Clustering Spectral avec Contraintes de Paires réglées par Noyaux Gaussiens

International audienceRésumé Nous considérons le problème du clustering spectral partielle-ment supervisé par des contraintes de la forme « must-link » et « cannot-link ». De telles contraintes apparaissent fréquemment dans divers pro-blèmes, comme la résolution de la coréférence en traitement automatique du langage naturel. L'approche développée dans ce papier consiste à ap-prendre une nouvelle représentation de l'espace pour les données, ainsi qu'une nouvelle distance dans cet espace. Cette représentation est ob-tenue via une transformation linéaire de l'enveloppe spectrale des don-nées. Les contraintes sont exprimées avec des fonctions Gaussiennes qui réajustent localement les similarités entre les objets. Un problème d'op-timisation global et non convexe est alors obtenu et l'apprentissage du modèle se fait grâce à des techniques de descentes de gradient. Nous évaluons notre algorithme sur des jeux de données standards et le com-parons à divers algorithmes de l'état de l'art, comme [14,18,32]. Les ré-sultats sur ces jeux de données, ainsi que sur le jeu de données de la tâche de coréférence CoNLL-2012, montrent que notre algorithme amé-liore significativement la qualité des clusters obtenus par les précédentes approches, et est plus robuste en montée en charge

Lactococci and lactobacilli as mucosal delivery vectors for therapeutic proteins and DNA vaccines

Food-grade Lactic Acid Bacteria (LAB) have been safely consumed for centuries by humans in fermented foods. Thus, they are good candidates to develop novel oral vectors, constituting attractive alternatives to attenuated pathogens, for mucosal delivery strategies. Herein, this review summarizes our research, up until now, on the use of LAB as mucosal delivery vectors for therapeutic proteins and DNA vaccines. Most of our work has been based on the model LAB Lactococcus lactis, for which we have developed efficient genetic tools, including expression signals and host strains, for the heterologous expression of therapeutic proteins such as antigens, cytokines and enzymes. Resulting recombinant lactococci strains have been tested successfully for their prophylactic and therapeutic effects in different animal models: i) against human papillomavirus type 16 (HPV-16)-induced tumors in mice, ii) to partially prevent a bovine β-lactoglobulin (BLG)-allergic reaction in mice and iii) to regulate body weight and food consumption in obese mice. Strikingly, all of these tools have been successfully transposed to the Lactobacillus genus, in recent years, within our laboratory. Notably, anti-oxidative Lactobacillus casei strains were constructed and tested in two chemically-induced colitis models. In parallel, we also developed a strategy based on the use of L. lactis to deliver DNA at the mucosal level, and were able to show that L. lactis is able to modulate the host response through DNA delivery. Today, we consider that all of our consistent data, together with those obtained by other groups, demonstrate and reinforce the interest of using LAB, particularly lactococci and lactobacilli strains, to develop novel therapeutic protein mucosal delivery vectors which should be tested now in human clinical trials

Mejoramiento del poblaciones de arroz de secano empleando selección recurrente y desarrollo de variedades

Improving upland rice populations using recurrent selection and varietal development The new breeding methods used by the collaborative rice improvement project carried out by CIAT and the French Agricultural Research Centre for International Development (CIRAD) are described: development of populations with a broad genetic base and recurrent selection. This project aims to continue to develop improved varieties while broadening the variability of germplasm available to farmers. A recessive male-sterile gene (ms) found in a mutant of variety IR36 facilitated the development of the rice population. Site-specific composite populations were developed with the national agricultural research institutes. In the case of Colombia, several composite populations were improved using two methods of recurrent selection. Several fertile plants were selected at each breeding stage and then used as a starting point to develop segregating and fixed lines using the conventional pedigree method. Since 2002, more than 90% of the lines in the selection process have come from original and improved recurrent populations. The most advanced lines are currently being evaluated in observation nurseries and yield trials in collaboration with different project partners in South America (Argentina, Bolivia, Brazil, Colombia, and Venezuela), Central America (Nicaragua), and the Caribbean (Cuba). Several promising lines, which could become commercial varieties, have been identified.Se describen los nuevos métodos de mejoramiento empleados dentro del proyecto de cooperación para el mejoramiento del arroz entre el CIAT y el Centro de Cooperación Internacional en Investigación Agrícola para el Desarrollo (CIRAD), de Francia, el cual busca dos objetivos: seguir produciendo variedades mejoradas y, al mismo tiempo, ampliar la variabilidad del germoplasma que se pone a disposición de los agricultores. Las nuevas estrategias de mejoramiento que se emplean en el arroz de secano son el desarrollo de poblaciones de amplia base genética y su mejoramiento mediante la selección recurrente. El gen recesivo de androesterilidad (ms), encontrado en un mutante de la variedad IR36, facilitó la creación de poblaciones. Se crearon así poblaciones compuestas para sitios específicos en colaboración con instituciones nacionales de investigación. En Colombia se mejoraron varias poblaciones compuestas empleando dos métodos de selección recurrente. En cada etapa del mejoramiento se seleccionaron algunas plantas fértiles, que se consideraban el punto de partida para el desarrollo de líneas segregantes y fijas mediante el método convencional de selección denominado pedigrí. Desde el año 2002, más del 90% de las líneas que están para selección provienen de las poblaciones recurrentes originales y mejoradas. Las líneas más avanzadas se evalúan actualmente en ensayos de observación y de rendimiento, en cooperación con los socios del proyecto en América del Sur (Argentina, Bolivia, Brasil, Colombia y Venezuela), América Central (Nicaragua) y el Caribe (Cuba). Ya han sido identificadas algunas líneas promisorias, que podrán convertirse en variedades comerciales

