovaram que sua colonização se dá pela formação de um biofilme que ocasiona o bloqueio dos vasos, dificultando a eficiência do transporte de água e seiva pela planta. Nesse contexto, o estudo da participação de proteínas de adesão, sejam elas fimbriais ou afimbriais, é fundamental para o entendimento da formação e estrutura do biofilme. Por apresentarem funções distintas, adesinas fimbriais e afimbriais são expressas em momentos diferentes durante a formação do biofilme. Diante do exposto acima, o objetivo desse trabalho foi monitorar a expressão de duas adesinas fimbriais e duas adesinas afimbriais de X. fastidiosa envolvidas com a formação do biofilme in vitro. Para tal, foram realizados Western blot e microscopia de fluorescência utilizando anticorpos desenvolvidos contra as proteínas alvo. Os resultados revelaram que adesinas fimbriais se expressam preferencialmente nas fases iniciais do bioflme, enquanto que adesinas afimbriais estão expressas nas fases mais tardias, quando o biofilme já apresenta traços de agregação celular. Esse padrão de expressão sugere que a adesão inicial da bactéria ao substrato seja mediada por proteínas fimbriais e a adesão célula a célula seja função de proteínas afimbriais. Além disso, uma maior ou menor quantidade de cada proteína se encontra expressa em todas as fases o biofilme, sugerindo haver uma regulação de expressão que resulta em interação biológica entre elas, a fim de manter a estabilidade e estruturação do biofilme. Com o objetivo de monitorar a expressão dessas adesinas in vivo, foram analisadas também secções ultrafinas de pecíolos de vinca, hibisco e citros infectados e apresentando sintomas da doença. Em todas as análises foi possível detectar a presença das proteínas alvo, comprovando que elas são necessárias para o processo de infecção da planta pela bactéria. Os resultados aqui apresentados demonstram que proteínas fimbriais e afimbriais, assim como em patógenos de humanos, são necessárias para a formação do biofilme de X. fastidiosa. Este é o único fitopatógeno cujo mecanismo de patogenicidade é a formação de um biofilme. Neste sentido, os resultados aqui apresentados são importantes no auxílio de possíveis controles de doenças formadas por biofilmes, uma vez que o tempo de expressão de cada adesina foi determinado, elas poderiam ser neutralizadas antes de desempenharem suas funções, quebrando a estabilidade do biofilme através da interrupção da interação entre as proteínas / Abstract: The importance of citriculture in Brazilian's economy is unquestionable. Brazil is the major exporter of concentrate juice in the world. In 2007, Brazilian exportations of orange almost reached 400 million boxes, reflecting the importance of a product that generates an enormous diversity of direct and indirect jobs, even helping the insums industry. In Brazil, São Paulo state has a great prominence in orange production. In the 80's, the citrus fields were severely harmed by Citrus Variegated Chlorosis (CVC), a disease that causes losses of million dollars since it affects the fruit size and, consequently, juice production. It was proved that the Xylella fastidiosa, a phytopathogen that grows limited to the xylem vessels, is the causal agent of CVC. Due to the importance of citriculture in the São Paulo state, the genome of X. fastidiosa was sequenced and there were found many genes related to adhesion, some of them similar to human and animal pathogens. This fact suggested that adhesion and biofilm formation were essential for the survey of the bacteria within the plant. This hypothesis is supported by the fact that symptomatic plants have colonies of bacteria adhered to the walls in xylem vessels. Subsequent works demonstrated that the colonization occurs through the formation of a biofilm that blocks the vessels, reducing the efficiency of water and sap transportation. In this context, the study of the role of the fimbrial or afimbrial adhesion proteins is fundamental to the elucidation of the biofilm structure and formation. These adhesins show different functions, and because of that they are not expressed at the same time during biofilm formation. In face of what was shown above, the aim of this work was to monitor the expression of two fimbrial and two non fimbrial adhesins involved in biofilm formation in vitro. Western blot and fluorescence microscopy using polyclonal antibodies developed against the target proteins were performed, and the results revealed that fimbrial adhesins are expressed preferentially at the initial phases of biofilm formation, while non fimbrial adhesins are expressed at the late phases, when the biofilm already presents cellular aggregation traits. This expression pattern suggests that the initial adhesion of the bacteria to the substrate is mediated by fimbrial adhesins and that the function of cell to cell adhesion is performed by non fimbrial adhesins. Besides, each protein studied is found more or less to be expressed during all stages of biofilm development, suggesting the existence of a regulatory mechanism that results in a biological interaction between these proteins, in order to keep the stability and structure of the biofilm. In order to accompany the expression of these adhesins in vivo, ultra thin sections of petioles of periwinkle, hibiscus