201 research outputs found
Supplemental Material for Roth, Florez-Rueda, and Städler, 2019
No full textSupplementary Figures S1-S2 and Tables S1-S5 for Roth et al., resubmission to Genetics 26 February 2019.<br
A Brief History of Human Time - Cross-verified Dataset
No full text
This cross-verified dataset contains 2.2 million individuals, it can be used for research purposes. This dataset is linked to the following paper that should be cited directly instead of the data itself:
Morgane Laouenan, Palaash Bhargava, Jean-Benoît Eyméoud, Olivier Gergaud, Guillaume Plique, Etienne Wasmer (2022) A cross-verified database of notable people, 3500BC-2018AD, Scientific Data, June 2022.
Bibtex:
@article{bhht3,
author = {Laouenan, Morgane and Bhargava, Palaash and Eyméoud, Jean-Benoît and Gergaud, Olivier and Plique, Guillaume and Wasmer, Etienne},
title = {A cross-verified database of notable people, 3500BC-2018AD},
journal = {Scientific Data},
publisher = {Nature Publishing Group},
year = {2022},
month = {Jun},
day = {09},
volume = {9},
number = {1},
pages = {290},
issn = {2052-4463},
doi = {10.1038/s41597-022-01369-4},
url = {https://doi.org/10.1038/s41597-022-01369-4}
}
This dataset is subject to CC-BY-SA licensing.
</p
A Brief History of Human Time - Codes & Datasets
No full text
This compressed folder includes the code used for scraping and building the dataset, the intermediate datasets and the (not cross-verified) exhaustive dataset. This dataset is linked to the following paper that should be cited directly instead of the data itself:
Morgane Laouenan, Palaash Bhargava, Jean-Benoît Eyméoud, Olivier Gergaud, Guillaume Plique, Etienne Wasmer (2022) A cross-verified database of notable people, 3500BC-2018AD, Scientific Data, June 2022.
Bibtex:
@article{bhht3,
author = {Laouenan, Morgane and Bhargava, Palaash and Eyméoud, Jean-Benoît and Gergaud, Olivier and Plique, Guillaume and Wasmer, Etienne},
title = {A cross-verified database of notable people, 3500BC-2018AD},
journal = {Scientific Data},
publisher = {Nature Publishing Group},
year = {2022},
month = {Jun},
day = {09},
volume = {9},
number = {1},
pages = {290},
issn = {2052-4463},
doi = {10.1038/s41597-022-01369-4},
url = {https://doi.org/10.1038/s41597-022-01369-4}
}
The intermediate files as well as the exhaustive database are not cross-verified and should not be used directly or under the full responsibility of users.
All datasets included in this folder are subject to CC-BY-SA licensing.
</p
Author response
Get PDFThe adult frog retina retains a reservoir of active neural stem cells that contribute to continuous eye growth throughout life. We found that Yap, a downstream effector of the Hippo pathway, is specifically expressed in these stem cells. Yap knock-down leads to an accelerated S-phase and an abnormal progression of DNA replication, a phenotype likely mediated by upregulation of c-Myc. This is associated with an increased occurrence of DNA damage and eventually p53-p21 pathway-mediated cell death. Finally, we identified PKNOX1, a transcription factor involved in the maintenance of genomic stability, as a functional and physical interactant of YAP. Altogether, we propose that YAP is required in adult retinal stem cells to regulate the temporal firing of replication origins and quality control of replicated DNA. Our data reinforce the view that specific mechanisms dedicated to S-phase control are at work in stem cells to protect them from genomic instability
Designing resilient stone fruit varieties via integrative phenotyping in low phytosanitary input orchards and association genetics
No full textDans un contexte marqué par des bouleversements épidémiologiques imprévisibles liés au changement climatique, les arbres fruitiers sont confrontés à l’attaque de multiples bioagresseurs qui sont responsables d’importants dégâts et menacent la durabilité des vergers. Sélectionner pour des résistances multiples par le biais du pyramidage des gènes est une stratégie efficace, mais particulièrement longue et complexe. Des cibles de sélection alternatives, plus intégratives, doivent être aujourd’hui envisagées pour trouver des alternatives durables à l'utilisation systématique de produits phytosanitaires dans les vergers. À ce titre la résilience est un concept séduisant encore trop peu exploré chez les arbres fruitiers. L’objectif principal de cette thèse est d’acquérir les connaissances clés sur la résilience des arbres fruitiers du genre Prunus grâce à l’exploitation de matériel végétal diversifié en conditions de basse protection phytosanitaire, et en développant des outils méthodologiques appropriés pour en caractériser les composantes.À travers une revue de littérature, nous avons tout d’abord montré l’intérêt de la résilience chez les arbres fruitiers comme nouvelle perspective concrète de sélection. Nous en avons proposé une définition claire s’appuyant sur trois composantes : résistance, tolérance et récupération. Grace à un suivi régulier des symptômes de 10 bioagresseurs dans deux core-collections de pêcher (P. persica) et d’abricotier (P. armeniaca) maintenues en conditions phytosanitaires réduites dans cinq lieux aux conditions environnementales contrastées, nous avons quantifié les cumuls de sensibilité des arbres vis-à-vis des multiples bioagresseurs qui s’attaquent aux vergers, ainsi que leur évolution au fil des années. Nous avons également caractérisé le comportement des arbres face à ces stress multiples en phénotypant des ‘biomarqueurs de la résilience’, i.e. des variables reflétant l'impact des différents bioagresseurs sur la santé et la performance des arbres, tels que la croissance du tronc, la densité des fleurs et la charge en fruits. Différents modèles de génétique d’association (GWAS) ont été testés pour disséquer l’architecture génétique des composantes de la résilience. En première approche, considérer les bioagresseurs individuellement a permis : i) de les classer en différentes typologies en fonction de l'influence de l’environnement et des interactions G×E, et ii) d’identifier des QTLs candidats, la majorité étant environnement spécifiques ou interactifs (i.e. avec des effets modulés par l'environnement). Nos résultats indiquent une sur-représentation de gènes issus de la famille des LRR-CRs et un rôle prépondérant des mécanismes