Reniform nematode, Rotylenchulus reniformis is a semi-endoparasitic nematode infecting over 300 plant species including important fiber crops like cotton. Introgression of reniform nematode resistance from a distantly-related resistant species Gossypium longicalyx into cultivated upland species Gossypium hirsutum has been a challenge. An approach towards achieving nematode resistance in crop plants has been to identify candidate parasitism genes expressed in the nematode facilitating infection of host plant species, and silencing the same through reverse genetic approaches like RNAi. A cDNA library constructed from the sedentary female stage of reniform nematode revealed an EST coding for C-type lectins and occurring in high frequency. Identification and characterization of C-type lectins in reniform nematode is important in understanding the immune system of nematode and in planning strategies for the development of reniform nematode resistant cotton varieties. A total of 11 C-type lectin gene family members were identified across six life stages of reniform nematode, with each member expected to play a significant role in the development and parasitic establishment with the host plant. Conserved sites characteristic of C-type lectins found in other organisms have been identified in the C-type lectin genes in reniform nematode for binding of Ca+2 and mannose. The highest level of expression of C-type lectins was observed in the sedentary female stage indicating it to be possibly the most sensitive stage to microbial infection and so a likely stage to target for its management. The site of secretion of C-type lectins in the sedentary female stage could be identified by in situ hybridization as the hypodermal region of the exposed posterior body region which is not inserted into the host root tissue. Phylogenetic analyses of C-type lectin domains of various nematode groups placed the plant-parasitic nematodes in one group indicating the possibility of co-evolution and probably carrying out a similar function aiding in the establishment of parasitism with host plants. Our findings now extend the spectrum of known nematode C-type lectin genes and suggest that lectin activity might be a more general feature of parasitism which could be explored in better understanding the interactions occurring at the host-nematode and nematode-pathogen interfaces.

SHP (Sphaeroides Heme Protein) is a monoheme cytochrome c of unknown function. In general, ligands cannot bind to ferric SHP, but some diatomic molecules, such as O2 or NO, can bind to ferrous SHP. The gene encoding SHP and genes encoding a diheme cytochrome c (DHC) and a b-type cytochrome (Cyt-b) are found in the same chromosome region in different species. In the case of Shewanella oneidensis MR-1, mRNA levels for SHP, DHC, and Cyt-b are up-regulated by nearly 10-fold when grown under anaerobic conditions using nitrate as the electron acceptor. Thus it is possible that the physiological role of SHP may be in nitrate metabolism. However, nitrate is too big to be a candidate substrate for SHP, and some nitrification steps need more than one electron transfer (SHP is a monoheme cytochrome). Therefore, we will focus on the nitrite reductase, nitric oxide reductase and nitric oxide dioxygenase activities of SHP. In this thesis it is shown that SHP can catalyse the reaction between oxygen and nitric oxide to give a nitrate ion as the final product. Thus a possible aerobic function for SHP as a nitric oxide dioxygenase is proposed. Aerobically, SHP is proposed to be a nitric oxide dioxygenase which utilizes the same mechanism as other NO dioxygenases, flavohemoglobin (HMP) and neuroglobin (Ngb). This mechanism is proposed to proceed via an oxy-ferrous complex (SHP2+-O2) which reacts with nitric oxide. A mechanism for the catalytic reaction with ferrous-NO complex is described. SHP2+-NO can be quickly converted back to ferrous SHP by reacting with superoxide liberated by SHP2+-O2 or from another source. In addition it is also found that Shewanella MR-1 wild type reveals a higher NO tolerance than the SHP knockout strain in aerobic conditions. The catalytic mechanism of NO dioxygenase is oxygen-dependent, but the SHP mRNA up-regulation in Shewanella oneidensis MR-1 grown with nitrate under anaerobic conditions indicates that SHP may also perform some anaerobic function and may possibly be involved in nitrate metabolism. This work found that SHP reveals anaerobic nitrite reductase activity. However, the catalytic efficiency of SHP is considerably lower than other nitrite reductases. This infers that although SHP can reduce nitrite in vitro, it is unlikely to function as a nitrite reductase in vivo. Ferrous SHP binds NO with a Kd of less than 1 μM, and does not auto-oxidise. Therefore, under anaerobic conditions SHP2+-NO must be processed by some other mechanism. In addition, biochemical results reveal that the SHP/DHC complex has NO reductase activity under anaerobic conditions. Unfortunately, this function was not proved in vivo. SHP was initially isolated from Rhodobacter sphaeroides and its structure was reported in 2000. Based upon this structure, SHP is clearly a class I cytochrome c with one axial histidine ligand to the heme iron. Unusually, however, it has an asparagine residue as the other axial heme ligand, and as such is unique among cytochromes c. For this reason it may be assumed that the asparagine plays a special role. This study reveals several potential reasons why SHP utilises asparagine as a heme ligand. Firstly, in the ferric form, asparagine 88 binds to the heme iron to prevent small molecules binding. Secondly, in the ferrous form it moves to allow oxygen to bind and form the oxy-ferrous complex, using hydrogen bonding for stability. Thirdly, using asparagine as a heme ligand creates a suitable redox potential for reduction by DHC, thus allowing NO dioxygenation.

