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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
71

Mapeamento global de interações proteicas nas vias de sinalização mediadas por c-di-GMP de Pseudomonas aeruginosa / Construction of a global map of protein-protein interactions in c-di-GMP signalling pathways of Pseudomonas aeruginosa

Andrea Rodrigues Cardoso 16 March 2016 (has links)
A persistência bacteriana correlacionada à formação de biofilmes bacterianos é, há algum tempo, fonte de grande preocupação médica em virtude de sua ampla associação com a dificuldade de tratamento de infecções crônicas. Por outro lado, as perspectivas de utilização de biofilmes bacterianos em novas aplicações biotecnológicas e até mesmo para fins terapêuticos são promissoras. Há, portanto, grande interesse em compreender os mecanismos que levam as células bacterianas a deixar o estado planctônico, de vida livre, e associarem-se nesses conglomerados celulares altamente complexos. Ao longo das últimas décadas, o segundo mensageiro c-di-GMP – em conjunto com as moléculas que catalisam sua síntese (diguanilato ciclases) e sua degradação (fosfodiesterases) e seus receptores – estabeleceu-se como um elemento central de regulação de uma série de respostas celulares que determinam a formação ou a dispersão de biofilmes. Curiosamente, as proteínas que participam do metabolismo deste segundo mensageiro estão, frequentemente, codificadas múltiplas vezes em um mesmo genoma bacteriano. Em vista dessa observação, estudos mais recentes apontam que, para reger paralelamente uma variedade tão ampla de fenótipos, este sistema opera em modo de alta especificidade de sinalização e que, portanto, o sinal metabolizado por determinados conjuntos de diguanilato ciclases e fosfodiesterases tem alvos celulares específicos. Evidências robustas, porém isoladas até o momento, apontaram que um dos meios pelo qual ocorre a segregação entre sinal produzido e alvo específico é a interação direta entre as proteínas componentes das vias de sinalização. Mais, demonstrou-se que, em algumas vias, a transmissão de sinal ocorre exclusivamente via interação proteica, dispensando a intermediação do sinalizador em si. Para avaliar a validade e relevância global deste mecanismo, propôs-se, neste estudo, a investigação da rede total de interações entre as proteínas tipicamente associadas às vias de sinalização por c-di-GMP em Pseudomonas aeruginosa, utilizando ensaios de duplo-hibrido bacteriano. Para tanto, foram construídas duas bibliotecas de DNA direcionadas e foram feitos testes de interação de forma estratégica para possibilitar o esgotamento e averiguação de todas as possíveis interações entre as proteínas alvo identificadas. O resultado obtido, um mapa inicial, porém abrangente, da rede de interações proteicas em P. aeruginosa, indica uma grande probabilidade de que os mecanismos previamente descritos sejam realmente recorrentes e relevantes para o intermédio da sinalização nesse organismo. Algumas das interações mais robustas encontradas são bastante interessantes e serão, em estudos futuros, mais extensivamente estudadas. / Persister bacteria are correlated to biofilm formation and have been a source of great medical concern due to its close association with the impairment of traditional treatment in combating chronic infections. On the other hand, using bacterial biofilms to create original biotechnological applications or even as a means of therapeutic treatment in medical settings constitutes a promising prospect. There is, therefore, a great interest in understanding the mechanisms that allow bacteria to leave the free-living planktonic lifestyle and associate in these highly complex cellular aggregates. Over the last decades, the second messenger c-di-GMP – and also the molecules involved in its synthesis (diguanylate ciclases) and degradation (phosphodiesterases) along with its receptors – has been established as a key element implicated in regulation of a series of cellular responses that determine biofilm formation or dispersion. Curiously, the proteins that play a part in the metabolism of this second messenger are frequently coded multiple times in single bacterial genomes. Taking this into account, recent studies indicate that, in order to control such a wide range of phenotypes, this system operates via high specificity of signaling – which means that the signal metabolized by a certain set of diguanylate ciclases and phosphodiesterases has specific cellular targets. Robust but yet isolated evidence indicate that a means by which a signal is segregated with its correlated phenotypic response is through direct protein-protein interaction involving the components of these signaling pathways. Even more, there has been strikingly evidence that, in some of these pathways, signal transduction occurs exclusively through protein-protein interaction, entirely dismissing any mediation by the signal molecule. In order to validate and evaluate the global relevance of this type of mechanism, this study proposed the investigation of the entire network of interactions between proteins typically associated with c-di-GMP signaling pathways of Pseudomonas aeruginosa by employing bacterial two-hybrid system assays. To make that possible, two DNA libraries were constructed and interaction essays were performed in a strategic way so that all possibilities of interaction between target proteins were explored. The results obtained from these experiments allowed the construction of a broad map of interactions that, although still primitive, indicates that, chances are, the mechanisms previously described are both recurrent and relevant to signaling regulation in this organism. Some of the interaction partners found are particularly interesting and will be further investigated in future studies.
72

Amphiphiles gemini cationiques : de l'auto-assemblage organique chiral aux micro- et nanomatériaux composites fonctionnels / Cationic gemini amphiphiles : from chiral organic self-assembly towards functional composite micro- and nanomaterials

