Two mechanisms of caspase 9 processing in double-stranded RNA- and virus-triggered apoptosis.

Viral double-stranded RNA (dsRNA) is a ubiquitous intracellular "alert signal" used by cells to detect viral infection and to mount anti-viral responses. DsRNA triggers a rapid (complete within 2-4 h) apoptosis in the highly-susceptible HeLa cell line. Here, we demonstrate that the apical event in this apoptotic cascade is the activation of procaspase 8. Downstream of caspase 8, the apoptotic signaling cascade bifurcates into a mitochondria-independent caspase 8/caspase 3 arm and a mitochondria-dependent, caspase 8/Bid/Bax/Bak/cytochrome c arm. Both arms impinge upon, and activate, procaspase 9 via two different cleavage sites within the procaspase 9 molecule (D330 and D315, respectively). This is the first in vivo demonstration that the "effector" caspase 3 plays an "initiator" role in the regulation of caspase 9. The dsRNA-induced apoptosis is potentiated by the inhibition of protein synthesis, whose role is to accelerate the execution of all apoptosis steps downstream of, and including, the activation of caspase 8. Thus, efficient apoptosis in response to viral dsRNA results from the co-operation of the two major apical caspases (8 and 9) and the dsRNA-activated protein kinase R (PKR)/ribonuclease L (RNase L) system that is essential for the inhibition of protein synthesis in response to viral infection.

Gestión de un proyecto de implantación de un repositorio de objetos de aprendizaje

El presente Trabajo Final de Carrera (TFC) está centrado en la Gestión de un Proyecto de Implantación de un Repositorio de Objetos Digitales de Aprendizaje en una Universidad, y queda englobado en el área de Gestión de Proyectos de la Ingeniería Técnica Informática de Gestión.

The processing limits the presentation of the melanoma-associated antigen Melan-A in vitro and in vivo

SUMMARY Both proteasomes and additional proteases play an essential role in the generation of most antigenic peptides presented by MHC class I molecules. Therefore, it is of major importance to characterize the mechanisms leading to the production of correct antigenic peptides to improve the design of vaccines. As a model determinant we used the melanoma-associated protein Melan-A, which contains the immunodominant CTL-epitope Melan-A26/27-35/HLA-A*0201 and against which a high frequency of T lymphocytes has been detected in many melanoma patients. In a first part, we have studied the effects of antigen processing on the induction of a specific T cell response in vivo. Our results have shown that the immunoproteasome, expressed in most cells after exposure to Interferon-γ (IFN-γ) and constitutively in some specialized cells such as dendritic cells, does not efficiently process the HLA¬A2-restricted peptide Melan-A26-35. We have produced recombinant lentiviral vectors (rec. 1v) and vaccinia virus (rec. vv) encoding either preprocessed Melan-A26-35(A27L) peptide or full-length Melan-A(A27L). The immunization of HLA-A2/Kb mice with thoses viruses indicates that immunoproteasomes negatively affect the induction of anti-Melan-A T cell responses in animals immunized with vectors coding for the full- length protein. This negative effect was abrogated in HLA-A2/Kb LMP2-/- mice, lacking the immunoproteasomes. Therefore, we can conclude that the expression of immunoproteasomes limits the induction of the anti-Melan-A T cell response. In a second part, we show that the in vitro degradation of a Melan-A26/27-35 precursor by the proteasomes produces both the final antigenic peptide and N-terminally extended intermediates. When human melanoma cells expressing the corresponding fragments were exposed to specific CTL, those expressing the minimal antigenic sequence were recognized more efficiently than those expressing the N-terminally extended intermediates. We demonstrated that the N-terminally extended intermediates were inefficiently trimmed by cytosolic proteases. These results imply that both proteasomes and post-proteasomal peptidases influence the availability of antigenic peptides and that the efficiency of presentation may be affected by conditions that alter the ratio between fully and partially processed proteasomal products. RESUME Le protéasome ainsi que d'autres protéases jouent un rôle essentiel dans l'apprêtement de la plupart des peptides antigéniques présentés par les molécules de MHC classe I. Il est donc particulièrement important de connaître les mécanismes menant à la production du peptide antigénique correct afin de pouvoir mieux définir de futurs vaccins. Nous avons utilisé la protéine associée au mélanome, Melan-A, contenant un épitope immunodominant Melan-A26/27-35/HLA-A*0201 contre lequel une fréquence élevée de lymphocytes T a été detectée dans plusieurs patients atteints de mélanome. Dans une première partie, nous avons étudié les effets de l'apprêtement du peptide antigéniques Melan-A26-35 sur l'induction de cellules T spécifiques dans la souris. Nos résultats ont démontré que l'immunoprotéasome, exprimé dans la plupart des cellules après exposition à de l'IFN-γ et exprimé constitutivement dans certaines cellules spécialisées, telles les cellules dendritiques, n'apprête pas efficacement le peptide antigénique Melan-A26-35 restreint par HLA-A2 in vitro. Nous avons produit des vecteurs lentiviraux recombinants ainsi que des virus vaccinia codant pour le peptide antigénique Melan-A26-35(A27L) et pour la protéine entière Melan-A(A27L). L'immunisation de souris HLA-A2/Kb avec ces virus démontre que l'immunoprotéasome affecte négativement l'induction d'une réponse T contre Melan¬-A dans les souris immunisées avec des virus contenant la séquence de la protéine entière. Cet effet négatif est complètement aboli dans les souris HLA-A2/Kb LMP2-/- qui n'expriment pas l'immunoprotéasome. Deuxièmement, nous avons demontré que la dégradation d'un peptide précurseur contenant Melan-A26/27-35 par le protéasome produit à la fois le peptide antigénique ainsi que des peptides rallongés à leurs extrémités N-terminales. Lorsque ces fragments sont exprimés dans des cellules humaines et exposés à des cellules T cytotoxiques (CTL), celles qui expriment le peptide antigénique final sont reconnus plus efficacement que celles exprimant les peptides rallongés en N-terminus. Nous avons démontré que les peptides rallongés en N-terminus ne sont pas apprêtés efficacement par les peptidases du cytosol. L'inefficacité de l'apprêtement des peptides rallongés dans le cytosol offre un certain avantage pour les peptides directement produits par le protéasome. Ces résultats impliquent donc que le protéasome ainsi que les peptidases post-proteasomales influencent l'accessibilité des peptides antigéniques.

