Dissertations / Theses on the topic 'SLH domain'

S-layer proteins of S. ureae ATCC 13881 form on the cell surface an S-layer lattice with p4 square type symmetry and a period of about 13.5 nm. These lattices were shown to be the excellent nanotemplates for deposition of regular metal clusters. The synthesis of the S. ureae S-layer protein is highly efficient, the protein accounts for approximately 10-15 % of the total cell protein content, judged by the SDS-PAGE results. Besides, the S-layer protein production is tightly regulated, since only negligible amounts of S-layer proteins are observed in the medium at different cell growth phases. At the same time, mechanisms of the regulation of S-layer protein synthesis are poorly understood. As several hundreds of S-layer proteins are produced per second during the cell growth, the S-layer gene promoters are among the strongest prokaryotic promoters at all. However, little is known about factors regulating the expression of S-layer genes, furthermore, no experimental identification of other upstream regulatory sequences except for -35/-10 and RBS sequences was presented to our knowledge to date. A sequence of the S-layer gene of S. ureae ATCC 13881, encoding the previously described S-layer protein, was identified in this work by combination of different approaches. The largest part of the gene, excluding its upstream regulatory and ORF 5’ regions, was isolated from a genomic library by hybridization. The sequence of the isolated fragment proved to contain additionally an 1.9 kb non-coding region and an incomplete 0.8 kb ORF region in its 3’-part. No RBS sequence and apparent promoter regions could be identified in front of the latter sequence, suggesting that it might represent a pseudogene sequence. The sequences of the 5’ and upstream regions of the S. ureae ATCC 13881 S-layer gene were identified by combination of PCR-sequencing and chromosome walking. Totally, a sequence of the 6.4 kb long region of S. ureae genomic DNA was established. The sequence of the S. ureae S-layer protein was deduced from the respective gene sequence and agreed with the peptide sequences, obtained after N-terminal sequencing of tryptic peptides of the S. ureae ATCC 13881 S-layer protein. For the protein the name SslA was proposed, which is an abbreviation for “Sporosarcina ureae S-layer protein A”. Several specific features were observed in gene organisation of sslA, which are also characteristic for other S-layer genes. The distance between the -35/-10 region and the ATG initiation codon is unusually long and a 41 bp palindromic sequence is present in the immediate vicinity of the -35/-10 region. Besides, a distant location of the rho-independent transcription terminator, which is 647 bp remote from the stop codon, will result in the mRNA transcripts with unusually long trailer region. Both the long 5’ UTR and the long 3’ trailer may have a regulatory function, either by conferring increased mRNA stability and/or by affecting translation efficiency. Potentially these sequences may define the binding sites of regulatory proteins. For example, palindromic sequences constitute the regulatory sites in several bacterial operons and may act as the binding sites of regulatory dimeric proteins. In respect to the conservation of the sslA sequence high similarity to the sequences of other functional S-layer genes, especially the slfA and slfB genes of B. sphaericus, was observed, whereas the results of phylogenetic analysis support the hypothesis that S-layer genes may have evolved via the lateral gene transfer. Based on the sslA sequence, several recombinant proteins with truncations of the terminal protein parts or C-terminal fusion of either EGFP or histidine tags were constructed. For all the truncated or EGFP-fusion SslA derivatives high level overexpression in E. coli was possible. For native SslA a moderate level of expression was observed suggesting that its high intracellular concentration may downregulate the protein synthesis. Interestingly, fluorescence microscopy indicates the same intracellular localization for heterologously produced recombinant proteins with fusions of EGFP either to the precursor or to the native SslA protein, suggesting that SslA secretion signal is not functional in E. coli. Heterologously produced SslA derivatives with truncations of N-, C- or both N- and C-terminal parts were shown to self- assemble in vitro, although the size of self-assembly structures was different from that observed upon the self-assembly of the native SslA. In the latter case extended self-assembly layers with the size up to 5x10 µm were observed, with a surface area of up to two orders of magnitude higher than that of S-layer patches, routinely isolated from S. ureae surface. Dependent on the applied recrystallization conditions preferential formation of single- or multilayer self-assembly structures was observed.

S-layer proteins of S. ureae ATCC 13881 form on the cell surface an S-layer lattice with p4 square type symmetry and a period of about 13.5 nm. These lattices were shown to be the excellent nanotemplates for deposition of regular metal clusters. The synthesis of the S. ureae S-layer protein is highly efficient, the protein accounts for approximately 10-15 % of the total cell protein content, judged by the SDS-PAGE results. Besides, the S-layer protein production is tightly regulated, since only negligible amounts of S-layer proteins are observed in the medium at different cell growth phases. At the same time, mechanisms of the regulation of S-layer protein synthesis are poorly understood. As several hundreds of S-layer proteins are produced per second during the cell growth, the S-layer gene promoters are among the strongest prokaryotic promoters at all. However, little is known about factors regulating the expression of S-layer genes, furthermore, no experimental identification of other upstream regulatory sequences except for -35/-10 and RBS sequences was presented to our knowledge to date. A sequence of the S-layer gene of S. ureae ATCC 13881, encoding the previously described S-layer protein, was identified in this work by combination of different approaches. The largest part of the gene, excluding its upstream regulatory and ORF 5’ regions, was isolated from a genomic library by hybridization. The sequence of the isolated fragment proved to contain additionally an 1.9 kb non-coding region and an incomplete 0.8 kb ORF region in its 3’-part. No RBS sequence and apparent promoter regions could be identified in front of the latter sequence, suggesting that it might represent a pseudogene sequence. The sequences of the 5’ and upstream regions of the S. ureae ATCC 13881 S-layer gene were identified by combination of PCR-sequencing and chromosome walking. Totally, a sequence of the 6.4 kb long region of S. ureae genomic DNA was established. The sequence of the S. ureae S-layer protein was deduced from the respective gene sequence and agreed with the peptide sequences, obtained after N-terminal sequencing of tryptic peptides of the S. ureae ATCC 13881 S-layer protein. For the protein the name SslA was proposed, which is an abbreviation for “Sporosarcina ureae S-layer protein A”. Several specific features were observed in gene organisation of sslA, which are also characteristic for other S-layer genes. The distance between the -35/-10 region and the ATG initiation codon is unusually long and a 41 bp palindromic sequence is present in the immediate vicinity of the -35/-10 region. Besides, a distant location of the rho-independent transcription terminator, which is 647 bp remote from the stop codon, will result in the mRNA transcripts with unusually long trailer region. Both the long 5’ UTR and the long 3’ trailer may have a regulatory function, either by conferring increased mRNA stability and/or by affecting translation efficiency. Potentially these sequences may define the binding sites of regulatory proteins. For example, palindromic sequences constitute the regulatory sites in several bacterial operons and may act as the binding sites of regulatory dimeric proteins. In respect to the conservation of the sslA sequence high similarity to the sequences of other functional S-layer genes, especially the slfA and slfB genes of B. sphaericus, was observed, whereas the results of phylogenetic analysis support the hypothesis that S-layer genes may have evolved via the lateral gene transfer. Based on the sslA sequence, several recombinant proteins with truncations of the terminal protein parts or C-terminal fusion of either EGFP or histidine tags were constructed. For all the truncated or EGFP-fusion SslA derivatives high level overexpression in E. coli was possible. For native SslA a moderate level of expression was observed suggesting that its high intracellular concentration may downregulate the protein synthesis. Interestingly, fluorescence microscopy indicates the same intracellular localization for heterologously produced recombinant proteins with fusions of EGFP either to the precursor or to the native SslA protein, suggesting that SslA secretion signal is not functional in E. coli. Heterologously produced SslA derivatives with truncations of N-, C- or both N- and C-terminal parts were shown to self- assemble in vitro, although the size of self-assembly structures was different from that observed upon the self-assembly of the native SslA. In the latter case extended self-assembly layers with the size up to 5x10 µm were observed, with a surface area of up to two orders of magnitude higher than that of S-layer patches, routinely isolated from S. ureae surface. Dependent on the applied recrystallization conditions preferential formation of single- or multilayer self-assembly structures was observed.

