RNA interference and nonviral targeted gene therapy of experimental brain cancer

According to isotopic labeling experiments, most of the carbon used by truffle (Tuber sp.) fruiting bodies to develop underground is provided by host trees, suggesting that trees and truffles are physically connected. However, such physical link between trees and truffle fruiting bodies has never been observed.We discovered fruiting bodies of Tuber aestivum adhering to the walls of a belowground quarry and we took advantage of this unique situation to analyze the physical structure that supported these fruiting bodies in the open air. Observation of transversal sections of the attachment structure indicated that it was organized in ducts made of gleba-like tissue and connected to a network of hyphae traveling across soil particles.Only one mating type was detected by PCR in the gleba and in the attachment structure, suggesting that these two organs are from maternal origin, leaving open the question of the location of the opposite paternal mating type

Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict

Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated

No effect of feedback, level of processing or stimulus presentation protocol on perceptual learning when easy and difficult trials are interleaved

The role of feedback during training is a topic of great theoretical importance in perceptual learning. Feedback can be provided externally by the environment or internally by the observer. In order to evaluate the effectiveness of learning with internal versus external feedback, we performed a large multi-level experiment, varying the type of training task (Motion or Form), the level of processing (Local or Global), the presence of feedback (With or Without) and finally the method of stimulus presentation (Adaptive staircase or Method of constant stimuli). 140 participants were randomly assigned to one of ten groups and undertook 3 days of training in one condition only. Detection thresholds were measured daily before and after training with a pre- and post-assessment. A 75% detection threshold was calculated and used to estimate that day’s training levels (65% and 85% accuracy for difficult and easy trials respectively). The group trained with MOCS were presented with predefined randomly interleaved easy and difficult trials ranging from 50% to 95% stimulus intensity. Our findings indicate that improvement was generally robust across training-tasks, processing levels and feedback conditions. This suggests that internal reinforcement is as effective as external feedback in a discrete-noise-paradigm for local and global tasks when easy and difficult trials are interleaved

Subclonal evolution in neuroblastoma

Le neuroblastome est le cancer solide extra-cranial le plus fréquent chez l’enfant. Il est caractérisé par une très grande hétérogénéité tant au niveau clinique que moléculaire. Alors que certains patients rentrent spontanément en rémission, on peut se demander quels facteurs permettent la réémergence du cancer chez d’autres malgré traitement. Pour répondre à cette question, il convient d’identifier chez les patients ayant rechuté, les différentes populations clonales coexistant au diagnostic et/ou à la rechute. Cela permet, entre autre, d’étudier les voies différemment altérées entre ces deux temps. Dans cette optique, nous présentons ici QuantumClone, un algorithme de reconstruction clonal à partir de données de séquençage, ainsi que son application à une cohorte de patients souffrant d’un neuroblastome. Sur ces données, l’application de notre méthode a permis d’identifier des différences dans le ratio de variants prédits fonctionnels par rapport à ceux prédits passagers entre les populations ancestrales, enrichies à la rechute ou appauvries à la rechute.Neuroblastoma is the most frequent solid extra-cranial cancer of childhood. This cancer displays a high heterogeneity both at clinical and molecular levels. Even though in some patients spontaneous remission can be observed, some others relapse despite treatment and surgical resection. It may be wondered which are the factors that distinguish these two cases. In order to answer this question, identification of populations coexisting at diagnosis and/or relapse in the patients which have relapsed is a prerequisite. This would allow, between other things, to study the pathways differently altered in clones that are specific to each time point. With this in mind, we hereby present QuantumClone, a clonal reconstruction algorithm from sequencing data. In addition, we applied this method to a cohort of patients suffering from neuroblastoma. On these data, our method identified differences in the functional mutation rate, i.e. the number of putative functional variants by total number of variants, between the ancestral clones, clones expanding at relapse, and clones shrinking at relapse