Dedovets, Dmytro 10 February 2014 (has links)
En raison de leurs propriétés physiques uniques, les matériaux chiraux trouvent des applications aussi bien en physique, qu’en chimie ou biologie. Ici, nous nous intéressons à la synthèse de nanoobjets inorganiques chiraux et à leur utilisation en tant que systèmes nano-électromécaniques.Différents auto-assemblages à base de surfactants Gemini et de contre-ions chiraux (nucleotide ou tartrate) formant dans l’eau des hélices micrométriques et nanométriques sont étudiés. Ces auto-assemblages sont ensuite utilisés comme structures directrices pour la formation d’hélices de silice par transcription inorganique. Le contrôle de la réactivité du précurseur inorganique est crucial pour parvenir aux caractéristiques mécaniques souhaitées.Enfin, une minéralisation secondaire des nano-hélices avec du TiO2 et du ZnO a lieu afin de créer des matériaux fonctionnels aux propriétés électroniques ou piézoélectriques. Différentes approches de synthèse et l’optimisation des procédés sont présentées. / Due to their unique physical properties chiral materials are used in a wide range of applications in chemistry, physics and biology. In this work we focus on the fabrication of chiral functional materials for NanoElectroMechanical systems based on the inorganic transcription of self-assembled surfactants.At first we introduce a new Nucleoamphiphile based system that self-assembles into micrometer sized helical fibers in aqueous medium. The effect of a wide range of chemical and physical parameters on the morphology of the aggregates was investigated. Then the synthesis of chiral silica structures based on the organic micro- and nanohelices as templates was studied to achieve the required mechanical properties of the material. Control over the precursor reactivity is crucial for the transcription of the morphology of the template into the silica replica. Secondary mineralization with TiO2 or ZnO was performed to provide the necessary electrical properties and functionality to the chiral material. Different approaches and the optimization parameters are described in detail. Finally the measurement of the mechanical properties of the silica nanotubes and nanohelices by AFM as the first step of the NEMS development will be described.
73