The assurance of Quality of Service (QoS) to the applications, although identified as a key feature since long ago [1], is one of the fundamental challenges that remain unsolved. In the Cloud Computing context, Quality of Service is defined as the measure of the compliance of certain user requirement in the delivery of a cloud resource, such as CPU or memory load for a virtual machine, or more abstract and higher level concepts such as response time or availability. Several research groups, both from academia and industry, have started working on describing the QoS levels that define the conditions under which the service need to be delivered, as well as on developing the necessary means to effectively manage and evaluate the state of these conditions. [2] propose Service Level Agreements (SLAs) as the vehicle for the definition of QoS guarantees, and the provision and management of resources. A Service Level Agreement (SLA) is a formal contract between providers and consumers, which defines the quality of service, the obligations and the guarantees in the delivery of a specific good. In the context of Cloud computing, SLAs are considered to be machine readable documents, which are automatically managed by the provider's platform. SLAs need to be dynamically adapted to the variable conditions of resources and applications. In a multilayer architecture, different parts of an SLA may refer to different resources. SLAs may therefore express complex relationship between entities in a changing environment, and be applied to resource selection to implement intelligent scheduling algorithms. Therefore SLAs are widely regarded as a key feature for the future development of Cloud platforms. However, the application of SLAs for Grid and Cloud systems has many open research lines. One of these challenges, the modeling of the landscape, lies at the core of the objectives of the Ph. D. Thesis.
García García, A. (2014). SLA-Driven Cloud Computing Domain Representation and Management [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/36579
TESIS

Thesis (M.A.)--City University of Hong Kong, 2005.
Title from title screen (viewed on 27 Mar. 2006) "Master of arts in arbitration and dispute resolution research paper." Includes bibliographical references.

Clostridium difficile is the leading cause of death from gastrointestinal infections in Canada. Current antiobiotic treatment is non-ideal due to the high incidence of relapse and the rise in hyper-virulent antibiotic-resistant strains. Surface layer proteins (SLPs) cover the entire bacterial surface and mediate adherence to host cells. Passive and active immunization against SLPs greatly enhances survival in hamsters, suggesting that antibody-mediated bacterial neutralization may be an effective alternative therapeutic strategy. Using a recombinant-antibody phage display library, and SLPs from strain QCD 32g58 as bait antigen, we isolated and extensively characterized 11 SLP-specific recombinant single-domain antibodies (sdAbs), in terms of affinity and specificity, intrinsic stability, and ability to inhibit cell motility. Several sdAbs exhibit promising characteristics for a potential oral therapeutic based on their high affinity, high thermal stability, and resistance to pepsin digestion. Our study provides the basis of a proof-of-principle model with which to develop specific, broadly neutralizing and intrinsically stable antibodies for the oral therapy of C. difficile infections, as an alternative to conventional antibiotic treatment.

This work presents the mathematical and computational aspects of a smooth dissipative particle dynamics with dynamic virtual particle allocation method (SDPD-DV) for modeling and simulation of mesoscopic fluids in wall-bounded domains. The SDPD-DV method is realized with fluid particles, boundary particles and dynamically allocated virtual particles near solid boundaries. The physical domain in SDPD-DV contains external and internal solid boundaries, periodic inlets and outlets, and the fluid region. The solid boundaries of the domain are represented with boundary particles which have an assigned position, wall velocity, and temperature upon initialization. The fluid domain is discretized with fluid particles placed in a global index. The algorithm for nearest neighbor particle search is based on a combination of the linked-cell and Verlet-list approaches and utilizes large rectangular cells for computational efficiency. The density model of a fluid particle in the proximity of a solid boundary includes the contribution from the virtual particles in its truncated support domain. The thermodynamic properties of a virtual particle are identical to those of the corresponding fluid particle. A periodic boundary particle allocation method is used at periodic inlets and outlets. Models for the conservative and dissipative forces on a fluid particle in the proximity of a solid boundary are presented and include the contributions of the virtual particles in its truncated support domain. The integration of the fluid particle position and momentum equations is accomplished with an implementation of the velocity-Verlet algorithm. The integration is supplemented by a bounce-forward algorithm in cases where the virtual particle force model is not able to prevent particle penetration. The integration of the entropy equation is based on the Runge-Kutta scheme. In isothermal simulations, the pressure of a fluid particle is obtained by an artificial compressibility formulation for liquids and the ideal gas law for compressible fluids. Sampling methods used for particle properties and transport coefficients in SDPD-DV are presented. The self-diffusion coefficient is obtained by an implementation of the generalized Einstein and the Green-Kubo relations. Field properties are obtained by sampling SDPD-DV outputs on a post-processing grid that allows harnessing the particle information on desired spatio-temporal scales. The isothermal (without the entropy equation) SDPD-DV method is verified and validated with simulations in bounded and periodic domains that cover the hydrodynamic and mesoscopic regimes. Verification is achieved with SDPD-DV simulations of transient, Poiseuille, body-force driven flow of liquid water between plates separated. The velocity profiles from the SDPD-DV simulations are in very good agreement with analytical estimates and the field density fluctuation near solid boundaries is shown to be below 5%. Additional verification involves SDPD-DV simulations of transient, planar, Couette liquid water flow. The top plate is moving and separated from the bottom stationary plate. The numerical results are in very good agreement with the analytical solutions. Additional SDPD-DV verification is accomplished with the simulation of a body-force driven, low-Reynolds number flow of water over a cylinder of radius R=0.02m. The SDPD-DV field velocity and pressure are compared with those obtained by FLUENT. An extensive set of SDPD-DV simulations of liquid water and gaseous nitrogen in mesoscopic periodic domains is presented. For the SDPD-DV simulations of liquid water the mass of the fluid particles is varied between 1.24 and 3.3e-7 real molecular masses and their corresponding size is between 1.08 and 323 physical length scales. For SDPD-DV simulations of gaseous nitrogen the mass of the fluid particles is varied between 6.37e3and 6.37e6 real molecular masses and their corresponding size is between 2.2e2 and 2.2e3 physical length scales. The equilibrium states are obtained and show that the particle speeds scale inversely with particle mass (or size) and that the translational temperature is scale-free. The self-diffusion coefficient for liquid water is obtained through the mean-square displacement and the velocity auto-correlation methods for the range of fluid particle masses (or sizes) considered. Various analytical expressions for the self-diffusivity of the SDPD fluid are developed in analogy to the real fluid. The numerical results are in very good agreement with the SDPD-fluid analytical expressions. The numerical self-diffusivity is shown to be scale dependent. For fluid particles approaching asymptotically the mass of the real particle the self-diffusivity is shown to approach the experimental value. The Schmidt numbers obtained from the SDPD-DV simulations are within the range expected for liquid water. The SDPD-DV method (with entropy) is verified and validated with simulations with an extensive set of simulations of gaseous nitrogen in mesoscopic, periodic domains in equilibrium. The simulations of N2(g) are performed in rectangular domains. The self-diffusion coefficient for N2(g) at equilibrium states is obtained through the mean-square displacement for the range of fluid particle masses (or sizes) considered. The numerical self-diffusion is shown to be scale dependent. The simulations show that self-diffusion decreases with increasing mass ratio. For a given mass ratio, increasing the smoothing length, increases the self-diffusion coefficient. The shear viscosity obtained from SDPD-DV is shown to be scale free and in good agreement with the real value. We examine also the effects of timestep in SDPD-DV simulations by examining thermodynamic parameters at equilibrium. These results show that the time step can lead to a significant error depending on the fluid particle mass and smoothing length. Fluctuations in thermodynamic variables obtained from SDPD-DV are compared with analytical estimates. Additional verification involves SDPD-DV simulations of steady planar thermal Couette flow of N2(g). The top plate at temperature T1 =330K is moving at Vxw =30m/s and is separated by 10-4 m from the bottom stationary plate at T2=300K. The SDPD-DV velocity and temperature fields are in excellent agreement with those obtained by FLUENT.