C-type natriuretic peptide (CNP) is synthesised and released by the endothelium and plays a vital role in the maintenance of vascular homeostasis (Moyes et al., 2014). However, a similar regulatory role of endogenous CNP in the heart has yet to be elucidated. Therefore, I have used three unique mouse strains with endothelium (Tie2-Cre), cardiomyocyte (αMHC-Cre) and fibroblast (Col1α2-Cre)-restricted deletion of CNP to investigate if the peptide modulates coronary vascular reactivity and cardiac function. Methods: Langendorff isolated hearts were used to investigate the effect of CNP deletion on coronary vascular reactivity in response to the endothelium-dependent vasodilators bradykinin (10nmol) and acetylcholine (0.1-1nmol). Vasodilatation associated with reperfusion was investigated by transient cessation of flow (20-80 seconds). Ischaemia reperfusion (IR) injury (35 minutes ischaemia followed by 60 minutes reperfusion) was also investigated in cell-specific knockout (KO) animals. Isoprenaline (ISO; 20mg/kg/day, 7days)- and pressure overload (abdominal aortic constriction [AAC]; 6 weeks)-induced heart failure were used to study the effect of CNP deletion during cardiac stress, with cardiac function assessed by echocardiography. Cardiac fibrosis and hypertrophy were determined by picro-sirius red and wheat-germ agglutinin fluorescence staining, respectively. A subset of experiments was repeated in mice with global deletion of natriuretic peptide receptor-C (NPR-C) to delineate the signalling pathway triggered by CNP. Real time qPCR was used to determine hypertrophic and fibrotic gene expression in left ventricles isolated from mice subjected to AAC or sham. Neonatal cardiomyocytes were isolated to investigate angiotensin (Ang)II-induced hypertrophy. Results: Coronary endothelial reactivity was reduced in endothelial CNP (ecCNP) KO mice compared to wild type (WT) in response to bradykinin, acetylcholine and reperfusion-induced vasodilatation. These observations were paralleled in NPR-C KO animals. ecCNP KO did not exacerbate IR injury, whilst mice with cardiomyocyte-restricted deletion of CNP (cmCNP KO) and NPR-C KO animals exhibited a larger infarct size compared to WT. cmCNP KO mice also displayed greater cardiac dysfunction and fibrosis after ISO infusion or AAC compared to WT; similar results were observed in fbCNP KO and NPR-C KO animals. Infusion of CNP (0.2mg/kg/day; osmotic mini-pump, s.c.) in WT, but not NPR-C KO, animals rescued the decline in cardiac function. CNP (1μM) administration in isolated cardiomyocyte also blunted Ang II-induced hypertrophy. Pro-hypertrophic and pro-fibrotic gene expression (ANP, β-MHC and MMP-2) was augmented in cmCNP KO and NPR-C KO mice compared to littermate controls following AAC. Conclusions: Endothelial, cardiomyocyte and fibroblast-derived CNP have distinct, complementary roles in the heart, modulating cardiac function by influencing coronary vascular tone and protecting against heart failure and IR injury. These protective effects of CNP are mediated, at least in part, via NPR-C activation. Developing CNP mimetics or selective NPR-C agonists could be a novel therapeutic intervention in cardiovascular disease.