and citrus infected by X. fastidiosa and presenting symptoms were prepared. All the sections showed the presence of the target proteins, suggesting that they are necessary to the infectious process of the plants. The results demonstrated that fimbrial and non fimbrial proteins, as well as in human pathogens, are necessary for the biofilm formation by X. fastidiosa. This is the only phytopathogen which requires the formation of a biofilm to cause the disease. In this way, the results obtained in this work may contribute with the development of possible approaches to control diseases caused by biofilm formation, once the expression profile of each adhesin was determined. In a possible attempt to prevent the symptoms, the interaction between these adhesins could be blocked, breaking the stability of biofilm / Mestrado / Genetica de Microorganismos / Mestre em Genética e Biologia Molecular

F4 positive enterotoxigenic Escherichia coli (ETEC) is the most common pathogen causing neonatal diarrhea in piglets. The pathogenesis requires the attachment of ETEC to the intestinal brush border, mediated by F4 fimbria. Colostral anti-F4 antibodies and some non-immunoglobulin porcine skim milk proteins can bind F4 and prevent colonization and infection by F4-positive ETEC. Little is known, however, about the F4-binding ability of porcine milk fat globule membrane (MFGM) proteins. In addition, the knowledge of the absorption of porcine colostral proteins into the blood of neonatal piglets is limited, despite the well accepted concept that in neonatal piglets, protein absorption from the intestine is non-selective.<p> In this study, the ability of porcine MFGM proteins to bind purified F4ac (one of the three subtypes of F4 fimbriae) was investigated. Porcine MFGM proteins were first separated by 2D SDS-PAGE and subsequently identified by mass spectrometry. Overlay western Blot was then employed to demonstrate the interaction between porcine MFGM proteins and purified F4ac. Several proteins from porcine MFGM reacted with F4ac, and of these, lactadherin, butyrophilin, adipophilin, and acyl-CoA synthetase 3 reacted strongly. The biological function of these proteins in vivo was not investigated but it is possible that their interaction with F4ac positive ETEC interferes with bacterial attachment and colonization. In order to investigate protein absorption by neonatal piglets after natural suckling, the protein profiles of the plasma of pre-suckling and 24 h post-suckling neonatal piglets were studied by 2D SDS-PAGE. Those plasma proteins that increased prominently after suckling were then identified by mass spectrometry. Only immunoglobulins were unequivocally determined to be absorbed, because they were absent before suckling and present in large quantity in plasma 24 h after suckling. The absorption of other colostral proteins was either equivocal or not detectable by our detection methods. These results suggest that, unlike immunoglobulins, major non-immunoglobulin proteins in porcine colostrum may not be absorbed into systemic circulation in substantial amounts.

F4 positive enterotoxigenic Escherichia coli (ETEC) is the most common pathogen causing neonatal diarrhea in piglets. The pathogenesis requires the attachment of ETEC to the intestinal brush border, mediated by F4 fimbria. Colostral anti-F4 antibodies and some non-immunoglobulin porcine skim milk proteins can bind F4 and prevent colonization and infection by F4-positive ETEC. Little is known, however, about the F4-binding ability of porcine milk fat globule membrane (MFGM) proteins. In addition, the knowledge of the absorption of porcine colostral proteins into the blood of neonatal piglets is limited, despite the well accepted concept that in neonatal piglets, protein absorption from the intestine is non-selective.<p> In this study, the ability of porcine MFGM proteins to bind purified F4ac (one of the three subtypes of F4 fimbriae) was investigated. Porcine MFGM proteins were first separated by 2D SDS-PAGE and subsequently identified by mass spectrometry. Overlay western Blot was then employed to demonstrate the interaction between porcine MFGM proteins and purified F4ac. Several proteins from porcine MFGM reacted with F4ac, and of these, lactadherin, butyrophilin, adipophilin, and acyl-CoA synthetase 3 reacted strongly. The biological function of these proteins in vivo was not investigated but it is possible that their interaction with F4ac positive ETEC interferes with bacterial attachment and colonization. In order to investigate protein absorption by neonatal piglets after natural suckling, the protein profiles of the plasma of pre-suckling and 24 h post-suckling neonatal piglets were studied by 2D SDS-PAGE. Those plasma proteins that increased prominently after suckling were then identified by mass spectrometry. Only immunoglobulins were unequivocally determined to be absorbed, because they were absent before suckling and present in large quantity in plasma 24 h after suckling. The absorption of other colostral proteins was either equivocal or not detectable by our detection methods. These results suggest that, unlike immunoglobulins, major non-immunoglobulin proteins in porcine colostrum may not be absorbed into systemic circulation in substantial amounts.