The connectome mapper: an open-source processing pipeline to map connectomes with MRI.

Researchers working in the field of global connectivity analysis using diffusion magnetic resonance imaging (MRI) can count on a wide selection of software packages for processing their data, with methods ranging from the reconstruction of the local intra-voxel axonal structure to the estimation of the trajectories of the underlying fibre tracts. However, each package is generally task-specific and uses its own conventions and file formats. In this article we present the Connectome Mapper, a software pipeline aimed at helping researchers through the tedious process of organising, processing and analysing diffusion MRI data to perform global brain connectivity analyses. Our pipeline is written in Python and is freely available as open-source at www.cmtk.org.

Bone tissue engineering using foetal cell therapy.

Different cell sources for bone tissue engineering are reviewed. In particular, adult cell source strategies have been based on the implantation of unfractionated fresh bone marrow; purified, culture expanded mesenchymal stem cells, differentiated osteoblasts, or cells that have been modified genetically to express rhBMP. Several limiting factors are mentioned for these strategies such as low number of available cells or possible immunological reaction of the host. Foetal bone cells are presented as an alternative solution and review of actual treatments using these cells is presented. Finally, foetal cells used specifically for bone tissue engineering are characterised and potentially interesting therapeutic options are proposed.

Engineering the thermal emission of macroporous silicon

Todos los cuerpos emiten luz espontaneamente al ser calentados. El espectro de radiacion es una funcion de la temperatura y el material. Sin embargo, la mayoria de los materiales irradia, en general, en una banda espectral amplia. Algunas matereiales, por el contrario, son capaces de concentrar la radiacion termica en una banda espectral mucho mas estrecha. Estos materiales se conocen como emisores selectivos y su uso tiene un profundo impacto en la eficiencia de sistemas sistemas tales como iluminacion y conversion de energia termofotovoltaica. De los emisores selectivos se espera que sean capaces de operar a altas temperaturas y que emitan en una banda espectral muy concisa. Uno de los metodos mas prometedores para controlar y disenar el espectro de emision termico es la utilizacion de cristales fotonicos. Los cristales fotonicos son estructuras periodicas artificiales capaces de controlar y confinar la luz de formas sin precedentes. Sin embargo, la produccion de dichas estructuras con grandes superficies y capaces de soportar altas temperaturas sigue siendo una dificil tarea. Este trabajo esta dedicada al estudio de las propiedades de emision termica de estructuras 3D de silicio macroporoso en el rango espectral mid-IR (2-30 m). En particular, este trabajo se enfoca en reducir la elevada emisividad del silicio cristalino. Las muestras estudiadas en este trabajo tienen una periodicidad de 4 m, lo que limitan los resultados obtenidos a la banda del infrarrojo medio, aunque estructuras mucho mas pequenas son tecnologicamente realizables con el metodo de fabricacion utilizado. Hemos demostrado que el silicio macroporoso 3D puede inhibir completamente la emision termica en su superficie. Mas aun, esta banda se puede ajustar en un amplio margen mediante pequenos cambios durante la formacion de los macroporos. Tambien hemos demostrado que tanto el ancho como la frecuencia de la banda de inhibicion se puede doblar mediante la aplicacion de tecnicas de postprocesado adecuadas. Finalmente hemos mostrado que es posible crear bandas de baja emisividad arbitrariamente anchas mediante estructuras macroporosas aperiodicas.

Characterization of SKI-1/S1P-mediated processing of Arenavirus glycoprotein precursors