La turbine Pelton est une turbine hydraulique dont le fonctionnement se caractérise par l'interaction d'un jet d'eau avec les augets d'une roue. Cette étude a pour but de comprendre les phénomènes influençant le jet et son interaction avec les augets. Pour cela deux actions différentes ont été menées. Une première a visé à caractériser expérimentalement la fragmentation d'un jet de turbine Pelton. La seconde s'est attachée à développer une méthode numérique pouvant mener'à la simulation précise de jets réels de turbines Pelton. La partie expérimentale a permis de déterminer le mode de fragmentation de ces jets (atomisation turbulente), mais aussi l'influence de la rugosité des parois de l'injecteur sur les performances de la turbine. La participation de ce travail à un projet expérimental a permis de montrer l'influence de l'écoulement en sortie d'injecteur sur la fragmentation du jet. Les phénomènes physiques influençant principalement l'évolution du jet ont ainsi été déterminés. La partie numérique a eu pour but de mettre en place une méthode permettant de simuler l'évolution d'un jet de turbine Pelton (fragmentation) et son interaction avec un auget. Etant donnés les progrès de la méthode SPH-ALE pour la simulation d'impact de jets pour les turbines Pelton, il a été décidé d'adapter cette méthode pour les simulations visées. Ainsi une étude du choix de la vitesse des interfaces de problème de Riemann a permis de réaliser un modèle multiphase stable pour les forts rapports de densité (eau-air). Cette méthode s'est avérée garantir les propriétés de continuité de vitesse normale et de pression à l'interface entre les fluides. L'ajout des phénomènes de tension de surface s'est fait par l'adaptation du modèle CSF (Continuum Surface Force) et le développement d'un second modèle nommé Laplace Law Pressure Correction (LLPC).L'intégration du saut de pression dans le solveur de Riemann a nécessité une étude précise du calcul de la courbure et a permis d'améliorer la simulation de loi de Laplace. La méthode numérique a été ensuite validée sur les cas académiques d'onde gravitaire, de rupture de barrage et d'oscillation de goutte. Les ressources en mémoire et le temps de calcul associé à cette méthode ont nécessité la parallélisation du code de calcul. Le caractère lagrangien de la méthode a très largement influencé la méthode de découpe de domaine pour permettre une bonne répartition de la charge de calcul entre les différents processeurs. En conclusion les phénomènes physiques influençant la fragmentation de jets issus d'injecteurs de turbine Pelton sont désormais mieux connus et ils ont pu être introduits dans la méthode numérique. Les prochains développements porteront sur la simulation de jets dont la condition d'entrée s'attachera à être représentative des caractéristiques d'un écoulement en sortie d'un injecteur de turbine Pelton.

La Qualité de Service (Quality of Service - QoS) est une garantie de paramètres réseau (bande passante élevée, délai court, etc.). Dans un réseaux inter-domaine, elle peut être assurée par des contrats entre domaines appelés Service Level Agreements (SLA). Dans cette thèse, nous nous intéressons d’abord à l’étape de négociation de SLA : la sélection des SLA proposés par un domaine. Nous proposons des méthodes exactes et approchées permettant aux domaines de proposer les SLA qui maximisent leurs revenus. Nous étudions également l'impact de la réputation des domaines sur cette négociation. Au niveau de l’instanciation des SLA, nous nous intéressons au calcul de chemins qui prennent en compte les encapsulations de protocoles (afin de pallier l’hétérogénéité technologique des domaines). En utilisant des outils de théorie des langages, nous proposons la première solution polynomiale au calcul de chemins dans un tel contexte
Quality of Service (QoS) is a guarantee of network parameters (high bandwidth, short delay, etc.). In an inter-domaine network, it can be provided by contracts between domains, called Service Level Agreements (SLAs). In this thesis, we first focus on the SLA negotiation step, i.e., the selection of SLAs proposed by a domain. We provide exact and approximate methods that allow the domains to propose the SLAs that maximize their revenues. We also study the impact of the domain reputation on the negotiation process. Regarding the SLA instantiation step, we focus on path computation processes that take into account the encapsulation of protocols (in order to overcome the domain technological heterogeneity). Using tools from Language Theory, we provide the first polynomial solution to the path computation problem in this context

