Especificación del comportamiento de un avatar en un mundo virtual mediante una ontología

El presente trabajo describe la construcción de una aplicación que controla a un Non Player Character (NPC), en un mundo virtual. La aplicación desarrollada, que tiene como nombre BotManager, realiza dos tareas fundamentales: 1) conectarse al repositorio de conocimiento, que en esta implementación es una ontología expresada en OWL, para obtener las acciones que debe realizar el NPC dentro del mundo virtual; y 2) ordenar al NPC que realice estas acciones en un mundo virtual creado con la plataforma OpenSimulator. BotManager puede tener variadas aplicaciones, por lo tanto puede ser usada como complemento en mundos virtuales aplicados a la educación, simulación, ocio, etc. Ahora bien, la principal razón que motivó el desarrollo del BotManager fue la de crear un sistema de demostración automática de tareas en un mundo virtual destinado a la educación/ entrenamiento. De esta forma, un Sistema Inteligente de Tutoría integrado con un mundo virtual podría demostrar paso a paso a un estudiante cómo realizar una tarea en el mundo virtual. La ontología que lee el BotManager extiende la ontología propuesta en la tesis “Una propuesta de modelado del estudiante basada en ontologías y diagnóstico pedagógico-cognitivo no monótono” de Julia Parraga en el 2011 (Ontología de Julia). La construcción y las pruebas del BotManager se llevaron a cabo en tres etapas: 1) creación de la Ontología de Acciones del NPC que extiende la Ontología de Julia; 2) diseño e implementación de la aplicación en C# que lee la ontología que contiene el plan de acción del NPC, y ordena al NPC realizar las acciones en el mundo virtual; y 3) pruebas de la aplicación con la práctica “preparación de una taza de cafe”, que es parte de un Laboratorio Virtual de Biotecnología. El BotManager se ha diseñado como una aplicación cliente que se conecta a un servidor de Open- Simulator. Por lo tanto, puede ejecutarse en una máquina distinta a la del servidor. Asimismo, en la implementación del BotManager se ha utilizado una librería gratuita denominada LibOpenMetaverse que permite controlar un NPC de forma remota.---ABSTRACT---This paper describes the construction of an application that controls a Non Player Character (NPC), in a virtual world. The application developed, called BotManager, performs two main tasks: 1) the connection to the repository of knowledge, which in this implementation is an ontology expressed in OWL, and retrieving the actions to be performed by the NPC within the virtual world; and 2) commanding the NPC to perform these actions in a virtual world created with the OpenSimulator platform. BotManager can have diverse applications, therefore it can be used as a complement in virtual worlds applied to education, simulation, entertainment, etc. However, the main reason behind the development of BotManager was to create an automatic demonstration of tasks in a virtual world for education / training. Thus, a virtual world integrated with an Intelligent Tutoring Systems could demonstrate step by step to a student how to perform a task in the virtual world. The ontology used by the BotManager extends ontology proposed in the thesis “A proposal for modeling ontologies based student and not monotonous teaching-cognitive diagnosis” by Julia Parraga in 2011 (Julia’s Ontology). Construction and testing of BotManager were conducted in three stages: 1) creation of the NPC Actions Ontology by extending the Julia’s Ontology; 2) design and implementation of the application in C# that reads the ontology containing the plan of action of the NPC, and commands the NPC to perform the read plan in the virtual world; and 3) testing of the application with the practice “preparing a cup of coffee”, which is part of a Virtual Laboratory of Biotechnology. The BotManager has been designed as a client application that connects to an OpenSimulator server. Therefore, it can run on a different machine to the server. To implement the BotManager we have used a free library called libopenmetaverse that allows us to control a NPC remotely.

Nuclear hourglass technique: An approach that detects electrically open nuclear pores in Xenopus laevis oocyte