Arenaviruses are rodent-born world-wide distributed negative strand RNA viruses that comprise a number of important human pathogens including Lassa virus (LASV) which causes more than 3 00'000 infections annually in Western Africa. Lymphocytic choriomeningitis virus (LCMV) is the prototypic member of the arenavirus family, which is divided in two major subgroups according to serological properties and geographical distribution, the Old World and New World arenaviruses. The envelope glycoprotein precursors (GPCs) of arenaviruses have to undergo proteolytic processing to acquire biological function and to be incorporated into progeny virions. A cellular enzyme is responsible for this processing: the Subtilisin Kexin Isozyme-1 or Site-1 protease (SKI- 1/S1P). In this thesis we have studied the relationship between SKI-1/S1P and the envelope GPs of arenaviruses. In a first project, we investigated the molecular interactions between SKI-1/SIP and arenavirus GPCs. Using SKI-1/SIP mutants, we confirmed previously published observations locating LCMV GPC and LASV GPC processing in the Late Golgi/TGN and ER/cis-Golgi, respectively. A single mutation in the cleavage site of LCMV was sufficient to re-locate SKI- 1/SIP-mediated processing from the late Golgi/TGN to the ER/cis-Golgi. We then demonstrated that the transmembrane domain, the C-terminal tail and the phosphorylation sites of SKI-1/S1P are dispensable for GPC processing. Additionally we identified a SKI- 1/S1P mutant defective for autoprocessing at site Β, B' that was selectively impaired in processing of viral GPCs but not cellular substrates. We also showed that a soluble variant of SKI-1/SIΡ was unable to cleave envelope GPs at the cell surface when added in the culture medium. This study highlighted a new target for small molecule inhibitors that would specifically impair GPC but not cellular substrate processing. In a second project, we identified and characterized two residues: LASV GPC Y253 and SKI-1/S1P Y285 that are important for the SKI-1/SIP-mediated LASV GPC cleavage. An alignment of GPC sequences revealed a conserved aromatic residue in P7 position in the GPCs of Old World and Clade C of New World arenaviruses. Mutations in GPC at position P7 impaired processing efficiency. In SKI-1/S1P, mutating Y285 into A negatively affected processing of substrates containing aromatic residues in P7, without affecting others. This property could be used to develop specific drugs targeting SKI-1/SIP-mediated cleavage of LASV GPC without affecting cellular substrates. As a third project we studied the role of the SKI-1/SIP-mediated processing and the unusual stable signal peptide (SSP) for the folding and secretion of soluble forms of the ectodomain of LASV and LCMV glycoproteins. We provide evidence that the transmembrane domain and the cytosolic tail are crucial for the stability of the prefusion conformation of arenavirus GP and that the SSP is required for transport and processing of full-length GP, but not the soluble ectodomain per se. Taken together, these results will lead to a better understanding of the complex interactions between arenavirus GPCs and SKI-1/S IP, paving the avenue for the development of novel anti-arenaviral therapeutics. - Les Arenavirus sont des virus à ARN négatif distribués mondialement et portés par les rongeurs. Cette famille de virus comprend des virus hautement pathogènes pour l'homme