Couverture)Les rétrovirus sont des virus enveloppés à ARN simple brin omniprésents dans le monde animal et sources de nombreuses pathologies. Les rétrovirus de vertébrés comprennent sept genres dont les gamma et deltarétrovirus qui sont l’objet de ces travaux. Les rétrovirus dits endogènes (ERV), par opposition à leurs homologues infectieux exogènes, sont présents dans les cellules germinales et font partie intégrante du patrimoine génétique, avec transmission mendélienne. Au cours de l'évolution, les ERV ont fait l'objet de mutations, rendant défectives la plupart des copies dans les génomes de vertébrés, avec quelques exceptions notoires. De fait, certaines copies maintiennent de larges cadres de lecture suite à une pression de sélection positive.Rétrovirus exogènes et ERV partagent une organisation génétique similaire. Leurs glycoprotéines d’enveloppe (Env), dont une des propriétés est de lier un récepteur cellulaire, comprennent une composante de surface (SU) associée à une partie transmembranaire (TM). La SU des Env γ et -rétrovirales porte un module RBD (Receptor-Binding Domain) qui lie un récepteur appartenant à la famille SLC (Solute Carriers) des transporteurs de nutriments. Les SLC présents à la surface cellulaire conditionnent le métabolisme des cellules. Afin de pallier l'absence d'anticorps fiables reconnaissant les parties extracellulaires (exofaciales) des SLC, le laboratoire a dérivé des RBD solubles comme ligands des SLC, permettant de suivre leur expression à la surface cellulaire et ainsi, évaluer le métabolisme cellulaire.Parmi les ERV, certaines env partiellement ou entièrement conservées jouent un rôle physiologique essentiel dans les organismes qui les portent. Une hypothèse de mon laboratoire d’accueil est l’existence de RBD endogènes de mammifères capables de moduler le métabolisme cellulaire de leurs hôtes. Dans ce contexte, mes travaux sont articulés autour de deux axes : (i) identifier et produire de nouveaux RBD dérivés des ERV et (ii) identifier de nouveaux transporteurs de type SLC reconnus par des RBD issus de rétrovirus exogènes et ERV de mammifères. Nous avons identifié et caractérisé deux nouveaux RBD humains endogènes (HERV-41 et HERV-89), entrés et conservés chez les primates de l’Ancien Monde il y a environ 35 millions d’années. Nous avons caractérisé leurs séquences PBS (Primer Binding Site), amorces putatives de la réplication rétrovirale, comme étant complémentaires de l’ARNtLeu ou ARNtArg pour HERV-89, et de l'ARNtGlu pour HERV-41. Les séquences env les plus proches dans le génome humain présentent respectivement 38% et 69% d'identité, indiquant l'appartenance de HERV-89 à deux nouvelles familles d'Env. Nous avons pu produire le RBD soluble de HERV-89, montrer que son récepteur est distinct de l'Env HERV ayant la séquence la plus homologue, et étudier sa distribution tissulaire. Le RBD HERV-89 lie un récepteur sur de nombreuses cellules souches et lignées cellulaires établies et nous avons montré par immunohistochimie que le récepteur est exprimé de manière différentielle dans les tissus humains sains et tumoraux. Parallèlement, nous avons dérivé une banque d'expression de 170 SLC que nous avons utilisée pour le criblage à haut-débit de récepteurs des Env gamma et deltarétrovirales. Cette banque nous a permis d'identifier le récepteur, longtemps recherché, de l’Env du virus de la leucémie bovine (BLV). De plus, en utilisant la transfection d'une banque d’expression d’ADNc dans des cellules de hamster, nous avons aussi identifié le récepteur du virus endogène félin ERV-DC14/FeLV-D comme étant le transporteur de cuivre et de cisplatine CTR1/SLC31A1.L’identification du récepteur de BLV pourrait notamment aider dans la lutte contre la transmission du virus et les pathologies associées qui affectent environ 5% du bétail infecté. De plus, les BLV-RBD et DC14-RBD constituent respectivement de nouveaux marqueurs et modulateurs potentiels du métabolisme, dont celui du cuivre
Retroviruses are enveloped, single-stranded RNA viruses, that are omnipresent in animals and the causal agents of a large array of pathologies. Vertebrate retroviruses are divided into seven genera, including the γ and -retroviral groups, which we study particularly. Endogenous retroviruses (ERV), as opposed to exogenous infectious viruses, are present in germline cells and as such are bona fide components of the host genome, with Mendelian transmission. Most ERV have been inactivated by purifying mutations during evolution, although a few copies have been subjected to positive selection pressure with conserved open reading frames (ORFs).Exogenous viruses and ERV that belong to gamma and deltaretroviruses share similar genetic organization and their envelope glycoproteins (Env) comprises a transmembrane (TM) and a surface (SU) component, which binds a specific receptor on the host cell membrane. The SU contains a receptor-binding domain (RBD), responsible for receptor recognition, while TM engages membrane fusion and harbors an immunosuppressive domain. Noticeably, some ERVs have maintained entire or partial ORFs in env, which have been shown, in certain cases, to have essential physiological functions.Another common feature of gamma and deltaretroviral Env is the nature of their receptors, which, when identified, all belong to the solute carrier family of nutrient transporters (SLCs). The laboratory derived soluble RBDs from complete Env that can bind cognate receptors and be used to monitor SLC receptor expression at the cell surface. This important property of RBDs overcomes the notorious lack of reliable anti-SLC exofacial antibodies and provides a new way to evaluate, or even modulate, cell metabolism.Our laboratory postulates that some endogenous RBD-coding genes have been positively selected in their hosts for properties linked to binding SLCs and modulating host cell metabolism. In this context, the aim of my work was to: (i) search for new natural endogenous RBDs and (ii) characterize SLC transporters recognized by RBDs derived from ERVs or exogenous infectious mammalian retroviruses.Here, we describe the identification of two novel human endogenous RBDs (HERV-41 and HERV-89), which each harbor a significant ORF. We estimated that both RBDs have been introduced into Old World primate genomes 35 MYA ago, after the separation with New World monkeys. HERV-89 and HERV-41 are included within retroviral elements that comprise potential primer binding sites (PBS) complementary to tRNALeu or tRNAArg, for HERV-89, and tRNAGlu, for HERV-41. The envs of HERV-89 and HERV-41 do not share more than 38% and 69% amino acid identity with the closest known HERVs, respectively, which indicates that they belong to two new Env families. We derived a soluble HERV-89 RBD and monitored its receptor cell and tissue distribution. Using the ligand by flow cytometry, we observed that a HERV-89 receptor is expressed in a large panel of established cell lines and stem cells. Immunohistochemistry on 94 healthy and tumor human tissue samples showed that HERV-89 receptor is largely distributed, with distinct expression patterns in healthy and tumor tissues. In parallel, we derived a 170 gene-containing SLC expression library for high throughput screening of SLC/ligand interactions. Using this partial human SLC library, we identified the long-sought receptor for bovine leukemia virus (BLV). Moreover, transfection of a cDNA library expression into hamster cells, led us to identify CTR1/SLC31A1, the copper and cisplatin transporter, as the receptor for the feline ERV-DC14/FeLV-D.As a ligand for the BLV receptor, BLV-RBD may be used to help controlling BLV transmission and prevent associated pathologies that affect 5% of infected cattle. Also, BLV-RBD and DC14-RBD can now be used as metabolic markers and modulators of their SLC cognate receptors, including copper metabolism, in the case of DC14-RBD

La recherche de nouveaux moyens de sélectivité pour les traitements laser dans le domaine biomédical n'est pas actuellement une thématique active, contrairement à l'analyse par la lumière des cellules et des tissus qui connaît une phase intense d'évolution. Mon travail a consisté à proposer un système sélectif de dépôt de lumière et à chercher les applications potentielles d'un tel dispositif. J'ai réalisé un montage expérimental utilisant un modulateur spatial de lumière à cristaux liquides et permettant de contrôler l'asservissement de la lumière traitante sur l'imagerie vidéo de la surface à traiter. Ce contrôle fait appel à un traitement automatique des images. Les résultats expérimentaux ont permis d'évaluer les performances pouvant être atteintes par le dispositif. En effet nous obtenons une résolution spatiale de l'ordre de 30 æm sans avoir atteint les limites de notre montage, et une robustesse et simplicité de mise en œuvre grâce à l'absence de parties mobiles dans le dispositif. Par contre notre solution est limitée quant à la dose maximale d'énergie délivrable. Fonction des performances actuelles et de celles que nous jugeons accessibles moyennant améliorations, nous nous sommes attachés à rechercher l'application pour laquelle ce dispositif pouvait avoir un apport conséquent. Nous avons été amené à mettre de côté les applications les plus courantes actuelles de traitement laser pour des raisons, soit de processus biologiques mis en œuvre, soit de limitations du dispositif. Par contre il est apparu que les caractéristiques d'un tel dispositif semblent tout à fait adaptées à la manipulation de la croissance cellulaire et tissulaire
Research of new selectivity means for laser treatment in the biomedical domain is not currently an active field, contrary to the analysis of cells and tissues by light which is in an intense phase of evolution. My work consisted of proposing a selective light deposition system and of looking for the potential applications of such a device. I have achieved an experimental setup using a liquid crystal spatial light modulator and allowing the control of the light repartition relating to the video image of the surface to be treated. This control uses an automatic image analysis. Experimental results have allowed the evaluation of the performances that can be actually reached by the irradiation system. In fact we get a spatial resolution about 30 æm without having reached the limits of our system, and a hardiness and a simplicity of implementation because we use no mobile parts in the system. On the other hand our solution is limited as for the maximal dose of the deliverable energy. Function of the actual performances and those that we think accessible after adding improvement, we have tried to look for the application for which this irradiation system could have a consequent contribution. We have been brought to put a side the most current applications of laser treatments because of either the implemented biologic processes or the limitations of the system. However it appears that the characteristics of the system seem to be perfectly adapted to the manipulation of the cellular and tissular growth

The Ste20-like kinase SLK plays a pivotal role in cell migration and focal adhesion turnover. SLK activity is regulated by the LIM domain-binding proteins Ldb1/2. In addition to playing role in tumor initiation and progression, these proteins have been demonstrated to interact with LMO4. Therefore, this project assessed the ability of LMO4 to interact and regulate SLK activity. Results show that LMO4 can directly bind to SLK and activate its kinase activity. LMO4 can be co-precipitated with SLK following the induction of cell migration by scratch wounding. Cre deletion of LMO4 inhibits cell migration and SLK activation, and impairs Ldb1 and SLK recruitment to the leading edge of migrating cells. Src/Yes/Fyn-deficient cells (SYF) express very low levels of LMO4 and do not recruit SLK to the leading edge. Src-family kinase inhibition impairs SLK recruitment to the leading edge, suggesting that both expression of LMO4 and the recruitment of SLK to the leading edge require c-Src activity. In conclusion, cell migration and activation of SLK requires its recruitment to the leading edge by LMO4 in a Src-dependent manner. This study also investigated whether LMO4 deletion through MMTV-Cre-driven excision would impair mammary tumorigenesis in a PyMT mouse model of breast cancer. No difference in Overall Survival was observed between animals with and without LMO4 expression. Western blot analysis and IHC showed that tumors expressed LMO4 protein in animals genotyped as Cre-positive. This result suggests that expression of LMO4 is required for tumor initiation in the PyMT model of murine mammary carcinoma. This project has established a novel cytosolic role for the transcriptional co-activator LMO4 and validated it’s involvement in the regulation of SLK and cell migration. This pathway may provide a novel therapeutic strategy as LMO4 appears to be critical to the initiation and progression of breast cancer.