Dissecting the C-DI-GMP Signaling Pathways : Tools and Tales

Sharma, Indra Mani January 2014 (has links) (PDF)
Evaluating aerodynamic noise from aircraft engines is a design stage process, so that it conform to regulations at airports. Aerodynamic noise is also a principal source of structural vibration and internal noise in short/vertical take off and landing and rocket launches. Acoustic loads may be critical for the proper functioning of electronic and mechanical components. It is imperative to have tools with capability to predict noise generation from turbulent flows. Understanding the mechanism of noise generation is essential in identifying methods for noise reduction. Lighthill (1952) and Lighthill (1954) provided the first explanation for the mechanism of aerodynamic noise generation and a procedure to estimate the radiated sound field. Many such procedures, known as acoustic analogies are used for estimating the radiated sound field in terms of the turbulent fluid flow properties. In these methods, the governing equations of the fluid flow are rearranged into two parts, the acoustic sources and the propagation terms. The noise source terms and propagation terms are different in different approaches. A good description of the turbulent flow field and the noise sources is required to understand the mechanism of noise generation. Computational aeroacoustics (CAA) tools are used to calculate the radiated far field noise. The inputs to the CAA tools are results from CFD simulations which provide details of the turbulent flow field and noise sources. Reynolds-Averaged Navier Stokes (RANS) solutions can be used as inputs to CAA tools which require only time-averaged mean quantities. The output of such tools will also be mean quantities. While complete unsteady turbulent flow details can be obtained from Direct Numerical Simulation (DNS), the computation is limited to low or moderate Reynolds number flows. Large eddy simulations (LES) provide accurate description for the dynamics of a range of large scales. Most of the kinetic energy in a turbulent flow is accounted by the large-scale structures. It is also the large-scale structures which accounts for the maximum contribution towards the radiated sound field. The results from LES can be used as an input to a suitable CAA tool to calculate the sound field. Numerical prediction of turbulent flow field, the acoustic sources and the radiated sound field is at the focus of this study. LES based on explicit filtering method is used for the simulations. The method uses a low-pass compact filter to account for the sub-grid scale effects. A one-parameter fourth-order compact filter scheme from Lele (1992) is used for this purpose. LES has been carried out for four different flow situations: (i) round jet (ii) plane jet (iii) impinging round jet and (iv) impinging plane jet. LES has been used to calculate the unsteady flow evolution of these cases and the Lighthill’s acoustic sources. A compact difference scheme proposed by Hixon & Turkel (1998) which involves only bi-diagonal matrices are used for evaluating spatial derivatives. The scheme provides similar spectral resolution as standard tridiagonal compact schemes for the first spatial derivatives. The scheme is computationally less intensive as it involves only bi-diagonal matrices. Also, the scheme employs only a two-point stencil. To calculate the radiated sound field, the Helmholtz equation is solved using the Green’s function approach, in the form of the Kirchhoff-Helmholtz integral. The integral is performed over a surface which is present entirely in the linear region and covers the volume where acoustic sources are present. The time series data of pressure and the normal component of the pressure gradient on the surface are obtained from the CFD results. The Fourier transforms of the time series of pressure and pressure gradient are then calculated and are used as input for the Kirchhoff-Helmholtz integral. The flow evolution for free jets is characterised by the growth of the instability waves in the shear layer which then rolls up into large vortices. These large vortical structures then break down into smaller ones in a cascade which are convected downstream with the flow. The rms values of the Lighthill’s acoustic sources showed that the sources are located mainly at regions immediately downstream of jet break down. This corresponds to the large scale structures at break down. The radiated sound field from free jets contains two components of noise from the large scales and from the small scales. The large structures are the dominant source for the radiated sound field. The contribution from the large structures is directional, mainly at small angles to the downstream direction. To account for the difference in jet core length, the far field SPL are calculated at points suitably shifted based on the jet core length. The peak value for the radiated sound field occurs between 30°and 35°as reported in literature. Convection of acoustic sources causes the radiated sound field to be altered due to Doppler effect. Lighthills sources along the shear layer were examined in the form of (x, t) plots and phase velocity pattern in (ω, k) plots to analyse for their convective speeds. These revealed that there is no unique convective speeds for the acoustic sources. The median convective velocity Uc of the acoustic sources in the shear layer is proportional to the jet velocity Uj at the center of the nozzle as Uc ≈ 0.6Uj. Simulations of the round jet at Mach number 0.9 were used for validating the LES approach. Five different cases of the round jet were used to understand the effect of Reynolds number and inflow perturbation on the flow, acoustic sources and the radiated sound field. Simulations were carried out for an Euler and LES at Reynolds number 3600 and 88000 at two different inflow perturbations. The LES results for the mean flow field, turbulence profiles and SPL directivity were compared with DNS of Freund (2001) and experimental data available in literature. The LES results showed that an increase in inflow forcing and higher Reynolds number caused the jet core length to reduce. The turbulent energy spectra showed that the energy content in smaller scale is higher for higher Reynolds number. LES of plane jets were carried out for two different cases, one with a co-flow and one without co-flow. LES of plane jets were carried out to understand the effect of co-flow on the sound field. The plane jets were of Mach number 0.5 and Reynolds number of 3000 based on center-line velocity excess at the nozzle. This is similar to the DNS by Stanley et al. (2002). It was identified that the co-flow leads to a reduction in turbulence levels. This was also corroborated by the turbulent energy spectrum plots. The far field radiation for the case without co-flow is higher over all angles. The contribution from the low frequencies is directional, mainly towards the downstream direction. The range of dominant convective velocities of the acoustic sources were different along shear layers and center-line. The plane jet results were also used to bring out a qualitative comparison of flow and the radiation characteristics with round jets. For the round jet, the center-line velocity decays linearly with the stream-wise distance. In the plane jet case, it is the square of the center-line velocity excess which decays linearly with the stream-wise distance. The turbulence levels at any section scales with the center-line stream-wise velocity. The decay of turbulence level is slower for the plane jet and hence the acoustic sources are present for longer distance along the downstream direction. Subsonic impinging jets are composed of four regions, the jet core, the fully developed jet, the impingement zone and the wall jet. The presence of the second region (fully developed free jet) depends on the distance of the wall from the nozzle and the length of the jet core. In impinging jets, reflection from the wall and the wall jet are additional sources of noise compared to the free jets. The results are analysed for the contribution of the different regions of the flow towards the radiated sound field. LES simulations of impinging round jets and impinging plane jet were carried out for this purpose. In addition, the results have been compared with equivalent free jets. The directivity plots showed that the SPL levels are significantly higher for the impinging jets at all angles. For free jets, a typical time scale for the acoustic sources is the ratio of the nozzle size to the jet velocity. This is ro/Uj for round jets and h/Uj for plane jets. For impinging jets, the non-dimensionlised rms of Lighthill’s source indicates that the time scale for acoustic sources is the ratio of the height of the nozzle from the wall to the jet velocity be L/Uj. LES of impinging round jets was carried out for two cases with different inflow perturbations. The jets were at Reynolds number of 88000 and Mach number of 0.9, same as the free jet cases. The impingement wall was at a distance L = 24ro from the nozzle exit. For impinging round jets, the SPL levels are found to be higher than the equivalent free jets. From the SPL levels and radiated noise spectra it was shown that the contribution from the large scale structures and its reflection from the wall is directional and at small angles to the wall normal. The difference in the range of angles where the radiation from the large scale structures were observed shows the significance of refraction of sound waves inside the flow. The rms values of the Lighthill’s sources indicate two dominant regions for the sources, just downstream of jet breakdown and in the impingement zone. The LES of impinging plane jet was done for a jet of Mach number 0.5 and Reynolds number of 6000. The impingement wall was at a distance L = 10h from the nozzle exit. The radiated sound field appears to emanate from this impingement zone. The directivity and the spectrum plots of the far field SPL indicate that there is no preferred direction of radiation from the impingement zone. The Lighthill’s sources are concentrated mainly in the impingement zone. The rms values of the sources indicate that the peak values occur in the impingement zone. The results from the different flow situations demonstrates the capability of LES with explicit filtering method in predicting the turbulent flow and radiated noise field. The method is robust and has been successfully used for moderate Reynolds number and an Euler simulation. An important feature is that LES can be used to identify acoustic sources and its convective speeds. It has been shown that the Lighthill source calculations, the calculated sound field and the observed radiation patterns agree well. An explanation for these based on the different turbulent flow structures has also been provided.
74