Ce travail a pour objet l’étude et le développement d’un capteur électrochimique pour la détection sélective quantitative des analytes biologiques à l’échelle nano. Il se divise en deux parties après une présentation de l’état de l’art sur les maladies nosocomiales et les capteurs électrochimiques. Tout d’abord, nous avons développé un protocole spécifique qui repose sur la fonctionnalisation localisée de la microélectrode de travail par dépôt électrophorétique d'oxyde de graphène réduit/polyéthylènimine (rGO/PEI) pour amplifier le signal de détection. Le microsystème réalisé en salle blanche, a été exploité avec succès pour la détection sélective de la dopamine avec une limite de détection de 50 nM.Ensuite, nous avons utilisé la même plateforme constituée d’électrodes de plus grande taille (mm) pour la réalisation d’un capteur immunologique. Il a démontré son efficacité, de manière spécifique et sélective, pour discriminer la souche sauvage E. Coli UTI89 de UTI89 Δfim (sans opéron), avec une limite de détection de 10 cfu mL−1. En outre, le concept d’utilisation d’une électrode modifiée par rGO/PEI par la modification covalente avec des anticorps pathogènes est général. Il peut être facilement adapté à toute autre espèce pathogène, rendant l’approche générique. Le capteur a donc abouti à des résultats intéressants en milieu aqueux, sérique et urinaire, ce qui est essentiel pour son utilisation potentielle pour le diagnostic clinique des maladies pathogènes. / The purpose of this work concerns the study and development of an electrochemical sensor for both quantitative and selective detection of biological analytes at the nanoscale. It is divided into two parts after a presentation of the state of the art on nosocomial diseases and electrochemical sensors. First, we have developed a specific protocol based on the localized functionalization of the working microelectrode by electrophoretic deposition. The strategy is based on the localizedfunctionalization of the working microelectrode by electrophoretic deposition of reduced graphène oxide / polyethyleneimine (rGO / PEI) to amplify the detection signal. The microsystem built in a clean room has been successfully tested for the selective detection of dopamine with a detection limit of 50 nM. In addition, the microsystem showed good performance in detecting dopamine levels.Then, we have also used the same electrode platform at a larger scale (mm) for the specific and selective detection of the immunological sensor which has demonstrated its effectiveness in distinguishing the UTI89 E. Coli wild-type strain of UTI89 Δfim (without operon), with a detection limit of 10. cfu mL-1. In addition, the concept of rGO / PEI modified electrode by covalent modification with pathogenic antibodies is general and can be easily transposed to any other pathogenic species, making the approach very versatile and generic.The sensor works in aqueous, serum and urinary media, which is essential for its potential use in clinical diagnosis of pathogenic diseases.