comme le virus de Lassa (LASV) qui cause plus de 300Ό00 infections par année en Afrique de l'Ouest. Le virus de la chorioméningite lymphocytaire (LCMV) est le représentant de cette famille qui est divisée en deux sous-groupes selon des critères sérologiques et de distributions géographiques: arenavirus du Nouveau et de l'Ancien monde. Les glycoprotéines d'enveloppe de ces virus (GPCs) doivent être clivées pour être incorporées dans le virus et ainsi lui permettre d'être infectieux. Une enzyme cellulaire est responsable de ce clivage : la Subtilisin Kexin Isozyme-1 ou protéase Site-1 (SKI-l/SlP). Dans cette thèse, nous avons étudié la relation entre cette enzyme cellulaire et les GPs des arenavirus. Dans un premier temps, nous avons étudié les interactions moléculaires entre SKI- 1/S1P et GPC. A l'aide de mutants de SKI-l/SlP, nous avons confirmé des résultats précédemment publiés montrant que les glycoprotéines d'enveloppe de LASV sont clivés dans le réticulum endoplasmique/cis-Golgi alors que celles de LCMV sont clivées dans le Golgi tardif/TGN. Une seule mutation dans le site de clivage de la glycoprotéine de LCMV est suffisante pour changer le compartiment cellulaire dans lequel est clivée cette glycoprotéine. Ensuite, nous avons démontré que le domaine transmembranaire, la partie cytosolique C-terminale ainsi que les sites de phosphorylations de cette enzyme ne sont pas indispensables pour permettre le clivage de GPC. De plus, nous avons identifié un mutant de SKI-l/SlP dans lequel Γ autoprocessing au site B,B' est impossible, incapable de cliver GPC mais toujours pleinement fonctionnelle envers ses substrats cellulaires. Nous avons également démontré qu'une forme soluble de SKI-l/SlP ajoutée dans le milieu de culture n'est pas capable de couper GPC à la surface de la cellule. Cette étude a défini une nouvelle cible potentielle pour un médicament qui inhiberait le clivage des glycoprotéines des arenavirus sans affecter les processus normaux de la cellule. Dans un second project, nous avons identifié deux acides aminés, LASV GPC Y253 et SKI-l/SlP Y285, qui sont important pour le clivage de LASV GPC. Un alignement des séquences de clivage des GPCs a montré qu'un résidu aromatique est conservé en position P7 du site de clivage chez tous les arenavirus de l'Ancien monde et dans le clade C des arenavirus du Nouveau monde. Une mutation de cet acide aminée dans GPC réduit l'efficacité de clivage par SKI-l/SlP. Mutation de la tyrosine 285 de SKI-l/SlP en alanine affecte négativement le clivage des substrats contenant un résidu aromatique en position P7 sans affecter les autres. Cette propriété pourrait être utilisée pour le développement de médicaments spécifiques ciblant le clivage de GPC. Finalement, nous avons étudié le rôle du processing accomplit par SKI-l/SlP et du signal peptide pour le pliage et la sécrétion de formes solubles des glycoprotéines de LASV et LCMV. Nous avons montré que le domaine transmembranaire et la partie cytosolique de GP sont crucials pour la stabilité de la conformation pre-fusionnelle des GPs et que SSP est nécessaire pour le transport et le processing de GP, mais pas de son ecto-domaine soluble. En conclusion, les résultats obtenus durant cette thèse permettrons de mieux comprendre les interactions complexes entre SKI-l/SlP et les glycoprotéines des arenavirus, ouvrant le chemin pour le développement de nouveaux médicaments anti-arénaviraux.