Molecular Phenotyping of Mutations in Guanylyi Cyclase C Associated with Congenital Diarrhea

Rasool, Insha January 2014 (has links) (PDF)
Guanylyl cyclase C (GC-C) is a member of particulate guanylyl cyclases, discovered primarily as the target of a family of heat stable enterotoxins (ST), produced by enterotoxigenic Escherichia coli (ETEC). ST is acknowledged as a prime cause of traveller’s diarrhea and the leading cause of child mortality under the age of 5 years in developing nations. The bacterial expression of ST peptides represents molecular mimicry where the pathogen has exploited a gastrointestinal tract-signaling pathway to disperse and propagate. GC-C is primarily expressed on the apical or the brush border membranes of intestinal epithelial cells. GC-C agonists elaborated in the gastrointestinal tract are a family of guanylin peptides, which are responsible for maintaining fluid-ion homeostasis, essential for normal gut physiology. The signal of liigand binding to the extracellular domain of GC-C is transduced to the catalytic guanylyl cyclase domain, which results in production of intracellular cGMP. The elevated levels of cGMP influence multiple downstream targets, which finally regulate ion-flux through the transporters present on the membrane of an enterocyte. The ST peptide, a GC-C superagonist, produces physiologically abnormal levels of cGMP that manifest as secretory diarrhea. The purview of GC-C misregulation was confined to the notion of its hyperactivation caused by ETEC infection and the ensuing diarrhea. Recently, two seminal studies widened the scope of pathologies associated with GC-C. Studies described point mutations in GUCY2C, which were associated with human disease. One study identified a Norwegian family whose members demonstrated a dominantly inherited syndrome of frequent diarrhea associated with hyperactive GC-C. Following this study, inactivating mutations in GC-C in a small Bedouin population was reported. The current study reports the molecular phenotypes associated with the first germ line mutations in GC-C that result in a severe form of congenital sodium diarrhea. Our collaborators from Austria (Thomas Muller & Andreas Janecke, Department of Pediatrics Innsbruck Medical University) communicated to us their study of patients who had clinical diagnosis of congenital sodium diarrhea, with proportionally high fecal sodium loss, metabolic acidosis and dehydration. Exome sequencing in a cohort of 6 unrelated patients revealed four heterozygous missense mutations in GC-C (R792S, L775P, K507E, N850D). Novel GC-C mutations were de novo spontaneous mutations with the carrier being the only affected family member in contrast to the previous two reports with familial history. Biochemical characterization revealed that the mutants (GC-CR792S, GC-CL775P) were constitutively active with GC-CR792S, GC-CK507E, and GC-CN850D showing further stimulation upon treatment with ST and guanylin family of peptides. Interestingly, there was no change in the binding affinities of the ligands for the mutant receptors compared to wild type. However, a significant decrease (ranging from 10-100 fold) in ligand EC50 for the mutant GC-C receptors was prominent. The in vitro assays suggested that the mutations occupying different domains of GC-C might have resulted in distinct structural consequences reflected in the repertoire of phenotypes that were observed. The results presented in this thesis illustrate the molecular basis of the severe form of congenital diarrhea associated with the GC-C gain-of-function mutations. This study has also elaborated our understanding of the regulation of GC-C activity by its various domains.
75

Regulation of Ecdysone 20-Monooxygenase Activity in the Tobacco Hornworm, Manduca sexta and the Apparent Occurrence of this Activity in Ascaris suum (Nematoda)

Drummond, Christopher Anson 14 March 2011 (has links)
No description available.
76

Deciphering Structure-Function Relationships in a Two-Subunit-Type GMP Synthetase by Solution NMR Spectroscopy