Cette thèse porte sur les relations entre les processus SLE, les ensembles CLE et le champ libre Gaussien. Dans le chapitre 2, nous donnons une construction des processus SLE(k,r) à partir des boucles des CLE(k) et d'échantillons de restriction chordale. Sheffield et Werner ont prouvé que les CLE(k) peuvent être construits à partir des processus d'exploration symétriques des SLE(k,r).Nous montrons dans le chapitre 3 que la configuration des boucles construites à partir du processus d'exploration asymétrique des SLE(k,k-6) donne la même loi CLE(k). Le processus SLE(4) peut être considéré comme les lignes de niveau du champ libre Gaussien et l'ensemble CLE(4) correspond à la collection des lignes de niveau de ce champ libre Gaussien. Dans la deuxième partie du chapitre 3, nous définissons un paramètre de temps invariant conforme pour chaque boucle appartenant à CLE(4) et nous donnons ensuite dans le chapitre 4 un couplage entre le champ libre Gaussien et l'ensemble CLE(4) à l'aide du paramètre de temps. Les processus SLE(k) peuvent être considérés comme les lignes de flot du champ libre Gaussien. Nous explicitons la dimension de Hausdorff de l'intersection de deux lignes de flot du champ libre Gaussien. Cela nous permet d'obtenir la dimension de l'ensemble des points de coupure et des points doubles de la courbe SLE, voir le chapitre 5. Dans le chapitre 6, nous définissons la mesure de restriction radiale, prouvons la caractérisation de ces mesures, et montrons la condition nécessaire et suffisante de l'existence des mesures de restriction radiale.

Les opérations de préparation ou de FAO en fabrication additive (FA) par fusion sur lit de poudre (FLP) consistent en des opérations complexes telles que la définition de l’orientation des pièces, la conception des supports, l’imbrication ou le nesting des pièces, etc. La définition de l’orientation des pièces dans l’espace de production est la première étape et plusieurs études ont montré que toutes les étapes restantes dépendent d’elle tout comme la qualité, le coût ainsi que le temps de production de la pièce. Sa définition n’est donnée que par deux paramètres d’angle de rotation dans la référence globale de la machine, mais leur définition est complexe et nécessite de fortes compétences dans le domaine. Des études dans la littérature ont montrées que les utilisateurs industriels se basent sur leurs connaissancesmétier pour y parvenir. Aujourd’hui, malgré les progrès techniques, il y aencore un manque d’outils et de méthodes pour prendre en compte cette expertise formalisée. Dans ce contexte, cette thèse (issue du projet ANR COFFA) propose des méthodes et des outils pour intégrer efficacement les connaissances formalisées des experts dans le processus de prise de décision sur les paramètres de la FAO dans le domaine de FLP et de la FA en général.Dans un premier temps, la revue des méthodes d’utilisation d’expertise dansla prise de décision en FAO de fabrication traditionnelle est présentée dans le but de trouver les inconvénients et possibilités pour une intégration en FA. En deuxième lieu, une investigation des types de connaissances pouvant être utilisés pour l’aide à la prise de décision est effectuée. Cette partie du travail explore également les ressources en connaissances disponibles pour la définition de l’orientation des pièces dans la littérature mais aussi dans la pratique industrielle. La troisième partie du travail présente une nouvelle approche pour transformer les connaissances de type règle d’action en des fonctions de désirabilité. Cette approche permet notamment d’évaluer ces règles d’action sur des pièces et d’obtenir une appréciation quantitative qui est considérée comme le niveau de respect de la règle (lorsque les paramètres de la FAO s’appliquent à la pièce). Ensuite cette approche est appliquée aux règles d’action trouvées dans la deuxième partie du travail pour établir des modèles quantitatifs destinés au calcul de la désirabilité d’orientation des pièces. Enfin, un outil de calcul de cette désirabilité d’orientation et d’aide à la décision est présenté. L’utilisation de l’outil est illustrée par des études de cas de pièces industrielles dont les résultats sont comparés à ceux d’outils commerciaux, et à travers des tests réalisés avec des étudiants en écoles l’ingénieurs.La principale sortie de ce projet est la fourniture de moyens numériques pour aider les opérateurs de FAO à prendre des décisions sur les paramètres de fabrication optimaux en fonction de l’expertise de l’entreprise. De plus, l’approche présentée offre la possibilité de re-concevoir des pièces en ciblant les surfaces qui ont une faible désirabilité par rapport à l’orientation de la pièce
Pre-processing or CAM operations in additive manufacturing (AM) by powder bedfusion (PBF) include complex operations such as the definition of part orientation, the design of support structures, the nesting of parts, etc. The definition of the parts orientation in the manufacturing build space is the first step and several studies have shown that all of the remaining steps depend on it as well as the quality, cost and production time of the part. Its definition is given by only two rotation angle parameters in the global machine reference, but their definition is complex and requires strong skills in the field. Studies in the literature have shown that industrial users rely on their knowledge or expertise of the process to achieve this. Today, despite the technical advances, there is still a lack of tools or methods to take into account this formalized expertise. In this context, this thesis (from ANR COFFA project) proposes methods and tools to efficiently include the formalized knowledge of experts in the decision making process of CAM parameters, in PBF and AM in general.As a first step, the review of methods to use expertise in decision making in traditional manufacturing CAM is presented in order to find the disadvantages and possibilities for integration in AM. Secondly, an investigation of the types of knowledge that can be used for decision support is carried out. This part of the work also explores the knowledge resources available for the definition of part orientation in the research literature but also in the industrial practice. The third part of the work presents a new approach for transforming knowledge of action rule type into desirability functions. This approach allows in particular to evaluate these action rules on parts and to obtain a quantitative appreciation which is considered as the level of respect of the rule (when the CAM parameters applied to the part). Then, this approach is applied to the action rules found in the second part of the work to establish quantitative models for the calculation of orientation desirability. Finally, a tool for the calculation of this orientation desirability and decision-making support is presented. The use of the tool is illustrated through case studies of industrial parts benchmarked with commercial tools, and through tests carried out with engineering school students.The main output of this project is the provision of numerical means to assistCAM operators in their decision-making on optimal manufacturing parameters based on the company expertise. In addition, the approach presented offers the possibility of redesigning parts by targeting surfaces that have a low desirability with respect to the part orientation