This thesis is concerned with the first ever X-ray crystallographic and complimentary solution studies on mycobacterial lectins. Lectins, described as multivalent carbohydrate binding proteins of non-immune origin, are found in all kingdoms of life. As explained in the introductory chapter, those from plants and animals are the best characterized in terms of structure and function. Although not that extensive, important studies have been carried out on viral, fungal and parasite lectins as well. Bacterial lectins studied so far can be classified in to fimbrial, surface and secretory (or toxic). Applications of lectins include blood typing, cell separation and purification of glycoconjugates, mitogenic stimulation of lymphocytes, mapping of neuronal pathways and drug targeting and delivery. The work reported in the thesis lies at the intersection of two major long range programs in this laboratory, one on lectins and the other on mycobacterial proteins. Three putative lectins Rv1419 and Rv2813 from M. tuberculosis and MSMEG_3662 from M. smegmatis were chosen for exploratory studies on the basis of preliminary genomic searches. Exploratory studies on Rv1419, Rv2813 and MSMEG_3662 are described in the second chapter. MSMEG_3662 contains two domains, a LysM domain and a lectin domain (MSL) connected by a long polypeptide chain. The two M. tuberculosis proteins, full length MSMEG_3662 and MSL were cloned, expressed, purified and characterized. Rv2813 did not show any appreciable agglutination activity. It showed ATPase activity. Clearly the protein was not a lectin. Rv1419, full length MSMEG_3662 and MSL exhibited lectin characteristics. Among them, Rv1419 and MSL could be crystallized. Preliminary X-ray diffraction studies on them were carried out. Rv1419 could be successfully expressed only once. However, that was enough for the determination of crystal structure and the glycan array analysis of the lectin (Chapter 3). The monomeric lectin has a β-trefoil fold. It has high affinity for LacNAc and its Neu5Ac derivatives. Modeling studies using complexes of homologous structures, led to the identification of two carbohydrate binding sites on the lectins. Sequence comparisons of Rv1419 with homologous proteins with known structures and phylogenetic analysis involving them provide interesting insights into the relationship among trefoil lectins from different sources. X-ray crystal structure analysis of MSL and its complexes with mannose and methyl-α-mannose, the first comprehensive effort of its kind on a mycobacterial lectin, reveals a structure very similar to β-prism II fold lectins from plant sources, but with extensive unprecedented domain swapping in dimer formation (Chapter 4). The two subunits in a dimer often show small differences in structure, but the two domains, not always related by 2-fold symmetry, have the same structure. Each domain carries three sugar-binding sites, similar to those in plant lectins, one on each Greek key motif. The occurrence of β-prism II fold lectins in bacteria, with characteristics similar to those from plants, indicates that this family of lectins is of ancient origin and had evolved into a mature system before bacteria and plants diverged. In plants, the number of binding sites per domain varies between one and three, whereas the number is two in the recently reported lectin domains from Pseudomonas putida and Pseudomonas aeruginosa. An analysis of the sequences of the lectins and the lectin domains shows that the level of sequence similarity among the three Greek keys in each domain has a correlation with the number of binding sites in it. Furthermore, sequence conservation among the lectins from different species is the highest for that Greek key which carries a binding site in all of them. Thus, it would appear that carbohydrate binding influences the course of the evolution of the lectin. LysM domains have been recognized in bacteria and eukaryotes as carbohydrate-binding protein modules, but the mechanism of their binding to chitooligosaccharides is underexplored. Binding of a full length MSMEG_3662 containing LysM and lectin (MSL) domains to chitooligosaccharides has been studied using isothermal titration calorimetry and fluorescence titration (Chapter 5). This investigation demonstrates the presence of two binding sites of non-identical affinities per dimeric MSL-LysM molecule. Affinity of the molecule for chitooligosaccharides correlates with the length of the carbohydrate chain. Its binding to chitooligosaccharides is characterized by negative cooperativity in the interactions of the two domains. Apparently, the flexibility of the long linker that connects the LysM and MSL domains plays a facilitating role in this recognition. The LysM domain in MSL-LysM, like other bacterial domains but unlike plant LysM domains, recognizes equally well peptidoglycan fragments as well as chitin polymers. Interestingly, in the present case two LysM domains are enough for binding to peptidoglycan in contrast to the three reportedly required by the LysM domains of Bacillus subtilis and Lactococcus lactis. Also, the affinity of MSL-LysM for chitooligosaccharides is higher than that of LysM-chitooligosaccharide interactions reported so far. A part of the work presented in this thesis has been reported in the following publications: • Patra D, Mishra P, Surolia A, Vijayan M. 2014. Structure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis. Glycobiology, 24:956-965. • Patra D, Sharma A, Chandran D, Vijayan M. 2011. Cloning, expression, purification, crystallization and preliminary X-ray studies of the mannose-binding lectin domain of MSMEG_3662 from Mycobacterium smegmatis. Acta Crystallogr Sect F Struct Biol Cryst Commun, 67:596-599. • Patra D, Srikalaivani R, Misra A, Singh DD, Selvaraj M, Vijayan M. 2010. Cloning, expression, purification, crystallization and preliminary X-ray studies of a secreted lectin (Rv1419) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun, 66:1662-1665.