Members of the C-type lectin domain (CTLD) superfamily are metazoan proteins functionally important in glycoprotein metabolism, mechanisms of multicellular integration and immunity. This thesis presents the results of several computational and experimental studies of the CTLD structure, function and evolution.¶ Core structural properties of the CTLD fold were explored in a comparative analysis of the 37 distinct CTLD structures available publicly, which demonstrate significant structural conservation despite low or undetectable sequence similarity. Pairwise structural alignments of all CTLD structures were created with three different methods (DALI, CE and LOCK) and analysed manually and using a computational algorithm developed for this purpose. The analysis revealed a set of conserved positions and interactions, which were classified based on their role in CTLD structure maintenance.¶ The CTLD family is large and diverse. To organize and annotate the several thousand of known CTLD-containing protein sequences and integrate the information on their evolution, structure and function a local database and a web-based interface to it were developed. The software is written in Perl, is based on bioperl, bioperl-db and Apache::ASP modules, and can be used for collaborative annotation of any collection of phylogenetically related sequences.¶ Several studies of CTLD genomics were performed. In one such study, carried out in collaboration with the RIKEN structural genomics centre, CTLD sequences from the Caenorhabditis elegans genome were identified and clustered into groups based on similarity. The most representative members of the groups were then selected, which if characterized structurally would tell most about the C. elegans CTLDs and provide templates for homology modelling of all C. elegans CTLD structures.¶ In the other whole-genome study, the CTLD family in the puffer fish Fugu rubripes was analysed using the draft genome sequence. This work extended and complemented three genome-level surveys on human, C. elegans and D. melanogaster reported previously. The study showed that the CTLD repertoire of Fugu rubripes is very similar to that of mammals, although several interesting differences exist, and that Fugu CTLD-encoding genes are selectively duplicated in a manner suggesting an ancient large-scale duplication event. Another important finding was the identification of several new CTLDcps, which had mammalian orthologues not recognized previously.¶ CBCP, a novel CTLD-containing protein highly conserved between fish and mammals with previously unknown domain architecture, was predicted in the Fugu study based solely on ab initio gene models from the Fugu locus and cross-species genomic DNA alignments. To test if the prediction was correct, a full-length cDNA of the mouse CBCP was cloned, its tissue distribution characterized and untranslated regions determined by RACE. The full-length mCBCP transcript is 10 kb long, encodes a protein of 2172 amino acids and confirms the original prediction. The presence of a large N-terminal NG2 domain makes CBCP a member of a small but very interesting family of Metazoan proteins.

C-type Natriuretic Peptide (CNP), a relatively new member of the natriuretic peptide family, is found throughout the central nervous system. Circumstantial evidence associates CNP with learning and memory, as its expression is highest in brain regions known to be involved in memory and associated with hippocampal physiology. Here, the first study housed rats in an enriched environment, regarded as providing an 'informal' learning experience, for either 14 or 28 days of housing in enrichment in six regions of interest, which was attributed to changes in the degradation of CNP. The second study examined a group of rats trained on object -recognition task – the bow-tie maze. A difference was found in CNP production in the limbic medial prefrontal cortex over repeated exposures to novel objects relative to controls that received 'yoked learning' an exposure only to the test room. CNP concentrations also tended to be lower in rats with better levels of discrimination between familiar objects. Together, these studies provide some initial evidence that CNP influences learning –induced plasticity in the intact brain.

Recognition of microbial components by germ-line encoded pattern recognition receptors (PRR) initiates immune responses to infectious agents. We and others have proposed that pairs or sets of PRR mediate host immunity. One such pair comprises the fungal β-glucan receptor, Dectin-1, which collaborates through an undefined mechanism with Toll-like receptor 2 (TLR2) to induce optimal cytokine responses in macrophages. We show here that Dectin-1 signaling through the spleen tyrosine kinase (Syk) pathway is required for this collaboration, which can also occur with TLR4, 5, 7 and 9. Deficiency of either Syk or the TLR adaptor MyD88 abolished collaborative responses, which include TNF,MIP-1α andMIP-2 production, and which are comparable to the previously described synergy between TLR2 and TLR4. Collaboration of the Syk and TLR/MyD88 pathways results in sustained degradation of the inhibitor of kB (IkB), enhancing NFkB nuclear translocation. These findings establish the first example of Syk-and MyD88-coupled PRR collaboration, further supporting the concept that paired receptors collaborate to control infectious agents.