Specific processing of tenascin-C by the metalloprotease meprin beta neutralizes its inhibition of cell spreading

The metalloprotease meprin has been implicated in tissue remodelling due to its capability to degrade extracellular matrix components. Here, we investigated the susceptibility of tenascin-C to cleavage by meprin beta and the functional properties of its proteolytic fragments. A set of monoclonal antibodies against chicken and human tenascin-C allowed the mapping of proteolytic fragments generated by meprin beta. In chicken tenascin-C, meprin beta processed all three major splicing variants by removal of 10 kDa N-terminal and 38 kDa C-terminal peptides, leaving a large central part of subunits intact. IN similar cleavage pattern was found for large human tenascin-C variant where two N-terminal peptides (10 or 15 kDa) and two C-terminal fragments (40 and 55 kDa) were removed from the intact subunit. N-terminal sequencing revealed the exact amino acid positions of cleavage sites. In both chicken and human tenascin-C N-terminal cleavages occurred just before and/or after the heptad repeats involved in subunit oligomerization. In the human protein, an additional cleavage site was identified in the alternative fibronectin type III repeat D. Whereas all these sites are known to be attacked by several other proteases, a unique cleavage by meprin beta was located to the 7th constant fibronectin type III repeat in both chicken and human tenascin-C, thereby removing the C-terminal domain involved in its anti-adhesive activity. In cell adhesion assays meprin beta-digested human tenascin-C was not able to interfere with fibronectin-mediated cell spreading, confirming cleavage in the anti-adhesive domain. Whereas the expression of meprin beta and tenascin-C does not overlap in normal colon tissue, inflamed lesions of the mucosa from patients with Crohn's disease exhibited many meprin beta-positive leukocytes in regions where tenascin-C was strongly induced. Our data indicate that, at least under pathological conditions, meprin beta might attack specific functional sites in tenascin-C that are important for its oligomerization and anti-adhesive activity. (C) 2009 Elsevier B.V. All rights reserved.

A neuron-specific deletion of the microRNA-processing enzyme DICER induces severe but transient obesity in mice.

MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression post-transcriptionally. MiRNAs are implicated in various biological processes associated with obesity, including adipocyte differentiation and lipid metabolism. We used a neuronal-specific inhibition of miRNA maturation in adult mice to study the consequences of miRNA loss on obesity development. Camk2a-CreERT2 (Cre+) and floxed Dicer (Dicerlox/lox) mice were crossed to generate tamoxifen-inducible conditional Dicer knockouts (cKO). Vehicle- and/or tamoxifen-injected Cre+;Dicerlox/lox and Cre+;Dicer+/+ served as controls. Four cohorts were used to a) measure body composition, b) follow food intake and body weight dynamics, c) evaluate basal metabolism and effects of food deprivation, and d) assess the brain transcriptome consequences of miRNA loss. cKO mice developed severe obesity and gained 18 g extra weight over the 5 weeks following tamoxifen injection, mainly due to increased fat mass. This phenotype was highly reproducible and observed in all 38 cKO mice recorded and in none of the controls, excluding possible effects of tamoxifen or the non-induced transgene. Development of obesity was concomitant with hyperphagia, increased food efficiency, and decreased activity. Surprisingly, after reaching maximum body weight, obese cKO mice spontaneously started losing weight as rapidly as it was gained. Weight loss was accompanied by lowered O2-consumption and respiratory-exchange ratio. Brain transcriptome analyses in obese mice identified several obesity-related pathways (e.g. leptin, somatostatin, and nemo-like kinase signaling), as well as genes involved in feeding and appetite (e.g. Pmch, Neurotensin) and in metabolism (e.g. Bmp4, Bmp7, Ptger1, Cox7a1). A gene cluster with anti-correlated expression in the cerebral cortex of post-obese compared to obese mice was enriched for synaptic plasticity pathways. While other studies have identified a role for miRNAs in obesity, we here present a unique model that allows for the study of processes involved in reversing obesity. Moreover, our study identified the cortex as a brain area important for body weight homeostasis.

Antiviral activity of a small-molecule inhibitor of arenavirus glycoprotein processing by the cellular site 1 protease.