Nuclear pore complexes (NPCs) mediate both active transport and passive diffusion across the nuclear envelope (NE). Determination of NE electrical conductance, however, has been confounded by the lack of an appropriate technical approach. The nuclear patch clamp technique is restricted to preparations with electrically closed NPCs, and microelectrode techniques fail to resolve the extremely low input resistance of large oocyte nuclei. To address the problem, we have developed an approach for measuring the NE electrical conductance of Xenopus laevis oocyte nuclei. The method uses a tapered glass tube, which narrows in its middle part to 2/3 of the diameter of the nucleus. The isolated nucleus is sucked into the narrow part of the capillary by gentle fluid movement, while the resulting change in electrical resistance is monitored. NE electrical conductance was unexpectedly large (7.9 ± 0.34 S/cm2). Evaluation of NPC density by atomic force microscopy showed that this conductance corresponded to 3.7 × 106 NPCs. In contrast to earlier conclusions drawn from nuclear patch clamp experiments, NPCs were in an electrically “open” state with a mean single NPC electrical conductance of 1.7 ± 0.07 nS. Enabling or blocking of active NPC transport (accomplished by the addition of cytosolic extracts or gp62-directed antibodies) revealed this large NPC conductance to be independent of the activation state of the transport machinery located in the center of NPCs. We conclude that peripheral channels, which are presumed to reside in the NPC subunits, establish a high ionic permeability that is virtually independent of the active protein transport mechanism.

The Integral Membrane Protein Snl1p Is Genetically Linked to Yeast Nuclear Pore Complex Function

Integral membrane proteins are predicted to play key roles in the biogenesis and function of nuclear pore complexes (NPCs). Revealing how the transport apparatus is assembled will be critical for understanding the mechanism of nucleocytoplasmic transport. We observed that expression of the carboxyl-terminal 200 amino acids of the nucleoporin Nup116p had no effect on wild-type yeast cells, but it rendered the nup116 null strain inviable at all temperatures and coincidentally resulted in the formation of nuclear membrane herniations at 23°C. To identify factors related to NPC function, a genetic screen for high-copy suppressors of this lethal nup116-C phenotype was conducted. One gene (designated SNL1 for suppressor of nup116-C lethal) was identified whose expression was necessary and sufficient for rescuing growth. Snl1p has a predicted molecular mass of 18.3 kDa, a putative transmembrane domain, and limited sequence similarity to Pom152p, the only previously identified yeast NPC-associated integral membrane protein. By both indirect immunofluorescence microscopy and subcellular fractionation studies, Snl1p was localized to both the nuclear envelope and the endoplasmic reticulum. Membrane extraction and topology assays suggested that Snl1p was an integral membrane protein, with its carboxyl-terminal region exposed to the cytosol. With regard to genetic specificity, the nup116-C lethality was also suppressed by high-copy GLE2 and NIC96. Moreover, high-copy SNL1 suppressed the temperature sensitivity of gle2–1 and nic96-G3 mutant cells. The nic96-G3 allele was identified in a synthetic lethal genetic screen with a null allele of the closely related nucleoporin nup100. Gle2p physically associated with Nup116p in vitro, and the interaction required the N-terminal region of Nup116p. Therefore, genetic links between the role of Snl1p and at least three NPC-associated proteins were established. We suggest that Snl1p plays a stabilizing role in NPC structure and function.

A Novel Fluorescence-based Genetic Strategy Identifies Mutants of Saccharomyces cerevisiae Defective for Nuclear Pore Complex Assembly

Nuclear pore complexes (NPCs) are large proteinaceous portals for exchanging macromolecules between the nucleus and the cytoplasm. Revealing how this transport apparatus is assembled will be critical for understanding the nuclear transport mechanism. To address this issue and to identify factors that regulate NPC formation and dynamics, a novel fluorescence-based strategy was used. This approach is based on the functional tagging of NPC proteins with the green fluorescent protein (GFP), and the hypothesis that NPC assembly mutants will have distinct GFP-NPC signals as compared with wild-type (wt) cells. By fluorescence-activated cell sorting for cells with low GFP signal from a population of mutagenized cells expressing GFP-Nup49p, three complementation groups were identified: two correspond to mutant nup120 and gle2 alleles that result in clusters of NPCs. Interestingly, a third group was a novel temperature-sensitive allele of nup57. The lowered GFP-Nup49p incorporation in the nup57-E17 cells resulted in a decreased fluorescence level, which was due in part to a sharply diminished interaction between the carboxy-terminal truncated nup57pE17 and wt Nup49p. Interestingly, the nup57-E17 mutant also affected the incorporation of a specific subset of other nucleoporins into the NPC. Decreased levels of NPC-associated Nsp1p and Nup116p were observed. In contrast, the localizations of Nic96p, Nup82p, Nup159p, Nup145p, and Pom152p were not markedly diminished. Coincidentally, nuclear import capacity was inhibited. Taken together, the identification of such mutants with specific perturbations of NPC structure validates this fluorescence-based strategy as a powerful approach for providing insight into the mechanism of NPC biogenesis.