Optimisation des stratégies d'amélioration génétique du pin maritime grâce à l'utilisation de marqueurs moléculaires

Maritime pine (Pinus pinaster Ait.) is one of the main economical forest species in France, providing about twenty five percent of the national round wood production. A breeding program, implemented since the 60’s, offers genetically improved varieties for growth and stem straightness.This PhD explores the use of molecular markers in breeding strategies for maritime pine in Aquitaine. Molecular markers were used for pedigree recovery in a polycross progeny trial to test assumptions of backward selection on one hand, and to evaluate the feasibility of a new breeding strategy on the other hand. First, the pedigree of 984 progeny was recovered with 63 SNPs allowing to verify the assumptions of backward selection. We also showed that genetic parameters and maternal breeding value estimates were not much modified by inclusion of full pedigree information. Then, the best progenies in the polycross trial were preselected and genotyped to investigate the possibility of carrying out a forward selection strategy. Finally, establishment of clonal seed orchards were simulated from various breeding strategies (backward, forward, mixed) in order to compare genetic gains from the improved varieties obtained thereby.This study opens new perspectives towards an implementation of forward selection in the French maritime pine breeding program, to speed the selection cycles up and to increase the frequency of variety renewal. Moreover, the set of SNP markers developed is now used in different steps of the breeding program.Le pin maritime (Pinus pinaster Ait.) est l’une des principales espèces forestières en France, fournissant près d’un quart de la production nationale de bois. Un programme d’amélioration, mis en place dans les années 1960, propose des variétés génétiquement améliorées pour la croissance et la rectitude du tronc.Cette thèse explore la possibilité d’introduire les marqueurs moléculaires dans les stratégies d’amélioration génétique du pin maritime en Aquitaine. Les marqueurs sont utilisés afin de reconstituer a posteriori les pedigrees au sein d’un test de descendance « polycross », pour d’une part vérifier les hypothèses sur lesquelles repose la sélection backward, et d’autre part, pour proposer une stratégie de sélection innovante. Tout d’abord, la reconstitution du pedigree de 984 individus à l’aide de 63 marqueurs SNPs permet de valider les hypothèses de la sélection backward, et montre que les estimations des paramètres génétiques et des valeurs génétiques maternelles, basées sur l’information d’un pedigree partiel ou complet, diffèrent peu. Puis, les meilleurs descendants du test polycross sont présélectionnés et génotypés pour évaluer la faisabilité d’une stratégie de sélection forward. Enfin, des vergers à graines sont simulés selon différentes stratégies de sélection (backward, forward, mixte) afin de comparer les gains génétiques des variétés améliorées ainsi obtenues.Une stratégie de sélection forward chez le pin maritime permettrait d’accélérer les cycles de sélection et d’augmenter la fréquence des sorties variétales. De plus, le jeu de marqueurs SNPs développé dans cette étude est en cours de valorisation dans différentes étapes du programme d’amélioration

Le capital social comme outil d’intervention : accès et mobilisation dans une école secondaire en milieu défavorisé et multiethnique