de résistance basale et hôte spécifique dans la réponse aux stress biotiques chez ces deux espèces. En seconde approche, des méthodologies intégratives multi-trait ont permis de mettre en évidence des colocalisations de QTLs contrôlant différents bioagresseurs. Pour aller plus loin dans notre compréhension des mécanismes de la résilience, nous avons suivi la croissance de 10 accessions de pêcher via des mesures de longueur des pousses et de diamètres de rameaux tout au long de la saison. Nous avons ainsi déterminé les bioagresseurs ayant les impacts les plus prononcés sur la croissance des rameaux et identifié des indicateurs de résilience prometteurs basés sur les déviations entre les performances observées et attendues. Enfin, nous avons construit plusieurs index pour identifier les accessions résilientes au sein des core-collections étudiées, nous permettant ainsi d’alimenter la réflexion sur la construction d’idéotypes résilients.Ce travail représente une première étape prometteuse d’identification des composantes de la résilience et de compréhension des comportements résilients chez les arbres fruitiers à noyaux. Il contribue à accompagner une modification profonde et nécessaire des objectifs de création variétale pour tendre vers des systèmes agricoles résilients.Climate change leads to unpredictable epidemiological disturbances, and faces fruit trees with complex and fluctuating multi-disease and pest challenge year after year, incurring for significant damages and economic losses. In this context, breeding objectives aiming at reducing the dependency to phytosanitary products are difficult to address. While breeding for multiple disease resistance through gene pyramiding is an effective strategy, it remains particularly long and complex. It is therefore high time to consider more integrative breeding targets to find varieties adapted to more durable orchard management. As such, disease resilience is an appealing concept which still needs to be explored for fruit tree. The main objective of this PhD project is to gain key insights on disease resilience in stone fruit trees by exploiting genetically highly diverse plant material under low phytosanitary protection, and by developing appropriate methodological tools to characterize its components.Through a literature review, we first demonstrated the added-value of disease resilience in fruit trees as a novel and concrete breeding perspective. We proposed a clear definition of disease resilience relying on 3 components: resistance, tolerance and recovery. Next, based on a regular monitoring of 10 biotic stresses symptoms in a peach (P. persica) and an apricot (P. armeniaca) core collection deployed under low phytosanitary conditions in five environmentally contrasted locations in South-East of France, we quantified the cumulative susceptibility to the multiple pests and diseases attacking orchards, as well as their evolution over the years. We characterized tree behaviour in response to these multiple biotic stresses by phenotyping 'resilience biomarkers', i.e. variables reflecting the impact of the different pests and diseases on tree health and performance, such as trunk growth, flower density and fruit load. Several genome-wide association models (GWAS) were tested to dissect the genetic architecture of disease resilience components. As a first approach, the individual study of each biotic stress allowed to: i) classify them into different typologies according to the influence of the environment and G×E interactions, and ii) identify candidate QTLs, the majority being environment-specific or interactive (i.e. with effects modulated by the environment). Our results indicate an over-representation of genes from the LRR-CRs family and a combination of both basal and host-specific resistance mechanisms in biotic stress response for peach and apricot. Secondly, the combined use of several multi-trait GWAS approaches proved to be relevant for detecting co-localized peaks controlling a diverse range of pests or diseases. To deepen our understanding of resilience mechanisms, we measured the growth of 10 peach accessions by recording shoot length and twig diameter throughout the season. This allowed us to identify the most harmful biotic stresses to twig growth, and to develop promising resilience indicators based on deviations between observed and expected performance. Last, thanks to the development of several indexes based on the combination of disease symptoms and biomarkers, we successfully identified resilient accessions able to cope with the multiple biotic stress context of low phytosanitary protection, thus fuelling the reflection on the design of resilient ideotypes.This work pioneers the exploration of the resilience ability in stone fruit trees while providing a framework for the identification of disease resilience components. It contributes to a profound and necessary shift in breeding targets to reach more resilient agricultural systems
Role of saturated covers as oxygen buffers in cold climates
No full text[T]his report explores a hybrid-applied solution: the use of saturated covers, which involve lifting an elevated water table into a tailing impoundment that maintains saturation within the tailing profile without allowing excess water directly along the surface of the embankment. The objective of this project is to evaluate the efficacy of saturated covers in Northern regions by testing oxygen diffusion in a series of experiments with two levels of saturation using an instrumented column. While there has been some research detailing the beneficial use of saturated covers, such as in the Oxygen diffusion in saturated covers methodology and literature review (Gagne Turcotte et al., 2020) completed prior to this lab scale study, the methodology used within this study relied heavily on prediction variables/models: De and Kr, but
these proved to be more complicated than expected (Gagne Turcotte et al., 2020). Additionally, mine tailings by nature are rather unique and each sample of tailings has its own unique characteristics that need to be accounted for. Thus, the creation of this methodology occurred, with a specific emphasis on applied methods.--from IntroductionPublication is a an outcome of the oxygen diffusion in saturated covers project
- …