La méthode SPH (Smoothed Particle Hydrodynamics) est une méthode numérique sans maillage utilisée dans cette étude pour la discrétisation spatiale des équations de la mécanique des fluides (essentiellement les équations d 'Euler). La méthode SPH rencontre depuis quelques années un certain succès dans la simulation d’écoulements à surface libre car son formalisme lagrangien facilite le traitement et le suivi des interfaces. Cette étude a pour but d’appliquer cette méthode pour la simulation des écoulements â surface libre se produisant dans les turbines Pelton. Le formalisme SPH standard est tout d’abord testé, il permet de valider la faisabilité de ce choix mais montre également les limites de la méthode SPH standard, en terme de précision et de fiabilité notamment. Le choix s'est alors porté vers une formulation hybride SPH-ALE (Arbitrary Lagrange Euler) qui entretient une certaine filiation avec le formalisme des volumes finis. SPH-ALE utilise en effet une formulation conservative des équations du mouvement et est capable théoriquement de décrire l'écoulement quelque soit le déplacement des points de discrétisation. Par ailleurs, sur un plan purement numérique, ce formalisme permet l'utilisation de schémas numériques décentrés, en particulier les schémas de type Godunov et leurs variantes d’ordre supérieur. Cette méthode hybride se révèle en pratique nettement supérieure A la méthode standard pour les applications visées. La stabilité des simulations est largement renforcée, et la précision des résultats est fortement améliorée. En particulier le champ de pression retrouve une forme satisfaisante sans lissage numérique particulier. La méthode hybride facilite également le traitement des conditions limites. Alors que ce point constitue une difficulté majeure pour la méthode SPH standard, la méthode SPH-ALE permet de traiter les conditions limites à travers des flux aux frontières qui peuvent être eux-aussi décentre��s. La mise en place d’un traitement cohérent et rigoureux des conditions limites constitue la principale contribution de ce travail de thèse. La méthode SPH-ALE est finalement testée sur des cas représentatifs des applications visées et fournit des résultats satisfaisants. En particulier le champ de pression en paroi solide est prédit correctement. En conclusion, les développements effectués dans cette étude ont été guidés par l'application en turbine Pelton qui était visée. La nécessité de manipuler des géométries complexes et d'obtenir un niveau de précision correct ont conduit à privilégier et à développer la méthode hybride SPH-ALE. Ce travail ouvre des perspectives prometteuses de développement rapide grâce au lien existant entre SPH-ALE et la méthode des volumes finis
The SPH (Smoothed Particle Hydrodynamics) method is a meshless numerical method used in this study to spatially discret ize fluid mechanics equations ( mostly 'Euler equations). Sin ce few years, SPH is becoming successfull in simulating free surface flows thanks to its lagrangian formalism , which eases the handling of interfaces. This study aims at applying this method to simulate free surface flows as those happening in Pelton turbines. The standard SPH formalism is first tested. This validates the feasability of using SPH for this application but also underlines the weaknesses of the standard method, notably in terms of accuracy and reliabili ty. A hybrid formulation called SPH-ALE (Arbitrary Lagrange Euler) has then been chosen. This method has many similarities with the Finite Volume method. Indeed it uses the conservation form of flow equations and is theoretically able to handle properly any smooth transport field of the discretization points. In addition, from a purely numerical point of view, the SPH-ALE formalism allows a proper use of upwind numerical schemes, and in particular Godunov and higher order schemes. In practice, this hybrid method behaves better than the standard one for the targeted applications. Stability and accuracy of the simulations are greatly improved. In particular the pressure field can be correctly predicted without resorting to any numerical smoothing. . The introduction of boundary conditions is also easier with the hybrid method. Whereas this is one major challenge for the standard SPH method, SPH-ALE can handle boundary conditions through boundary fluxes which can also be computed in an upwind fashion. The setting of a consistent and rigorous boundary treatment is the main contribution of this study. The SPH-ALE method is tested and validated on typical cases, giving satisfacory results, particularly for the pressure field on solid boundaries. To conclude, developments presented in this study have been driven by the targeted application in Pelton turbines. The need for a proper handling of bodies with complex shapes and the requirement of accuracy have lead to a focus on the hybrid SPH-ALE method. This work opens the door to promising perspectives and quick developments thanks to the strong link with the Finite Volumes method

L'approche experimentale choisie consiste a etudier les proprietes spectroscopiques de l'emission spontanee et stimulee pour des composants deja realises. Parallelement, un modele realiste a ete elabore dont la nouveaute reside dans l'inclusion explicite des effets de la densite d'etats de la cavite optique. L'accord est excellent pour les lasers gaas/algaas; l'inclusion des courants associes a la recombinaison dans la cavite permet d'expliquer la superiorite des lasers grinsch sur les lasers sch. Des structures optimisees sont presentees pour les lasers a puits quantiques avec zone active en gainas. Les difficultes rencontrees dans ce systeme tiennent a l'effet auger et aux courants de cavite. D'autre part il persiste dans ce systeme des problemes d'elaboration du materiau et des interfaces auxquels les structures laser a puits quantiques sont plus sensibles que les structures dh traditionnelles a zone active large

L'etude d'un laser a semiconducteur de type a pompage electronique est presentee. Le but de ce travail est la realisation d'un laser compact emettant dans le visible (bleu). Deux aspects distincts ont ete consideres. 1 le pompage electronique du laser ainsi que la realisation d'un dispositif compact. Le faisceau d'electrons permettant le pompage du laser est obtenu a partir d'une cathode comportant des micropointes. Ce composant est une source d'electrons froide, utilisant le principe de l'emission par effet de champ, realise grace aux procedes de la microelectronique conventionnelles et deja utilise dans la fabrication d'ecrans plats. Les travaux presentes relatent l'etude des caracteristiques de ces sources et de leur interet dans le cadre de ce projet. La focalisation du faisceau d'electrons est decrites dans plusieurs cas de figure, et la realisation d'un dispositif compact scelle sous vide statique fonctionnant en mode cathodoluminescent est rapportee. 2 laser semiconducteur ii-vi a grand gap permettant l'emission lumineuse dans le visible. Les heterostructures laser doivent etre specialement adaptees au pompage electronique a cause de la relativement faible profondeur de penetration des electrons pour les energies considerees. La description du fonctionnement des lasers semiconducteurs est donnees dans un premier temps. Il apparait que pour notre application, les structures laser doivent etre de type grinsch (heterostructure a gradient de composition et a separation des confinements) a puits quantiques. Dans un deuxieme temps, les resultats de caracterisation des materiaux laser, par les techniques de cathodoluminescence, de microscopie, de spectroscopie de masse des ions secondaires (sims) et de pompage electronique sont donnes. L'evolution des seuils en fonction de la temperature et les problemes de duree de vie en fonctionnement des lasers semiconducteurs sont plus particulierement traites. Ces resultats sont compares a ceux des diodes laser ii-vi actuelles

L'objet de ce travail est le developpement et l'etude physique des structures lasers a base de composes semiconducteurs ii-vi. Ce sont des heterostructures a confinement separe (sch et grinsch) a puits quantique de cdte/cdmnte et cdte/cdmgte que nous avons etudiees par des mesures optiques. Leurs caracteristiques de gain et de perte ont ete determinees par la methode du ruban de longueur variable, en fonction de la densite d'excitation et de la temperature. Nous montrons que les alliages cdmgte ne sont pas encore de qualite suffisante pour etre utilises comme materiau laser. Par contre, avec cdmnte, nous sommes arrives a obtenir une structure laser fonctionnant a tres bas seuil a temperature ambiante. Ainsi un seuil de 1. 8kw/cm#2 a ete observe pour une cavite de 1300 micrometres de long. Nous avons trouve un tres bon accord entre les mesures d'emission laser en fonction de la longueur de la cavite et les mesures de gain net spectral par la methode du ruban. Nous montrons par ailleurs que cette methode permet d'estimer l'importance des pertes d'origine optique dans les pertes internes du materiau. Le probleme de mecanisme de gain a egalement ete aborde. Nous montrons que, dans notre meilleure structure cdte/cdmnte, l'exciton est toujours present dans le regime de fonctionnement laser entre 80 et 150-200k et participe a la stimulation via un processus de diffusion inelastique avec les electrons. A plus haute temperature, le gain est alors domine par le processus de recombinaison du plasma d'electrons et de trous. En revanche nous n'avons pas pu identifier clairement le mecanisme de gain a 4k. Nos resultats dans cdte/cdmgte montrent que certains mecanismes sont a rejeter (le modele de ding d'excitons distribues de facon inhomogene, le biexciton, etc), et semblent suggerer un mecanisme d'excitons localises dans une distribution d'etats de type exponentiel