Le postulat de départ de cette thèse est que « les ressources sociales comptent ». En milieu scolaire, ces ressources prennent plusieurs formes (enseignant, conseiller en orientation, psychoéducateur, travailleur social, surveillant, etc.) qui peuvent jouer un rôle compensatoire et aider les élèves qui présentent des conditions a priori défavorables à « s’en sortir » quand ils rencontrent des difficultés dans leur parcours éducatif. La thèse s’ancre ainsi dans la lignée de plusieurs écrits scientifiques (Kamanzi, et al., 2007) et rapports de recherche (Deniger et al., 2011) qui établissent un lien entre capital social et réussite scolaire. Plusieurs considèrent d’ailleurs la prise en compte du capital social comme un outil pour les politiques publiques éducatives (Leana et Pil, 2014; Spillane, 2013). Dans cette optique, l’objectif de cette thèse est de comprendre la mobilisation du capital social dans une école secondaire en milieu défavorisé et multiethnique. Pour appréhender ce phénomène complexe, le cadre théorique propose plusieurs entrées : les trois dimensions conceptuelles issues des principales approches du capital social : les dimensions cognitive (Nahapiet et Ghoshal, 1989), normative (Coleman, 1988 ; Putnam 2000) et structurelle (Bourdieu, 1986 ; Burt, 2000 ; Lin, 1999) permettent d’étudier le capital social accessible dans l’école. La théorie de la structuration (Giddens, 1984) offre un modèle d’action qui recentre la mobilisation sur les élèves et articule les dynamiques de structuration individuelles et collectives. L’étude de cas ethnographique (Merriam, 1998) est la démarche privilégiée. Elle a été mise en place dans une école secondaire située dans un quartier défavorisé et multiethnique de Montréal. Plusieurs méthodes de collecte de données ont été employées, en particulier une observation participante d’une durée de trois ans et demi, afin de documenter de la manière la plus exhaustive possible la mobilisation du capital social et répondre aux questions suivantes : quel est le contexte de mobilisation du capital social (médias) ? Quel est le capital social accessible (documents officiels de l’école) ? Quel est le capital social mobilisé (questionnaires sur les réseaux sociaux) ? Quels sont les processus de mobilisation du capital social (entretiens de groupe) ? Après avoir identifié les différents leviers socio-organisationnels dont l’école dispose pour favoriser la mobilisation du capital social, l’analyse thématique opérée révèle que les élèves ne mobilisent pas le capital social selon le cadre normatif de l’école, mais qu’ils négocient cette mobilisation. Ils mobilisent ainsi le capital social de l’école selon huit processus qui reposent sur la signification qu’ils attribuent aux ressources, la légitimation qu’ils confèrent à l’institution scolaire et le pouvoir qu’ils se dégagent dans la mobilisation. L’étude de ces processus de mobilisation permet de révéler l’importance des espaces de médiation, qui favorisent la négociation entre les élèves et l’école et souligne l’importance des agents de médiation du capital social. Ces agents, en grande partie issue du milieu communautaire jouent un rôle prépondérant dans cette mobilisation : ils peuvent renforcer le pouvoir des jeunes en leur donnant accès à d’autres ressources ou à de l’information pertinente. L’interprétation est l’occasion de revenir sur les multiples tensions internes qui naissent des « négociations de sens » (Morrissette, 2010) entre les élèves et l’institution. Dans cette optique, le concept de « forme scolaire » (Vincent, 1980) permet de renverser la perspective et d’interroger cette fois la capacité de l’école à générer ces espaces de médiation, et donc incidemment à produire du capital social pour les élèves qui rencontrent des difficultés. Mieux comprendre la mobilisation du capital social sur le plan organisationnel de l’école permet de parvenir à des pistes de propositions pour intervenir plus efficacement auprès du public étudié. Les pistes proposées reposent sur l’étude des espaces de médiation, qui fournissent des zones de manœuvre pour l’intervention (Fontaine, 2011) et le rôle particulier qu’y jouent les médiateurs de capital social, ces « agents institutionnels » (Stanton-Salazar, 2011) qui gravitent à la périphérie de la forme scolaire. Leurs interventions s’ancrent dans une approche plus globale et plus intégrée qui favorise le pouvoir des élèves, tout en renforçant leurs liens avec l’institution. Malheureusement, ces agents ne disposeraient pas de l’espace idéal pour leur action dans l’école.The premise of this research is that “social resources count”, meaning that they can play a compensating role and help students with a priori underprivileged conditions to “pull through” when they come up against difficulties during their educational path. It follows the lead of much scientific literature (Kamanzi & al., 2007) and research reports (Deniger & al., 2011) that establish a link between a school’s social capital and academic success. More precisely, this research aims to study the mobilization that students do with a school’s social capital (teacher, guidance counselor, psychoeducator, monitors, etc.) in an underprivileged and multiethnic school of Montreal. The suggested theoretical framework is multidimensional. It combines the three dimensions emerging from the main approaches of social capital: the cognitive (Nahapiet & Ghoshal, 1989), normative (Coleman, 1988 ; Putnam 2000) and structural dimensions (Bourdieu, 1986 ; Burt, 2000 ; Lin, 1999). Its main framework is structuration theory (Giddens, 1984): it articulates these constitutive dimensions of the suggested model by re-centering the action on students. The methodological approach consists of an ethnographic case study (Merriam, 1998). It lasted three years and a half and was done in a high school, in an underprivileged and multiethnic neighbourhood of Montreal. It is based on a variety of methods of data collection – in which participant observation is the common thread, and that allows the answering of several questions, constituting as many steps towards the study and production of social capital: what is the production context of social capital (media study)? What is the accessible social capital (study of the school’s official documents)? What is the mobilized social capital (study of surveys on social networks)? What are the mobilization processes of social capital (group interviews and spontaneous exchanges)? The thematic analysis revealed that students did not mobilize social capital according to the normative framework of the school, but that they mobilized the social resources according to eight processes that rest on their leeway and their adhesion to the school’s system. The interpretation is an occasion to revisit the multiple internal tensions that emerge from “meaning negotiations” (Morrissette, 2010) between students and the institution. With this in mind, the concept of “school form” (Vincent, 1980) allows the reversal of the perspective and questions the school’s capacity to produce social capital for students that encounter difficulties. Better understanding the production of social capital on the organizational level leads to potential propositions to intervene more effectively on behalf of the population being studied. One of the paths that is proposed focuses on mediation (Fontaine, 2011) ans the specific role that social capital mediators play, these “institutional agents” (Stanton-Salazar, 2011) that gravitate on the periphery of educational form. Their interventions take root in a more global approach that favours the students’ power, all while reinforcing their ties with the establishment. Unfortunately, these agents do not possess the ideal space for their action in the school