Ali, Rustam January 2013 (has links) (PDF)
The guanosine monophosphate synthetase (GMPS) is a class I glutamine amidotransferase, involved in the de-novo purine nucleotide biosynthesis. The enzyme catalyzes the biochemical transformation of xantosine (XMP) into guanosine monophosphate (GMP) in presence of ATP, Mg2+ and glutamine. All GMPSs consist of two catalytic sites 1) for GATase activity 2) for the ATPPase activity. The two catalytic sites may be housed in the same polypeptide (two-domain-type) or in separate polypeptides (two-subunit-type). Most of the studies have been performed on two-domain-type GMPSs, while only one study has been reported from two-subunit-type GMPS (Maruoka et al. 2009). The two-subunit-type GMPS presents an example where the component reactions of a single enzymatic reaction are carried out by two distinct subunits. In order to get better understanding of structural aspects and mechanistic principle that governs the GMPS activity in two-subunit-type GMPSs, we initiated the study by taking GMPS of Methanocaldococcus jannaschii as a model system. The GMPS of M. jannaschii (Mj) is a two-subunit-type protein. The GATase subunit catalyzes the hydrolysis of glutamine to produce glutamate and ammonia. The ATPPase subunit catalyses the amination of XMP to produce GMP using the ammonia generated in GATase subunit. Since the two component reactions are catalysed by two separate subunits and are coupled in the way that product of one reaction (ammonia) acts as a nucleophile in the second reaction. The cross-talk between these two subunits in order to maximise the efficiency of overall GMPS warrants investigation. The GATase activity is tightly regulated by the interaction with ATPPase domain/subunit, in all GMPS except in the case of P. falciparum. This interaction is facilitated by substrate binding to the ATPPase domain/subunit. Though, the conditions for the interaction between two subunits is known in a two-subunit-type GMP synthetase from P. horikoshii, the structural basis of substrate dependent interaction is not known. As a first step to understand the structural basis of interaction between the Mj GATase and Mj ATPPase subunits, we have determined the structure of Mj GATase (21 kDa) subunit using high resolution, multinuclear, multidimensional NMR spectroscopy. Sequence specific resonance assignments were obtained through analysis of various 2D and 3D hetero-nuclear multidimensional NMR experiments. NMR based distance restraints were obtained from assignment of correlations observed in NOE based experiments. Data were acquired on isotopically enriched samples of Mj GATase. The structure of Mj GATase (2lxn) was solved by using cyana-3.0 using NMR based restraints as input for the structure calculation. The ensemble of 20 lowest-energy structures showed root-mean-square deviations of 0.35±0.06 Å for backbone atoms and 0.8±0.06 Å for all heavy atoms. Attempts were also made to obtain assignments for the 69.6 kDa dimeric ATPPase subunit. Partial assignments have been obtained for this subunit. The GATase subunit is catalytically inactive. So far, there has been only one published report on a two-subunit-type GMPS from P. horikashii. The study has shown that the catalytic activity of GATase is regulated by the GATase-ATPPase interaction which is facilitated by the substrate binding to the ATPPase subunit. For the first time, we have provided the structural basis of interaction between GATase-ATPPase (112 kDa) in a two-subunit-type GMPS. Observed line width changes were used to identify residues in GATase residues that are involved in the Mj GATase-ATPPase interaction. Our data provides a possible explanation for conformational changes observed in the Mj GATase subunit upon GATase-ATPPase interaction that lead to GATase activation. Ammonia is generated in GATase subunit and is very reactive and labile. Thus, the faithful transportation of ammonia from GATase to ATPPase subunit is very crucial for optimal GMPS activity. Till date, a PDB query for GMPS retrieves only one structure which belongs to two-subunit-type GMPS, where authors have determined the structures of GATase and ATPPase subunits separately. However, the structure of holo-GMPS is not determined yet. Using interface information from experimental data and HADDOCK, we have constructed a model for the holo-GMPS from M. jannaschii. A possible ammonia channel has been deduced using the programs MOLE 2.0 and CAVER 2.0. This ammonia channel has a length of 46 Å, which is well within the range of the lengths calculated for similar channels in other glutamine amidotransferase. It had been suggested earlier that in addition to the magnesium required for charge stabilization of ATP, additional binding sites were present on GMPS. The effect of excess Mg2+ requirement on the GMPS activity has been studied in two-domain-type GMPS. However, the interaction between GATase and Mg2+ has been not investigated in any GMPS. This prompted us to investigate the effect of MgCl2 on Mj GATase subunit. For the first time, using chemical shift perturbation, we have established interaction between Mj GATase and Mg2+. The dissociation constant (Kd) of the Mj GATase-Mg2+ interaction was determined. The Kd value was found to be 1 mM, which indicates a very weak interaction. The substrate of the GATase subunit is glutamine. The condition of the hydrolysis of the glutamine is known in GMPS. However, the binding of the glutamine and associated conformational changes in GATase have been not studied in GMPS. Furthermore, till date there is no structure available for the glutamine bound GMPS/GATase. Using isotope edited one dimensional and two-dimensional NMR spectroscopy; we have shown that the Mj GATase catalytic residues are not in a compatible conformation to bind with glutamine. Thus, a conformational change in Mj GATase subunit is a pre-requisite condition for the binding of glutamine. These conformational changes are brought by the Mj GATase-ATPPase interaction.
77

An IL-4-dependent macrophage-iNKT cell circuit resolves sterile inflammation and is defective in mice with chronic granulomatous disease

Zeng, Melody Yue 03 February 2014 (has links)
Indiana University-Purdue University Indianapolis (IUPUI) / The immune system initiates tissue repair following injury. In response to sterile tissue injury, neutrophils infiltrate the tissue to remove tissue debris and subsequently undergo apoptosis. Proper clearance of apoptotic neutrophils in the tissue by recruited macrophages, in a process termed efferocytosis, is critical to facilitate the resolution of inflammation and tissue repair. However, the events leading to suppression of sterile inflammation following efferocytosis, and the contribution of other innate cell types are not clearly defined in an in vivo setting. Using a sterile mouse peritonitis model, we identified IL-4 production from efferocytosing macrophages in the peritoneum that activate invariant NKT cells to produce cytokines including IL-4 and IL-13. Importantly, IL-4 from macrophages functions in autocrine and paracrine circuits to promote alternative activation of peritoneal exudate macrophages and augment type-2 cytokine production from NKT cells to suppress inflammation. The increased peritonitis in mice deficient in IL-4, NKT cells, or IL-4Ra expression on myeloid cells suggested that each is a key component for resolution of sterile inflammation. The phagocyte NADPH oxidase, a multi-subunit enzyme complex we demonstrated to require a physical interaction between the Rac GTPase and the oxidase subunit gp91phox for generation of reactive oxygen species (ROS), is required for production of ROS within macrophage phagosomes containing ingested apoptotic cells. In mice with X-linked chronic granulomatous disease (X-CGD) that lack gp91phox, efferocytosing macrophages were unable to produce ROS and were defective in activating iNKT during sterile peritonitis, resulting in enhanced and prolonged inflammation. Thus, efferocytosis-induced IL-4 production and activation of IL-4-producing iNKT cells by macrophages are immunomodulatory events in an innate immune circuit required to resolve sterile inflammation and promote tissue repair.
78