Il lavoro è stato suddiviso in tre macro-aree. Una prima riguardante un'analisi teorica di come funzionano le intrusioni, di quali software vengono utilizzati per compierle, e di come proteggersi (usando i dispositivi che in termine generico si possono riconoscere come i firewall). Una seconda macro-area che analizza un'intrusione avvenuta dall'esterno verso dei server sensibili di una rete LAN. Questa analisi viene condotta sui file catturati dalle due interfacce di rete configurate in modalità promiscua su una sonda presente nella LAN. Le interfacce sono due per potersi interfacciare a due segmenti di LAN aventi due maschere di sotto-rete differenti. L'attacco viene analizzato mediante vari software. Si può infatti definire una terza parte del lavoro, la parte dove vengono analizzati i file catturati dalle due interfacce con i software che prima si occupano di analizzare i dati di contenuto completo, come Wireshark, poi dei software che si occupano di analizzare i dati di sessione che sono stati trattati con Argus, e infine i dati di tipo statistico che sono stati trattati con Ntop. Il penultimo capitolo, quello prima delle conclusioni, invece tratta l'installazione di Nagios, e la sua configurazione per il monitoraggio attraverso plugin dello spazio di disco rimanente su una macchina agent remota, e sui servizi MySql e DNS. Ovviamente Nagios può essere configurato per monitorare ogni tipo di servizio offerto sulla rete.

Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2007.
Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 1043. Adviser: Robert O. Bauer. Includes bibliographical references (leaves 78-79) Available on microfilm from Pro Quest Information and Learning.

A time-domain backprojection processor for airborne synthetic aperture radar (SAR) has been developed at the University of Massachusetts’ Microwave Remote Sensing Lab (MIRSL). The aim of this work is to produce a SAR processor capable of addressing the motion compensation issues faced by frequency-domain processing algorithms, in order to create well focused SAR imagery suitable for interferometry. The time-domain backprojection algorithm inherently compensates for non-linear platform motion, dependent on the availability of accurate measurements of the motion. The implementation must manage the relatively high computational burden of the backprojection algorithm, which is done using modern graphics processing units (GPUs), programmed with NVIDIA’s CUDA language. An implementation of the Non-Equispaced Fast Fourier Transform (NERFFT) is used to enable efficient and accurate range interpolation as a critical step of the processing. The phase of time- domain processed imagery is dif erent than that of frequency-domain imagery, leading to a potentially different approach to interferometry. This general purpose SAR processor is designed to work with a novel, dual-frequency S- and Ka-band radar system developed at MIRSL as well as the UAVSAR instrument developed by NASA’s Jet Propulsion Laboratory. These instruments represent a wide range of SAR system parameters, ensuring the ability of the processor to work with most any airborne SAR. Results are presented from these two systems, showing good performance of the processor itself.

The presence of photonic band gap in an arbitrarily shaped photonic structure, particularly structures that are fabricated by exploiting rolled-up nanotechnology, can be understood from the density of optical states. In this thesis, the density of optical states and the local density of optical states in finite-sized photonic structures are calculated using the finite difference time domain method together with a parallelized message passing interface. With this approach, a software package suitable for high-performance computing on multi-platform was published under GNU GPL license. When light is guided to propagate along a rolled-up thin film, whispering gallery mode resonances can be formed in a microtubular structure. Dynamic probing and tuning via a plasmonic nanoparticle-coated glass tip are investigated to demonstrate the transition from dielectric-dielectric to dielectric-plasmonic coupling in the tubular microcavity. The competition of these two coupling mechanisms allow the tuning of the optical cavity modes towards lower and then higher energies in a single coupling system. Moreover, three dimensionally confined higher order axial modes can be selectively coupled and tuned by the glass tip due to their unique spatial distribution of the optical field along the tube axis. In addition, the interaction between sharp optical cavity modes and broad plasmonic modes supported by silver nanoparticles leads to the occurrence of Fano resonance. In particular, Fano resonances occurring at higher-order axial modes has been observed as well. The experimental results are supported by numerical simulations based on the finite difference time domain method. In photonic lattice structures, light propagation behavior can be influenced and defined by the photonic band structure. By designing the unit cell with glide mirror symmetry, topologically protected edge states operating in the visible spectral range have been proposed in two dimensional photonic crystals which can be made of feasible materials. Topological phenomena such as unidirectional waveguiding and/or effective zero refractive index are presented. In addition, a scheme to study topological phase transition in a single photonic crystal device is proposed and studied via unevenly stretching photonic lattice. Moreover, a new method is explored to distinguish the topological phase from the bulk modes. The research presented in this thesis concerns molding the flow of light in specially designed photonic devices for various potential applications. The software package can be used to design and investigate finite-sized photonic structures with an arbitrary shape, which is much faster in terms of computation than other reported techniques and software packages. The rolled-up microcavities can be employed to trap and store light in the way of whispering gallery mode resonances, and the resonant light can be tuned and modulated by a plasmonic nanoparticles-coated glass tip. This research is particularly interesting for optical signal processing, slowing light via Fano resonances, and high sensitive sensing. In addition, the topological photonic crystal design and examination scheme presented in this thesis provide a simplified yet more efficient way to obtain non-trivial topological phase from a tunable photonic crystal that can be verified not only by edge modes but also by bulk modes.:Bibliographic record 1 Abstract 1 LIST OF ABBREVIATIONS and Symbols 3 1 Introduction 9 1.1 Introduction and Motivation 9 1.2 Objectives 11 1.3 Organization of the thesis 12 2 Density of optical states in rolled-up photonic crystals and quasi crystals 15 2.1 Introduction 15 2.1.1 background 17 2.1.2 Infinitely extended ideal photonic crystal 17 2.2 Finite-sized photonic crystal, photonic quasicrystal, and arbitrary photonics structures 20 2.2.1 Numerical algorithm 25 2.2.2 Rolled-up photonic crystals and quasi crystals 30 2.3 Software package 33 2.3.1 Computational performance 33 2.3.2 FPS User interface 35 2.3.3 Detailed tutorial 37 2.3.4 Alternative rolled-up photonic crystals 47 2.3.5 Beyond 3D photonic crystals. 48 2.4 Conclusion 49 3 Rolled-up microesonator 51 3.1 Introduction 51 3.2 Rolled-up microresonators 52 4 Tip-assisted photon-plasmon coupling in three-dimensionally confined microtube cavities 57 4.1 Introduction 57 4.2 Tube and plasmonic particle preparation and characterization 60 4.3 Results and discussion 62 4.4 Axial mode tuning 64 4.5 Fano resonance 65 4.5.1 Background 65 4.5.2 Fano resonance in the tip assisted coupling setup 68 4.6 Conclusion 71 5 Topological photonics 73 5.1 Introduction and motivation 73 5.2 Topological phase transition point 77 5.2.1 Fundamental phase transition point 77 5.2.2 Zero refractive index material 79 5.3 Non-trivial topology in realistic materials 80 6 Topological phase transition in stretchable photonic crystals 85 6.1 Introduction and motivation 85 6.2 SSH model 88 6.3 Photonic crystal 91 6.4 Band structure and end modes of the photonic crystal 99 6.5 Conclusion 101 7 Summary and outlook 103 7.1 Summary 103 7.2 Outlook 104 Bibliography 111 List of figures 127 Publications 133 Acknowledgments 136 Selbständigkeitserklärung 137 Curriculum Vitae 138