Les effets du financement par projet sur les organismes à but non lucratif : étude de cas de Déclic

Cet article explore les conséquences croissantes du financement par projet sur l’organisme communautaire Déclic, spécialisé dans le soutien au raccrochage scolaire. En se basant sur une étude de cas collaborative entamée à l’automne 2019, l’article examine les origines de ce changement et ses effets sur les activités de l’organisme. Il analyse également les impacts sur les pratiques de Déclic en fonction de recherches de projets et de partenaires financiers, en abordant les apports et défis que ce mode de financement engendre

Landscapes and bacterial signatures of mucosa-associated intestinal microbiota in Chilean and Spanish patients with inflammatory bowel disease

Inflammatory bowel diseases (IBDs), which include ulcerative colitis (UC) and Crohn’s disease (CD), cause chronic inflammation of the gut, affecting millions of people worldwide. IBDs have been frequently associated with an alteration of the gut microbiota, termed dysbiosis, which is generally characterized by an increase in abundance of Proteobacteria such as Escherichia coli, and a decrease in abundance of Firmicutes such as Faecalibacterium prausnitzii (an indicator of a healthy colonic microbiota). The mechanisms behind the development of IBDs and dysbiosis are incompletely understood. Using samples from colonic biopsies, we studied the mucosa-associated intestinal microbiota in Chilean and Spanish patients with IBD. In agreement with previous studies, microbiome comparison between IBD patients and non-IBD controls indicated that dysbiosis in these patients is characterized by an increase of pro-inflammatory bacteria (mostly Proteobacteria) and a decrease of commensal beneficial bacteria (mostly Firmicutes). Notably, bacteria typically residing on the mucosa of healthy individuals were mostly obligate anaerobes, whereas in the inflamed mucosa an increase of facultative anaerobe and aerobic bacteria was observed. We also identify potential co-occurring and mutually exclusive interactions between bacteria associated with the healthy and inflamed mucosa, which appear to be determined by the oxygen availability and the type of respiration. Finally, we identified a panel of bacterial biomarkers that allow the discrimination between eubiosis from dysbiosis with a high diagnostic performance (96% accurately), which could be used for the development of non-invasive diagnostic methods. Thus, this study is a step forward towards understanding the landscapes and alterations of mucosa-associated intestinal microbiota in patients with IBDs.This study was supported by Fondo Nacional De Desarrollo Científico y Tecnológico FONDECYT grant 1161161 to R. Vidal, CONICYT-PCHA/2014-21140975 fellowship to N. Chamorro, FONDECYT 1120577 and 1170648 to Hermoso MA and the Spanish Ministry of Economy projects CLG2015 66686-C3-1-P to Rosselló-Mora R., as well as funds from the European Regional Development Fund (FEDER) and NSF Dimensions in Biodiversity grant OCE-1342694. Support was also provided by a Millennium Science Initiative grant from the Ministry of Economy, Development and Tourism to Paredes-Sabja D