Current review of genetically modified lactic acid bacteria for the prevention and treatment of colitis using murine models

Inflammatory Bowel Diseases (IBD) are disorders of the gastrointestinal tract characterized by recurrent inflammation that requires lifelong treatments. Probiotic microorganisms appear as an alternative for these patients; however, probiotic characteristics are strain dependent and each probiotic needs to be tested to understand the underlining mechanisms involved in their beneficial properties. Genetic modification of lactic acid bacteria (LAB) was also described as a tool for new IBD treatments.The first part of this review shows different genetically modified LAB (GM-LAB) described for IBD treatment since 2000.Then, the two principally studied strategies are discussed (i) GM-LAB producing antioxidant enzymes and (ii) GM-LAB producing the anti-inflammatory cytokine IL-10. Different delivery systems, including protein delivery and DNA delivery, will also be discussed. Studies show the efficacy of GM-LAB (using different expression systems) for the prevention and treatment of IBD, highlighting the importance of the bacterial strain selection (with anti-inflammatory innate properties) as a promising alternative. These microorganisms could be used in the near future for the development of therapeutic products with anti-inflammatory properties that can improve the quality of life of IBD patients.Fil: de Moreno, Maria Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: del Carmen, Silvina Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Chatel, Jean Marc. Institut National de la Recherche Agronomique; FranciaFil: Miyoshi, Anderson. Universidade Federal do Minas Gerais; BrasilFil: Azevedo, Vasco. Universidade Federal do Minas Gerais; BrasilFil: Langella, Philippe. Institut National de la Recherche Agronomique; FranciaFil: Bermudez Humaran, Luis G.. Institut National de la Recherche Agronomique; FranciaFil: Leblanc, Jean Guy Joseph. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentin

Mejoramiento del arroz de secano para América Latina

Improving upland rice for Latin America The ecosystems for upland rice in Latin America and the Caribbean and their limitations for rice cultivation are analyzed. The sites where the CIAT rice program and the collaborative project that the Center carries out with the French Agricultural Research Centre for International Development (CIRAD) evaluate and select genetic materials for upland conditions are also described, as well as the conventional genetic improvement activities carried out by CIAT since 1981 and those carried out by CIRAD since 1996. These activities include population development through population improvement and recurrent selection. The advances made so far are reported. As a result of these research projects, lines have been developed that present high yield potential and new commercial varieties have been released that have been quickly adopted by farmers. This has allowed the opening of new agricultural frontiers in Colombia’s Eastern Plains, and northern coast regions. In Brazil, the production of upland rice has been stimulated and, in Bolivia, alternatives to upland rice cultivation are being offered.Se analizan los ecosistemas para el arroz de secano de América Latina y el Caribe, las limitaciones que presentan para el cultivo del arroz, y los sitios donde se evalúan y seleccionan materiales genéticos de arroz de secano del Programa de Arroz del CIAT y del proyecto de cooperación con el Centro de Cooperación Internacional en Investigación Agrícola para el Desarrollo (CIRAD), de Francia. Se describen también las actividades de mejoramiento genético convencional desarrolladas por el CIAT desde 1981, y las que realizó el CIRAD desde 1996, es decir, desarrollo de poblaciones mediante la implementación del mejoramiento poblacional y su mejora mediante la selección recurrente. También se presentan algunos datos de los avances obtenidos. Como resultado de estos proyectos de investigación se han desarrollado líneas de elevado potencial productivo y se han liberado nuevas variedades comerciales rápidamente adoptadas por los agricultores. Con ellas se han abierto nuevas fronteras agrícolas en los Llanos Orientales y en la costa norte de Colombia, se ha estimulado la producción del arroz de secano en Brasil y se han ofrecido alternativas al cultivo de arroz de secano en Bolivia

A new plasmid vector for DNA delivery using lactococci

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

A delay differential equation solver for MONOLIX & MLXPLORE

We describe the implementation of a Delay differential Equation (DDE) solver in Monolix, a platform for population modeling of longitudinal data, and MlxPlore, a tool for the exploration of complex models. We use explicit Runge-Kutta schemes. Several examples for MlxPlore and Monolix are proposed