Arenaviruses merit interest as clinically important human pathogens and include several causative agents, chiefly Lassa virus (LASV), of hemorrhagic fever disease in humans. There are no licensed LASV vaccines, and current antiarenavirus therapy is limited to the use of ribavirin, which is only partially effective and is associated with significant side effects. The arenavirus glycoprotein (GP) precursor GPC is processed by the cellular site 1 protease (S1P) to generate the peripheral virion attachment protein GP1 and the fusion-active transmembrane protein GP2, which is critical for production of infectious progeny and virus propagation. Therefore, S1P-mediated processing of arenavirus GPC is a promising target for therapeutic intervention. To this end, we have evaluated the antiarenaviral activity of PF-429242, a recently described small-molecule inhibitor of S1P. PF-429242 efficiently prevented the processing of GPC from the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) and LASV, which correlated with the compound's potent antiviral activity against LCMV and LASV in cultured cells. In contrast, a recombinant LCMV expressing a GPC whose processing into GP1 and GP2 was mediated by furin, instead of S1P, was highly resistant to PF-429242 treatment. PF-429242 did not affect virus RNA replication or budding but had a modest effect on virus cell entry, indicating that the antiarenaviral activity of PF-429242 was mostly related to its ability to inhibit S1P-mediated processing of arenavirus GPC. Our findings support the feasibility of using small-molecule inhibitors of S1P-mediated processing of arenavirus GPC as a novel antiviral strategy.

A Negotiation Style Recommender Based on Computational Ecology in Open Negotiation Environments

The system described herein represents the first example of a recommender system in digital ecosystems where agents negotiate services on behalf of small companies. The small companies compete not only with price or quality, but with a wider service-by-service composition by subcontracting with other companies. The final result of these offerings depends on negotiations at the scale of millions of small companies. This scale requires new platforms for supporting digital business ecosystems, as well as related services like open-id, trust management, monitors and recommenders. This is done in the Open Negotiation Environment (ONE), which is an open-source platform that allows agents, on behalf of small companies, to negotiate and use the ecosystem services, and enables the development of new agent technologies. The methods and tools of cyber engineering are necessary to build up Open Negotiation Environments that are stable, a basic condition for predictable business and reliable business environments. Aiming to build stable digital business ecosystems by means of improved collective intelligence, we introduce a model of negotiation style dynamics from the point of view of computational ecology. This model inspires an ecosystem monitor as well as a novel negotiation style recommender. The ecosystem monitor provides hints to the negotiation style recommender to achieve greater stability of an open negotiation environment in a digital business ecosystem. The greater stability provides the small companies with higher predictability, and therefore better business results. The negotiation style recommender is implemented with a simulated annealing algorithm at a constant temperature, and its impact is shown by applying it to a real case of an open negotiation environment populated by Italian companies

Time processing in visual cortices: How the visual brain encodes and keeps track of time

Time is embedded in any sensory experience: the movements of a dance, the rhythm of a piece of music, the words of a speaker are all examples of temporally structured sensory events. In humans, if and how visual cortices perform temporal processing remains unclear. Here we show that both primary visual cortex (V1) and extrastriate area V5/MT are causally involved in encoding and keeping time in memory and that this involvement is independent from low-level visual processing. Most importantly we demonstrate that V1 and V5/MT are functionally linked and temporally synchronized during time encoding whereas they are functionally independent and operate serially (V1 followed by V5/MT) while maintaining temporal information in working memory. These data challenge the traditional view of V1 and V5/MT as visuo-spatial features detectors and highlight the functional contribution and the temporal dynamics of these brain regions in the processing of time in millisecond range. The present project resulted in the paper entitled: 'How the visual brain encodes and keeps track of time' by Paolo Salvioni, Lysiann Kalmbach, Micah Murray and Domenica Bueti that is now submitted for publication to the Journal of Neuroscience.

Friction Stir Processing : a new microstructure improvement technique

In the present work, microstructure improvement using FSP (Friction Stir Processing) is studied. In the first part of the work, the microstructure improvement of as-cast A356 is demonstrated. Some tensile tests were applied to check the increase in ductility. However, the expected results couldn’t be achieved. In the second part, the microstructure improvement of a fusion weld in 1050 aluminium alloy is presented. Hardness tests were carried out to prove the mechanical propertyimprovements. In the third and last part, the microstructure improvement of 1050 aluminium alloy is achieved. A discussion of the mechanical property improvements induced by FSP is made. The influence of tool traverse speed on microstructure and mechanical properties is also discussed. Hardness tests and recrystallization theory enabled us to find out such influence