High prevalence of HIV-1 drug resistance among patients on first-line antiretroviral treatment in Lomé, Togo

<p>Abstract</p> <p>Background</p> <p>With widespread use of antiretroviral (ARV) drugs in Africa, one of the major potential challenges is the risk of emergence of ARV drug-resistant HIV strains. Our objective is to evaluate the virological failure and genotypic drug-resistance mutations in patients receiving first-line highly active antiretroviral therapy (HAART) in routine clinics that use the World Health Organization public health approach to monitor antiretroviral treatment (ART) in Togo.</p> <p>Methods</p> <p>Patients on HAART for one year (10-14 months) were enrolled between April and October 2008 at three sites in Lomé, the capital city of Togo. Plasma viral load was measured with the NucliSENS EasyQ HIV-1 assay (Biomérieux, Lyon, France) and/or a Generic viral load assay (Biocentric, Bandol, France). Genotypic drug-resistance testing was performed with an inhouse assay on plasma samples from patients with viral loads of more than 1000 copies/ml. CD4 cell counts and demographic data were also obtained from medical records.</p> <p>Results</p> <p>A total of 188 patients receiving first-line antiretroviral treatment were enrolled, and 58 (30.8%) of them experienced virologic failure. Drug-resistance mutations were present in 46 patients, corresponding to 24.5% of all patients enrolled in the study. All 46 patients were resistant to non-nucleoside reverse-transcriptase inhibitors (NNRTIs): of these, 12 were resistant only to NNRTIs, 25 to NNRTIs and lamivudine/emtricitabine, and eight to all three drugs of their ARV regimes. Importantly, eight patients were already predicted to be resistant to etravirine, the new NNRTI, and three patients harboured the K65R mutation, inducing major resistance to tenofovir.</p> <p>Conclusions</p> <p>In Togo, efforts to provide access to ARV therapy for infected persons have increased since 2003, and scaling up of ART started in 2007. The high number of resistant strains observed in Togo shows clearly that the emergence of HIV drug resistance is of increasing concern in countries where ART is now widely used, and can compromise the long-term success of first- and second-line ART.</p

Compreensão do sentimento materno na vivência no método canguru

Aim: to understand the maternal feelings experienced in different stages of Kangaroo-mother care method. Methods: descriptive qualitative study, conducted in a neonatal unit of a teaching hospital in southern Brazil, in which nine mothers participated. Data collection occurred during the second semester of 2013, through structured interviews. Data were analyzed using the method of content analysis. Results: the following categories emerged: Birth expectation: to be born at term, Approach of the mother with the baby, Feeling more like a mom and When I got home. Conclusion: the maternal feelings are closely related to the degree of knowledge and adaptability of the mother. It is a concern of the health professionals to provide information and support in an individualized manner, respecting the history of each mother and her familyObjetivo: comprender los sentimientos maternales en diferentes etapas del Método Madre Canguro. Métodos: estudio descriptivo, cualitativo, desarrollado en una unidad neonatal de un hospital escuela al sur de Brasil, con la participación de nueve madres. La recolección de datos ocurrió en el segundo semestre de 2013. Se realizaron entrevistas semiestructuradas. Los datos fueron analizados según el método de análisis de contenido. Resultados: emergieron las categorías: Expectativas del nacimiento: Nacer al término, Proximidad de la madre con el bebe, Sintiéndose más madre y Cuando llegue a casa. Conclusión: los sentimientos maternos se relacionan íntimamente con el grado de conocimiento y adaptación de la madre. Cabe al profesional de la salud informar y apoyar individualmente, respetando la historia de cada madre y su familia.Objetivo: compreender os sentimentos maternos vivenciados nas diferentes etapas do Método Canguru. Método: estudo descritivo, qualitativo, desenvolvido em uma unidade neonatal de um hospital escola no sul do Brasil, com a participação de nove mães. A coleta dos dados ocorreu no segundo semestre de 2013, quando foram aplicadas entrevistas semiestruturadas. Os dados foram submetidos à análise de conteúdo. Resultados: emergiram as seguintes categorias: Expectativas do nascimento: Nascer a termo, Aproximação da mãe com o bebê, Sentindo-se mais mãe e Quando cheguei em casa. Conclusão: os sentimentos maternos relacionam-se intimamente com o grau de conhecimento e adaptabilidade da mãe. Cabe ao profissional de saúde fornecer informações e apoio de forma individualizada, respeitando a história de cada mãe e sua família