Pneumocystis jirovecii causes fungal pneumonia in immunocompromised patients and can be fatal if left untreated. The global mortality rate is estimated to be over 200 000 in AIDS patients. In non-AIDS patients there is an estimated mortality rate of 50 000 cases. This rate is increasing in developed countries, attributed to an increase in disorders which require immunotherapy. These include hematologic malignancies, organ transplant, inflammatory disorders and pre-existing lung disease. Immediate immunity is initiated by receptors that recognize pathogen associated molecular patterns on the surface of pathogenic fungi. Specifically, C-type lectin receptors (CLRs) have been shown to be the principal initiators of innate immune response during fungal infection. Limited studies have focused on the role of CLRs in Pneumocystis infection. Dectin1and Mincle have been shown to recognise Pneumocystis surface antigens with Dectin-1 recognizing β-glucans on the Pneumocystis cell wall leading to an effective immune response. However, the role of a newly described CLR, the Dendritic Cell Immunoactivating Receptor (DCAR) remains undefined. For this reason, we investigated the potential role of this receptor in a mouse model of Pneumocystis murina infection. Wild type and DCAR-deficient C57BL/6 mice were infected with P. murina organisms via intratracheal instillation. Fungal burden was measured in the lung using quantitative Polymerase Chain Reaction. DCAR-deficient mice had a significantly reduced burden compared to wild type mice at Day 7 and 14 post-infection. To identify the immune components involved in pathogen clearance in these mice we measured cellular recruitment and cytokine production at both early (48 hours) and late (7, 14 and 21 days) time points. Flow cytometry analysis showed an increase in alveolar macrophage, dendritic cells, inflammatory monocytes, eosinophils and T cell recruitment to the lung. While ELISA showed increased levels of IL-1β and IFN-γ at 48 hours, and later on in infection IL-1β and IL-12p40 levels were also elevated. Histology analysis determined the localization of the recruited cells, and v interestingly showed an increase in mucus production at day 21 in DCARdeficient mice. In conclusion, we have identified DCAR deficiency as a potential driver of protective immunity in mice during P. murina infection. This may be associated with increased levels of IL-1β in DCAR-deficient mice. Furthermore, DCAR may also be important in adaptive inflammatory response regulation, as DCAR-deficient mice have increased cellular recruitment and mucus production later in infection. The mechanism by which the deletion of this receptor affords these mice the ability to efficiently clear P. murina remains to be determined.

Natural killer cells play a significant role in the immune response against tumor and infected cells. NK cells express a wide variety of surface receptors, including NKRP1, a C-type lectin-like family of both activating and inhibitory receptors. Recently, ligands have been found for some of these previously orphan molecules, some of them lying within the same family. This is also the case of rat Clr-b as a cognitive ligand for rat NKRP1B. It has been shown that in rat, this inhibitory NKRP1B-Clr-b mutual receptor system is subverted by rat cytomegalovirus protein RCTL, a viral version of Clr-b, which serves as a decoy ligand for NK cells. The aim of my diploma thesis was cloning and production of the above mentioned C-type lectin-like proteins based on transient transfection of HEK293T cell line in a suspension culture. This expression system allows us not only to obtain proteins of our interest with a satisfactory yield but also in their native conformation, removing the need for time consuming and often fruitless refolding procedures required in case of using the E. coli expression system. Success was achieved in case of Clr-b and NKRP1B receptors from both WAG and SD strains. Proteins were purified using IMAC followed by gel filtration, identified by mass spectrometry and characterized by disulfide...

In the post smallpox era, vaccinia virus (VACV) has emerged as an important candidate vaccine vector. As yet, the binding receptors and entry mechanisms utilised by the two infectious forms, IMV and EEV, in dendritic cells (DCs) are unknown. We have investigated the interactions between VACV and C-type lectin receptors (CLRs) that are known to be utilised by many other viruses for binding and entry in DCs. Using a variety of CLR ligands and inhibitors we were unable to inhibit IMV or EEV binding to MDDCs and we conclude that they do not bind to CLRs. We have also investigated VACV entry in MDDCs and show that both IMV and EEV enter MDDCs via an endocytic pathway. Using a variety of drugs that inhibit cellular processes we found IMV and EEV entry to be actin- and calcium-dependent. EEV entry was also cholesterol- and energy-dependent, whereas IMV entry was only partially dependent on these factors. Both IMV and EEV colocalised with endolysosomal markers. This data suggests that EEV may enter DCs via caveolin-mediated endocytosis whereas IMV entry can occur via multiple complementary mechanisms, including endocytosis and fusion. Macropinocytosis may also constitute a minor route of entry for IMV as entry was partially inhibited by dimethyl amiloride and the virus colocalised with dextran. Finally we have provided a comprehensive flow cytometric analysis of Toll-like receptor (TLR) expression at the protein level in MDDCs and monocyte-derived Langerhans cells (MDLCs) as models for different myeloid DC subsets. We found TLR expression to be cell type-specific and MDDCs expressed the full repertoire of TLRs 1-9, including small amounts of TLR8 and TLR9 on the cell surface. The expression of these TLRs that recognise nucleic acids on the surface of cells may constitute an early warning system for signalling the presence of viral invaders that would normally subvert the function of DCs. We also found TLR expression in mature cells to be dependent on the nature of the maturation stimulus (lipopolysaccharide versus cytokine/prostaglandin cocktail) and VACV infection induced profound down-regulation of all TLRs. These findings will have important implications for the rational design of VACV-vectored vaccines.