The signalling role of superoxide anion in vascular smooth muscle cells

Wu, Lingyun 05 1900 (has links)
Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal. / L'anion superoxyde peut agir comme une molécule de signalisation ou comme un facteur préjudiciable selon sa concentration, l'organe cible, et selon la présence ou non d'antioxydants neutralisants. Actuellement, dans les cellules musculaires lisses (CMLs) vasculaires, les effets de l'anion superoxyde sur les différentes voies de transduction du signal et sur les interactions croisées entre ces voies ne sont pas encore définies. Par conséquent, une meilleure connaissance des effets de l'anion superoxyde sur les différentes voies de signalisation pourrait fournir une meilleure compréhension des mécanismes sous-jacents aux fonctions altérées des CMLs vasculaires observées dans des conditions pathologiques. L'objectif général de cette étude était de caractériser et d'évaluer le rôle modulateur de l'anion superoxyde, produit par la réaction de l'hypoxanthine avec la xanthine oxidase, sur les activités de différentes voies de signalisation dans les CMLs vasculaires, et de déterminer si la sensibilité de différentes voies de signalisation à l'anion superoxyde était altérée dans l'hypertension artérielle. Le projet de ce programme de recherche était basé sur les principaux postulats suivants : (1) l'anion superoxyde pourrait affecter sélectivement la production d'inositol 1,4,5-triphosphates (IP3), de GMPc, ou d'AMPc dans les CMLs vasculaires; (2) le rôle modulateur de l'anion superoxyde pourrait être dû à une altération des interactions croisées entre différentes voies de signalisation; et (3) les anomalies observées dans les CMLs vasculaires chez le rat spontanément hypertendu (SHR) pourraient être reliées à des altérations des différentes voies de signalisation induites par l'anion superoxyde. Une production augmentée d'1P3induite par l'anion superoxyde dans les CMLs d'aorte de rat ou d'artère mésentérique en culture a été démontrée pour la première fois dans cette étude. L'anion superoxyde a augmenté la formation d'IP3d'une manière concentration-dépendante et temps-dépendante. La superoxyde dismutase (SOD), mais non la catalase, a inhibé significativement la formation d'IP3 induite par l'anion superoxyde. L'inhibition de la phospholipase C (PLC) a aboli l'effet de l'anion superoxyde sur la formation d'1P3. La génistéine et la tyrphostine A25, deux inhibiteurs de la tyrosine kinase, ont aussi inhibé significativement la formation d'IP3induite par l'anion superoxyde. L'utilisation d'anticorps anti-PLCy a atténué significativement la formation d'1P3induite par l'anion superoxyde. De plus, le taux d'expression des protéines de la PLCy a été augmenté après l'exposition des CMLs à l'anion superoxyde. Ces observations suggèrent donc que dans les CMLs vasculaires la formation d'1P3 induite par l'anion superoxyde pourrait être en grande partie secondaire à une augmentation de l'activité de la tyrosine kinase liée aux voies de signalisation de la PLCy. En ce qui concerne la voie du GMPc, l'anion superoxyde a diminué significativement les niveaux de base de GMPc et supprimé aussi l'augmentation des niveaux de GMPc induite par des stimulateurs de la guanylyl cyclase, le nitroprussiate de sodium (NPS) ou la s-nitroso-nacétylpénicillamine (SNAP). La formation d'1P3stimulée par l'anion superoxyde a été significativement inhibée par le NPS ou la SNAP, mais potentialisée de façon importante par un inhibiteur de la guanylyl cyclase l'ODQ ou par le KT5823 (un inhibiteur de la protéine kinase dépendant du GMPc). Cependant, l'anion superoxyde n'a pas eu d'effet sur les niveaux de base d'AMPc ou sur la production d'AMPc induite par la forskoline et de plus, l'inhibition de l'adénylyl cyclase ou de la protéine kinase dépendante de l'AMPe n'a pas affecté la formation d'lP3stimulée par l'anion superoxyde. Ces données, par conséquent, suggèrent que l'inhibition de la formation de GMPc par l'anion superoxyde contribue probablement à l'activation de la formation d'1P3induite par l'anion superoxyde en atténuant le rétrocontrôle inhibiteur du GMPc sur les voies de signalisation liées à la PLC, tandis que la voie de signalisation de l'AMPc ne serait pas impliquée dans la formation d'EP3induite par l'anion superoxyde. Dans les CMLs vasculaires de rat SHR, les effets de l'anion superoxyde ont été plus puissants que dans les CMLs de rat WKY, en ce qui concerne l'augmentation de formation d'1P3, la diminution des taux de GMPc et la facilitation induite par l'anion superoxyde des interactions croisées entre les voies du GMPc et de 1'IP3. Dans les CMLs vasculaires des deux souches de rat, la formation d'IP3induite par l'anion superoxyde a été inhibée par une variété d'antioxydants, dont la N-acétylcystéine, l'acide a-lipoïque, la mélatonine et la SOD. Il apparaît donc vraisemblable que l'hypersensibilité à l'anion superoxyde des voies de 1'IP3et du GMPc puissent contribuer à l'augmentation du tonus vasculaire et de la réactivité des CMLs dans l'hypertension artérielle. Nous avons aussi investigué si l'effet de la mélatonine était dû à ses propriétés antioxydantes. Un effet inhibiteur plus important de la mélatonine sur la contraction aortique induite par la norépinéphrine (NE) a été observé chez les rats SHR en comparaison avec les rats Wistar-Kyoto (WKY). L'inhibition par la mélatonine de la formation d'IP induite par la NE a été aussi plus importante dans les CMLs aortiques de rat SHR que dans celles de rat WKY. Les effets plus puissants de la mélatonine chez le rat SHR, qui ont été aussi observés avec la SOD, mais non avec la catalase, ne sont pas dûs à l'activation des récepteurs à la mélatonine ou des récepteurs a-adrénergiques. Ces résultats indiquent que les effets anti-hypertenseurs de la mélatonine sont largement dûs à l'inactivation de l'anion superoxyde, et que les niveaux endogènes d' antioxydants ne parviennent pas à contrecarrer les niveaux accrus d'anion superoxyde produits chez le rat SHR. En conclusion, cette étude révèle une variété de nouveaux mécanismes de signalisation de l'anion superoxyde. Pour la première fois, il a été démontré que l'anion superoxyde active l'hydrolyse des phosphoinositides et augmente les taux d'IP3dans les CMLs vasculaires, principalement par la stimulation de la tyrosine kinase liée à la voie de signalisation de la PLCy. Il a aussi été observé que l'anion superoxyde réduit la formation de GMPc et supprime l'inhibition croisée de 1'1P3par le GMPc, facilitant ainsi la formation d'1P3. Les effets sélectifs de l'anion superoxyde sur les voies de 1'IP3et du GMPc, ainsi que l'existence d'une inhibition croisée de la formation d'1P3par la voie du GMPc, révèlent des mécanismes nouveaux pour expliquer