Characterization of Adherent-Invasive Escherichia coli (AIEC) Outer Membrane Proteins Provides Potential Molecular Markers to Screen Putative AIEC Strains

Adherent-invasive E. coli (AIEC) is a pathotype associated with the etiopathogenesis of Crohn's disease (CD), albeit with an as-yet unclear role. The main pathogenic mechanisms described for AIEC are adherence to epithelial cells, invasion of epithelial cells, and survival and replication within macrophages. A few virulence factors have been described as participating directly in these phenotypes, most of which have been evaluated only in AIEC reference strains. To date, no molecular markers have been identified that can differentiate AIEC from other E. coli pathotypes, so these strains are currently identified based on the phenotypic characterization of their pathogenic mechanisms. The identification of putative AIEC molecular markers could be beneficial not only from the diagnostic point of view but could also help in better understanding the determinants of AIEC pathogenicity. The objective of this study was to identify molecular markers that contribute to the screening of AIEC strains. For this, we characterized outer membrane protein (OMP) profiles in a group of AIEC strains and compared them with the commensal E. coli HS strain. Notably, we found a set of OMPs that were present in the AIEC strains but absent in the HS strain. Moreover, we developed a PCR assay and performed phylogenomic analyses to determine the frequency and distribution of the genes coding for these OMPs in a larger collection of AIEC and other E. coli strains. As result, it was found that three genes (chuA, eefC, and fitA) are widely distributed and significantly correlated with AIEC strains, whereas they are infrequent in commensal and diarrheagenic E. coli strains (DEC). Additional studies are needed to validate these markers in diverse strain collections from different geographical regions, as well as investigate their possible role in AIEC pathogenicity

A Brazilian university hospital position regarding transplantation criteria for HIV-positive patients according to the current literature

Human immunodeficiency virus (HIV) infection was considered a contraindication for solid organ transplantation (SOT) in the past. However, HIV management has improved since highly active antiretroviral therapy (HAART) became available in 1996, and the long-term survival of patients living with HIV has led many transplant programs to reevaluate their policies regarding the exclusion of patients with HIV infection. Based on the available data in the medical literature and the cumulative experience of transplantation in HIVpositive patients at our hospital, the aim of the present article is to outline the criteria for transplantation in HIVpositive patients as recommended by the Immunocompromised Host Committee of the Hospital das Clı´nicas of the University of Sa˜o Paulo