Le premier but de mon projet de doctorat a ete la caracterisation moleculaire de l'interface entre les recepteurs activateurs des cellules Natural Killer (NK) et de leurs ligands exprimes dans les cellules infectees ainsi que l'implication de cette interaction sur la reponse a l'infection par le cytomegalovirus (MCMV). / J'ai tire un avantage de la variation naturelle au sein des membres lies aux recepteurs Ly49C ainsi que de la disponibilite des structures cristallines des Ly49 afin de comprendre les determinants moleculaires des interactions Ly49H-m157 et egalement identifier les residus des acides amines qui permettent de discriminer entre les recepteurs qui se lient et ceux qui ne se lient pas a m157. Mes decouvertes suggerent que le "site 2" du contact entre le CMH de classe I et Ly49 n'est visiblement pas implique dans la liaison avec m157. Au contraire, les residus localises au niveau de l'interface homodimere-recepteur seraient probablement critiques a la reconnaissance fonctionnelle de la glycoproteine m157. Notre approche fonctionnelle et de modelisation tridimensionnelle suggerent que l'architecture du dimere Ly49H est cruciale pour l'accessibilite de m157 mais non pour les molecules de CMH de classe I et relient la variabilite dans l'homodimerisation des Ly49 a la reconnaissance directe des produits pathogeniques. / Un autre mecanisme de la reponse de l'hote contre MCMV provient de l'etude de la souche de souris MA/My, laquelle, malgre l'absence du gene Ly49h ainsi que la proteine pour laquelle il code, y est hautement resistant. Des etudes anterieures ont demontre qu'une interaction epistatique entre un gene issu du groupe des genes Ly49 sur le chromosome 6 et le CMH (H2) sur le chromosome 17 est associee avec la resistance au virus. Utilisant une methode de co-culture de cellules reportrices NFAT-GFP exprimant les recepteurs activateurs Ly49 et de fibroblastes primaires infectes, j'ai montre que le recepteur activateur Ly49P des cellules NK reconnait specifiquement les cellules infectees par MCMV et que cette reconnaissance depend de la presence de l'haplotype H2k. Ce signal etait bloque par l'utilisation des anticorps anti-H2-D k mais non par anti-H2-Kk. Ces resultats indiquent l'existence d'un nouveau mecanisme des cellules NK implique dans la resistance au MCMV, lequel depend de l'interaction fonctionnelle entre le recepteur Ly49P et la molecule du MHC de classe I, H2-Dk, dans les cellules infectees par MCMV. Comme contribution directe de ce travail, nous avons demontre que la resistance chez MA/My est au moins partiellement dependante des interactions entre le recepteur Ly49P et la molecule H2-Dk modifiee par le virus dans les cellules infectees. Comme MCMV regule negativement l'expression des molecules du CMH de classe I, j'ai confirme la presence de H2-Dk dans les cellules infectees par l'utilisation d'un virus MCMV recombinant portant un gene rapporteur GFP. En permutant la plateforme peptidique de liaison, les domaines transmembranaires et intracellulaires entre les molecules H2-Db et H2-D k, j'ai demontre que la plateforme peptidique de liaison est critique pour la reconnaissance des cellules infectees. Par le criblage d'un panel de mutants MCMV portant des genes impliques dans l'evasion immune, j'ai demontre que l'infection de fibroblastes par le MCMV depourvu du gene m04 (Deltam04) abolit totalement l'activation de Ly49P. (Abstract shortened by UMI.)