Evolution sous-clonale dans le neuroblastome

Neuroblastoma is the most frequent solid extra-cranial cancer of childhood. This cancer displays a high heterogeneity both at clinical and molecular levels. Even though in some patients spontaneous remission can be observed, some others relapse despite treatment and surgical resection. It may be wondered which are the factors that distinguish these two cases. In order to answer this question, identification of populations coexisting at diagnosis and/or relapse in the patients which have relapsed is a prerequisite. This would allow, between other things, to study the pathways differently altered in clones that are specific to each time point. With this in mind, we hereby present QuantumClone, a clonal reconstruction algorithm from sequencing data. In addition, we applied this method to a cohort of patients suffering from neuroblastoma. On these data, our method identified differences in the functional mutation rate, i.e. the number of putative functional variants by total number of variants, between the ancestral clones, clones expanding at relapse, and clones shrinking at relapse.Le neuroblastome est le cancer solide extra-cranial le plus fréquent chez l’enfant. Il est caractérisé par une très grande hétérogénéité tant au niveau clinique que moléculaire. Alors que certains patients rentrent spontanément en rémission, on peut se demander quels facteurs permettent la réémergence du cancer chez d’autres malgré traitement. Pour répondre à cette question, il convient d’identifier chez les patients ayant rechuté, les différentes populations clonales coexistant au diagnostic et/ou à la rechute. Cela permet, entre autre, d’étudier les voies différemment altérées entre ces deux temps. Dans cette optique, nous présentons ici QuantumClone, un algorithme de reconstruction clonal à partir de données de séquençage, ainsi que son application à une cohorte de patients souffrant d’un neuroblastome. Sur ces données, l’application de notre méthode a permis d’identifier des différences dans le ratio de variants prédits fonctionnels par rapport à ceux prédits passagers entre les populations ancestrales, enrichies à la rechute ou appauvries à la rechute

Overdiagnosis of Asthma in the Community

BACKGROUND: Overdiagnosis of asthma may be an emerging problem after years of attention to the rising prevalence and reported underdiagnosis of the disease

Couplage et modélisation des flux d'eau et de carbone dans une plantation tropicale pérenne

National audienceLes flux d'énergie, d'eau et de carbone ont été mesurés en continu pendant deux ans dans une plantation tropicale de cocotiers (méthode CARBOEUROFLUX). A l'échelle foliaire, la réponse de la conductance stomatique (Gs) au climat a été mesurée et modélisée (Gsmod, Jarvis, 1976). La réponse de la photosynthèse foliaire (An) a été enregistrée, ainsi que l'effet de la température sur Vcmax et Jmax (Farquhar, 1981). Le modèle complet de photosynthèse foliaire prédit An en fonction des seules variables climatiques et de Gsmod par méthode analytique (Wang and Jarvis, 1993). L'effet du %N sur Vcmax et la distributions de %N dans la canopée est en cours de dépouillement. A l'échelle de l'arbre, les flux de sève mesurés ont été calibrés par des mesures d'évapotranspiration au-dessus et en-dessous de la canopée (eddycorrelation). La conductance de couvert (Gc) a été obtenue en inversant l'équation de Penman-Monteith. On a utilisé un modèle Sun/Shade (de Pury and Farqhuar, 1997) pour calculer la proportion de feuilles d'ombre et de lumière dans la canopée au pas de temps semi-horaire. Le coefficient d'extinction de la plantation a été calculé sur maquette 3D (Dauzat and Eroy, 1995) et le LAI obtenu par destruction. La conductance de couvert modélisée utilise les paramètres de Gsmod (foliaire) et les surfaces calculées respectives des feuilles d'ombre et de lumière. On obtient une bonne correlation entre Gc et Gcmod après ajustement des températures de feuilles (bilans d'énergie et radiatif). La photosynthèse de couvert (Acmod) a été modélisée à l'aide du même modèle Sun/Shade et des paramètres issus du modèle foliaire. La photosynthèse brute du couvert (GPP) est la différence des flux de carbone diurnes de la plantation et de la respiration de l'écosystème mesurée la nuit (Reco, filtrée pour U* et ajustée aux températures diurnes). On obtient une bonne correlation entre GPP et Acmod