USO DO TAMARINDO NO DESENVOLVIMENTO DE PRODUTOS ALIMENTÍCIOS: UMA REVISÃO

Tamarind stands out for its nutritional and medicinal properties, and is commonly used by the population in the preparation of homemade recipes. The objective of this study was to compile and analyze studies published in the years 2011 to 2021 that used tamarind to prepare food products and evaluated its physicochemical, microbiological and/or sensory characteristics. The literature review was integrative, applying the following descriptors with the respective operators: “Tamarindus indica” OR “products” AND “development” OR “sensory” AND “microbiological” OR “physicochemical”, and their combinations in Portuguese, English and Spanish, in the Google Scholar, SciELO and Capes Periodicals databases. Three selection filters were defined for analysis: title and keywords, abstract and methodology, and reading. The searches generated a total of 116 articles, 12 articles were selected that met the presented criteria, which were fully evaluated. It was observed that the studies are relevant, many formulations have already been made with tamarind pulp: candy, jelly, yogurt, fermented milk drink, juice and wine, providing excellent physical, physico-chemical, microbiological, sensory characteristics, capacity antioxidant and phenolic compounds, as specified in the legislation for each product type. In view of the evaluation of the studies, it was possible to observe the potential of use of tamarind in the incorporation of food formulations, promoting the valorization of the fruit, little exploited in the region. Furthermore, it guarantees the conservation of the fruit through the preparation of these products, and the supply of food using an alternative ingredient, in this case, tamarind pulp, promoting health and well-being.El tamarindo destaca por sus propiedades nutricionales y medicinales, siendo comúnmente utilizado por la población en la elaboración de recetas caseras. El objetivo de este estudio fue recopilar y analizar los estudios publicados en los años 2011 a 2021 que utilizaron tamarindo para la preparación de productos alimenticios y evaluaron sus características físico-químicas, microbiológicas y/o sensoriales. La revisión bibliográfica fue de tipo integrador, aplicando los siguientes descriptores con los respectivos operadores: "Tamarindus indica" O "productos" Y "desarrollo" O "sensorial" Y "microbiológico" O "fisicoquímico", y sus combinaciones en portugués, inglés y español, en las Bases de Datos Google Academic, SciELO y Capes Journals. Se definieron tres filtros de selección para el análisis: título y palabras clave, resumen y metodología, y lectura. Las búsquedas generaron un total de 116 artículos, seleccionando 12 artículos que cumplían con los criterios presentados, los cuales fueron completamente evaluados. Se observó que los estudios son relevantes, ya se han elaborado muchas formulaciones con la pulpa de tamarindo: dulce, mermelada, yogur, bebida láctea fermentada, jugo y vino, aportando excelentes características físicas, físico-químicas, microbiológicas, sensoriales, capacidad antioxidante y compuestos fenólicos, cumpliendo con la legislación especificada para cada tipo de producto. A la vista de la evaluación de los estudios, se pudo observar el potencial del uso del tamarindo en la incorporación de formulaciones alimenticias, promoviendo la valorización de la fruta, poco explorada en la región.O tamarindo destaca-se por suas propriedades nutricionais e medicinais, sendo comumente utilizado pela população no preparo de receitas caseiras. O objetivo deste estudo foi compilar e analisar os estudos publicados nos anos 2011 a 2021 que utilizaram o tamarindo para elaboração de produtos alimentícios e avaliaram suas características físico-químicas, microbiológicas e/ou sensoriais. A revisão bibliográfica de literatura foi do tipo integrativa, aplicando os seguintes descritores com os respectivos operadores: “Tamarindus indica” OR “products” AND “development” OR “sensory” AND “microbiological” OR “physicochemical”, e suas combinações em português, inglês e espanhol, nas bases de dados Google Acadêmico, SciELO e Periódicos Capes. Definiu-se três filtros de seleção para análise: título e palavras-chave, resumo e metodologia, e leitura. As buscas geraram um total de 116 artigos, selecionando-se 12 artigos que preenchiam os critérios apresentados, sendo estes avaliados de forma integral. Observou-se que os estudos são relevantes, muitas formulações já foram elaboradas com a polpa do tamarindo: doce, geleia, iogurte, bebida láctea fermentada, suco e vinho, proporcionando excelentes características físicas, físico-químicas, microbiológicas, sensoriais, capacidade antioxidante e compostos fenólicos, atendendo ao especificado na legislação para cada tipo de produto. Diante da avaliação dos estudos, foi possível observar o potencial da utilização do tamarindo na incorporação de formulações alimentícias, promovendo a valorização do fruto, pouco explorado na região. Além disso, garante a conservação do fruto através da elaboração desses produtos, e a oferta de alimentos com uso de um ingrediente alternativo, no caso, a polpa do tamarindo, promovendo saúde e bem-estar