Mycobacteria are multifaceted pathogens capable of causing both acute disease as well as an asymptomatic latent infection. Host immune responses during mycobacterial infection involve potent cell effector functions including that of CD4+, CD8+ and γδT cells, macrophages and dendritic cells (DCs). Further, the critical regulators of protective immunity to mycobacterial infection include IFN-γ, IL-12, IL-23, TNF-α, lymphotoxins, CD40, nitric oxide and reactive oxygen species. However, the success of mycobacterial infection often relies in its ability to evade immune surveillance mechanisms mediated by sentinels of host immunity by modulating host signal transduction pathways and expression of immunoregulatory molecules. Therefore, the key to control mycobacterial growth and limit pathogenesis lies in the understanding the interactions between Mycobacterium and primary responders like macrophages and DCs. In this scenario, the role of pattern recognition receptors (PPRs) in orchestrating host immune responses assumes central importance. The cell surface receptors play crucial role in influencing overall immune responses. Of the PRRs, the Toll-like receptors (TLRs) form key immune surveillance mechanisms in recognition as well as control of mycobacterial infection. Among them, TLR2 is the primary interacting receptor on antigen presenting cells that recognize the invading mycobacteria. Mycobacterial cell wall constituents such as LAM, LM, PIM and 19-kDa protein have been shown to activate TLR2 signaling leading to proinflammatory responses. Recent reports have suggested that PE_PGRS antigens of M. tuberculosis interact with TLR2. For example, RV0754, Rv0978c, RV1917c have been implicated in modulation of human DCs. The 19-kDa lipoprotein, LpqH (Rv3763) and LprG (Rv1411c) utilize TLR2 signaling to inhibit macrophage responsiveness to IFN-γ triggered MHC class II expression and mycobacterial antigen presentation. Interestingly, recognition and amplification of pathogenic-specific signaling events play important roles in not only discriminating the invading microbes, but also in regulating explicit immune responses. In this context, integration of key signaling centers, which modulate host immunity to pathogenic mycobacterial infections, remains unexplored. In accordance to above observations, signal transduction pathways downstream to TLRs play a critical role in modulation of battery of host cells genes in terms of expression and production of immune modulatory cytokines and chemokines, recruitment of cellular machineries to site of infections etc. This suggests the decisive role for TLRs in modulation of host cell fate decisions. However, during the ensuing immunity to invading pathogens, beside TLR signaling pathways, various other signaling molecules are thought to execute specific functions in divergent cellular contexts. Recent studies from our laboratory have clearly demarcated a novel cross talk of TLR2-NOTCH1 and TLR2-Wnt signaling pathways during mycobacterial infections. The current study primary focuses on the broad range of cross talk of TLR2 and Sonic hedgehog (SHH) signaling pathways and its functional significance. The present investigation demonstrates that M. bovis BCG, a vaccine strain, triggers a robust activation of SHH signaling in macrophages compared to infection with diverse Gram-positive or Gram-negative microbes. This observation was further evidenced by the heightened SHH signaling signatures during in vivo scenario in cells /tissues from pulmonary tuberculosis (TB) individuals as well as tuberculous meningitis (TBM) patients. Furthermore, we show that the sustained TNF-α secretion by macrophages upon infection with M. bovis BCG is a critical necessity for SHH activation. Significantly, perturbation studies implicate a vital role for M. bovis BCG stimulated TLR2/PI3K/PKC/MAPK/NF-κB axis to induce TNF-α, that contributes to enhance SHH signaling. The TNF-α driven SHH signaling downregulates M. bovis BCG induced TLR2 signaling events leading to modulation of battery of genes that regulate various functions of macrophages genes like Vegf-a, Socs-3, Cox-2, Mmp-9 and M1/M2 genes. Importantly, utilizing whole-genome microRNA (miRNA) profiling, roles for specific miRNAs were identified as the molecular regulators that bring about the negative-feedback loop comprising TLR2-SHH signaling events. Thus, the current study illustrates how SHH signaling tightly regulates the kinetics and strengths of M. bovis BCG specific TLR2 responses, emphasizing a novel role for SHH signaling in host immune responses to mycobacterial infections. As described, variety of host factors contributes for ensuing effective host defenses and modulation of host cell fate decisions. Interestingly, avirulent pathogenic mycobacteria, including the vaccine strain M. bovis BCG, unlike virulent M. tuberculosis, cause extensive apoptosis of infected macrophages, which suggests a significant contribution of the apoptosis process to the initiation and subsequent amplification of innate as well as adaptive immune responses. Among various cues that could lead to apoptosis of host cells, the initiation of the apoptotic machinery by posttranscriptional mechanisms assumes significant importance. Among posttranscriptional control mechanisms, miRNAs are suggested to regulate several biological processes including immune responses. Various effectors of host immunity are known to be regulated by several miRNAs, and a prominent one among them, miRNA-155 (miR-155), often exhibits crucial roles during innate or adaptive immune responses. In this perspective, we identified a novel role of miR-155 during M. bovis BCG induced apoptosis of macrophages. The genetic and signaling perturbations data suggested that miR-155 regulates PKA signaling by directly targeting a negative regulator of PKA, protein kinase inhibitor alpha (PKI-α). Enhanced activation of PKA signaling resulted in induced expression of the apoptotic genes as well as Caspase-3 cleavage and Cytochrome c translocation. Thus, augmented PKA signaling by M. bovis BCG-driven miR-155 dictates cell fate decisions of infected macrophages, emphasizing a novel role for miR-155 in host immunity to mycobacterial infections. In perspective of these studies, important directives are often comprised of sequential and coordinated activation of TLR and NLR-driven signal transduction pathways, thus exhibiting foremost influence in determining the overall strength of the innate immune responses. As described, TLR2 exhibits dominant role in sensing various agonists including pathogen-associated molecular patterns (PAMPs) of microbes at the cell surface and generally considered as major effectuator of proinflammatory responses. Interestingly, NLRs like NOD1 or NOD2 often act in contrary, thus regulating anti-inflammatory responses as well as polarization of T cells towards skewed Th2 phenotype. This presents an interesting conundrum to functionality of DCs or macrophages in terms of effector functions during rapidly evolving immunological processes including effects originating from immunosuppressive effectors such as CTLA-4 or TGF-. DCs like macrophages are important sentinels of innate immunity, possesses array of PRRs that include TLRs and NOD-like receptors (NLRs). Signaling events associated with innate sensors like TLRs and NLRs often act as regulatory circuits that modulate the overall functions of DCs in terms of maturation process, cytokine or chemokine production, receptor expression, migration to secondary lymphoid organs for antigen presentation for effectuating Th polarization. TLR2, while acting as sensors for extracellular cues or endocytic network, drives signaling events in response to recognition of PAMPs including mycobacterial antigens like ESAT-6, PE_PGRS antigens, while NOD1 and NOD2 operate as cytosolic sensors initiating signaling pathways upon recognition of diaminopimelic acid (DAP) and muramyl dipeptide (MDP), components of bacterial peptidoglycan. Thus, TLRs or NOD receptors could trigger similar or contrasting immune responses by cooperative or non-cooperative sensing, consequently exhibiting immense complexity during combinatorial triggering of host DCs-PRR repertoire. In view of these observations, our current investigation comprehensively demonstrated that maturation process of human DCs were cooperatively regulated by signaling cascades initiated by engagements of TLR2, NOD1 and NOD2 receptors. Importantly, combined triggering of TLR2 and NOD receptors abolished the TGF-β or CTLA-4-mediated impairment of human DCs maturation, which required critical participation of NOTCH1-PI3K signaling cohorts. Thus, our data delineated the novel insights in modulation of macrophages and DCs effector functions by mycobacterial TLR2 or NOD agonists and broaden our understanding on the signal dynamics and integration of multiple signals from PRRs during mycobacterial infections. Altogether, our findings establish the understanding of conceptual frame work in fine tuning of TLR2 responses by SHH signaling as well as potential co-operativity among TLRs and NODs to modulate NOTCH1 dependent DCs maturation. Importantly, our study provides mechanistic and functional insights into various molecular regulators of macrophage cell fate decisions like miR-31. miR-150 and miR-155, which can fuel the search for attractive and effective drug targets and novel therapeutics to combat diseases of the hour like tuberculosis.