le rôle modulateur de l'anion superoxyde sur les voies de signalisation dans les CMLs. Par conséquent, les effets plus puissants de l'anion superoxyde sur la signalisation de la voie de 1'IP3et de la voie du GMPc dans les CMLs vasculaires de rat SHR, effets qui ont été démontrés pour la première fois dans cette étude, pourraient être responsables des altérations des mécanismes de transduction du signal cellulaire chez le rat SHR et ainsi contribuer au développement et/ou au maintien de l'hypertension artérielle. Ces observations permettent donc d'imaginer de nouvelles orientations pour le développement de nouvelles stratégies pour la prévention ou le traitement de l'hypertension artérielle. / Superoxide anion can act as a signalling molecule or a detrimental factor depending on its concentration, the targeted organ, and the presence of counteracting antioxidants. The effects of superoxide on different signal transduction pathways and on the cross-talk interactions among these pathways in vascular smooth muscle cells (SMCs) are presently still unsettled. Therefore, a better knowledge on the effects of superoxide on different signalling pathways may provide a better understanding of the mechanisms underlying the altered functions in vascular SMCs observed in pathological conditions. The general objective of this study was to characterize and evaluate the modulating role of superoxide generated by the hypoxanthine and xanthine oxidase reaction on the activities of different signalling pathways in vascular SMCs and to investigate whether the sensitivities of different signalling pathways to superoxide were altered in hypertension. The design of the present research program was based on the following major postulates. (1) superoxide might selectively affect the generation of inositol 1,4,5-triphosphates (IP3), cGMP, or cAMP in vascular SMCs; (2) the modulating role of superoxide might be mediated by alteration in the cross-talk interactions among different signalling pathways; and (3) the abnormalities observed in vascular SMCs from spontaneously hypertensive rats (SHR) might be related to the alterations induced by superoxide on different signalling pathways. An enhanced production of 1P3induced by superoxide in cultured SMCs from rat aorta or mesenteric artery was demonstrated, for the first time, in this study. Superoxide increased 1P3 formation in a concentration- and time-dependent manner. Superoxide dismutase (SOD), but not catalase, significantly inhibited the superoxide-increased 1P3formation. The inhibition of phospholipase C (PLC) abolished the effect of superoxide on IP3formation. Genistein and tyrphostin A25, two tyrosine kinase inhibitors, also significantly inhibited the superoxideinduced IP3formation. The application of antibody against PLCI, significantly attenuated the superoxide-induced 1P3formation. Moreover, the expression level of PLC7proteins was increased after exposing SMCs to superoxide. These observations thus suggest that superoxideinduced IP3 formation may be in a great part secondary to an increase in the activity of tyrosine kinase-link PLCy signalling pathways in vascular SMCs. Concerning the cGMP pathway, superoxide significantly decreased the basal levels of cGMP and also suppressed the rise in cGMP levels induced by guanylyl cyclase stimulator sodium nitroprusside (SNP) or s-nitroso-n-acetylpenicillamine (SNAP). The superoxide-induced IP3 formation was significantly inhibited by SNP or SNAP, but markedly potentiated by a guanylyl cyclase inhibitor ODQ or KT5823 (a cGMP-dependent protein kinase inhibitor). However, superoxide had no effect on the basal levels of cAMP or the forskolin-induced cAMP production and moreover, the inhibition of adenylyl cyclase or cAMP-dependent protein kinase did not affect the superoxide-enhanced IP3formation. These data, therefore, suggest that the reduced cGMP formation by superoxide probably contributes to the superoxide induced activation of 1P3 formation by lifting the inhibitory feedback of cGMP on the PLC pathway(s), whereas, the cAMP pathway may not be involved in the superoxide-induced IP3formation. In vascular SMCs from SHR, the effects of superoxide were more potent than in SMCs from WKY, including the increase in 1P3 formation, the decrease in cGMP levels, and the superoxide-induced facilitation of the cross-talk interaction between cGMP and IP3pathways. The superoxide-induced 1P3formation was inhibited by a variety of antioxidants, including nacetylcysteine, cc-lipoic acid, melatonin and SOD, in vascular SMCs from both strains. It thus appears that the hypersensitivity of 1P3and cGMP pathways to superoxide is likely to contribute to the increased vascular tone and reactivity of SMCs in hypertension. Whether the effect of melatonin is due to its antioxidant properties was also explored. A greater inhibitory effect of melatonin on the norepinephrine (NE)-induced aortic contraction was observed in SHR than in Wistar-Kyoto rats (WKY). The inhibition of the NE-induced IP formation by melatonin was also greater in aortic SMCs from SHR than that from WKY. The enhanced effects of melatonin in SHR, which were found to be similarly enhanced with SOD but not with catalase, were not mediated by melatonin receptors or oc-adrenoceptors. These results indicate that the anti-hypertensive effects of melatonin are largely due to the scavenging of superoxide, and that the levels of endogenous antioxidants may not counteract the levels of overproduced superoxide in SHR. In conclusion, this study reveals a variety of novel signalling mechanisms for superoxide. For the first time, it was demonstrated that superoxide activates the hydrolysis of phosphoinositides and increases IP3levels in vascular SMCs mainly through the stimulation of tyrosine kinase-link PLCy signal pathway. It was also found that superoxide reduces cGMP formation and suppresses the cross-inhibition of IP3by cGMP, thus facilitating 1133formation. The selective effects of superoxide on 1133and cGMP pathways as well as the existence of a cross-inhibition of IP3formation by cGMP pathway provide novel mechanisms for the signalling role of superoxide in vascular SMCs. Therefore, the altered signalling effects of superoxide on the IP3pathway and the cGMP pathway, which were demonstrated in vascular SMCs from SHR for the first time in this study, could thus be responsible for the alterations in cellular signal transduction mechanisms in SHR and might contribute to the development and/or maintenance of hypertension. These observations could provide new avenues for the development of new strategies for the prevention or treatment of hypertension.
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Electrostaticanalisys the Ras active site