Correlation between fibronectin binding protein A expression level at the surface of recombinant lactococcus lactis and plasmid transfer in vitro and in vivo

Background: Fibronectin Binding Protein A (FnBPA) is an invasin from Staphylococcus aureus that allows this pathogen to internalize into eukaryote cells. It was previously demonstrated that recombinant Lactococcus lactis expressing FnBPA were invasive and able to transfer a plasmid to eukaryotic cells in vitro and in vivo. In this study, the invasivity of recombinant strains of Lactococcus lactis that express FnBPA under the control of its constitutive promoter or driven by the strong nisin inducible expression system (NICE) were studied.Results: It was demonstrated that the nisA promoter allows an increase of FnBPA expression on the surface of Lactococcus lactis surface, as shown by flow cytometry, which subsequently enhanced internalization and plasmid transfer properties in vitro in Caco2 cells and Bone Marrow Dendritic Cells. In vivo, the use of nisA promoter increase the plasmid transfer in cells of both the small and large intestine of mice.Conclusion: FnBPA expression at the surface of recombinant L. lactis is positively correlated to internalization and DNA transfer properties. The recombinant strains of L. lactis that expresses FnBPA under the control of the nisin inducible expression system could thus be considered as an improved tool in the field of DNA transfer.Fil: Almeida, Juliana F.. Institut National de la Recherche Agronomique; Francia. Institut des sciences et industries du vivant et de l; FranciaFil: Mariat, Denis. Institut National de la Recherche Agronomique; Francia. Institut des sciences et industries du vivant et de l; FranciaFil: Azevedo, Vasco. Universidade Federal Do Minas Gerais;Fil: Miyoshi, Anderson. Universidade Federal Do Minas Gerais;Fil: de Moreno, Maria Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; ArgentinaFil: del Carmen, Silvina Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; ArgentinaFil: Martin, Rebeca. Institut National de la Recherche Agronomique; Francia. Institut des sciences et industries du vivant et de l; FranciaFil: Langella, Philippe. Institut National de la Recherche Agronomique; Francia. Institut des sciences et industries du vivant et de l; FranciaFil: Leblanc, Jean Guy Joseph. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; ArgentinaFil: Chatel, Jean Marc. Institut National de la Recherche Agronomique; Francia. Institut des sciences et industries du vivant et de l; Franci

A novel interleukin-10 DNA mucosal delivery system attenuates intestinal inflammation in a mouse model

Inflammatory bowel diseases (IBD) describe a group of complex intestinal disorders characterized by inflammation in the gastrointestinal tract. Current treatments for IBD include the use of anti-inflammatory drugs; furthermore, recombinant lactic acid bacteria have been used as a therapeutic vehicle for anti-inflammatory agents in IBD models. Interleukin-10 (IL-10) is one of the most important anti-inflammatory cytokines; however, its oral administration is limited because it is quickly degraded in the gastrointestinal tract and systemic treatments have led to undesirable side effects. In this study, an engineered invasive strain of Lactococcus (L.) lactis producing Fibronectin Binding Protein A (FnBPA+), from Staphylococcus aureus capable of delivering, directly inside eukaryotic cells, an eukaryotic DNA expression vector containing the ORF coding for IL-10 of Mus musculus (pValac:il-10) was developed and its functionality was evaluated using in vitro and in vivo assays. Functionality of the plasmid and the invasive strain was demonstrated by transfection and invasiveness assays using cell cultures and in vivo in mice by fluorescence microscopy. TNBS inoculated mice that received this novel strain showed lower damage scores in their large intestines (at both macroscopic and microscopic levels), lower microbial translocation to liver, and increased anti-inflammatory/pro-inflammatory cytokine ratios compared to mice that received L. lactis FnBPA+ without the pValac:il-10 plasmid. The effectiveness was demonstrated of this novel DNA delivery therapeutic strategy in the prevention of inflammation using a murine model of colitis.Fil: del Carmen, Silvina Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Tucumán. Centro de Referencia para Lactobacilos (i); ArgentinaFil: Zurita-Turk, Meritxell. Universidade Federal Do Minas Gerais; Brasil;Fil: Alvarenga Lima, Fernanda. Universidade Federal Do Minas Gerais; Brasil;Fil: Coelho Dos Santos, Janete. No especifíca;Fil: Leclercq, Sophie Yvette. No especifíca;Fil: Chatel, Jean-Marc. Institut National de la Recherche Agronomique; Francia;Fil: Azevedo, Vasco. Universidade Federal Do Minas Gerais; Brasil;Fil: de Moreno, Maria Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Tucumán. Centro de Referencia para Lactobacilos (i); ArgentinaFil: Miyoshi, Anderson. Universidade Federal Do Minas Gerais; Brasil;Fil: Leblanc, Jean Guy Joseph. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Tucumán. Centro de Referencia para Lactobacilos (i); Argentina. Universidad Nacional de Tucuman. Facultad de Medicina. Departamento de Investigacion. Catedra de Metodologia de la Invest.cientifica; Argentin