Khan, Abdul Kareem 05 March 2009 (has links)
La preorganització electrostàtica del centre actiu s'ha postulat com el mecanisme genèric de l'acció dels enzims. Així, alguns residus "estratègics" es disposarien per catalitzar reaccions interaccionant en una forma més forta amb l'estat de transició, baixant d'aquesta manera el valor de l'energia dactivació g cat. S'ha proposat que aquesta preorientació electrostática s'hauria de poder mostrar analitzant l'estabilitat electrostàtica de residus individuals en el centre actiu.Ras es una proteïna essencial de senyalització i actúa com un interruptor cel.lular. Les característiques estructurals de Ras en el seu estat actiu (ON) són diferents de les que té a l'estat inactiu (OFF). En aquesta tesi es duu a terme una anàlisi exhaustiva de l'estabilitat dels residus del centre actiu deRas en l'estat actiu i inactiu. / The electrostatic preorganization of the active site has been put forward as the general framework of action of enzymes. Thus, enzymes would position "strategic" residues in such a way to be prepared to catalyze reactions byinteracting in a stronger way with the transition state, in this way decreasing the activation energy g cat for the catalytic process. It has been proposed thatsuch electrostatic preorientation should be shown by analyzing the electrostatic stability of individual residues in the active site.Ras protein is an essential signaling molecule and functions as a switch in thecell. The structural features of the Ras protein in its active state (ON state) are different than those in its inactive state (OFF state). In this thesis, an exhaustive analysis of the stability of residues in the active and inactive Ras active site is performed.
80

食品因子による生体防御を目的としたDNA傷害マ-カ-の開発と応用

大澤, 俊彦, 山下, かなへ, 三村, 精男, 中山, 勉, 豊國, 伸哉, 内田, 浩二 03 1900 (has links)
科学研究費補助金 研究種目:試験研究(B) 課題番号:05556021 研究代表者:大澤 俊彦 研究期間:1993-1995年度

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