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Investigation of molecular mechanisms involved in apple scab quantitative resistance using untargeted metabolic QTL mapping
No full textInternational audienceTo reduce the use of phytochemical treatments, apple scab resistant varieties have been deployed in orchards. They mostly rely on a single resistance gene Rvi6, which is now overcome by adapted Venturia inaequalis (Vi) isolates, thus challenging orchard durability. One way to improve durability would imply to diversify sources and mechanisms of genetic resistance within new varieties. Yet, efficiently pyramiding these different mechanisms means to first better characterize the molecular end-players of biotic stress resistance. We focused our study on complementary resistance quantitative trait loci (rQTL) to apple scab, segregating in a biparental population known as ‘TN 10-8 x Fiesta progeny’. The rQTL ‘qT1’ inherited from the hybrid ‘TN 10-8’ confers a high level of resistance to specific races of Vi while the epistatic rQTL ‘qF11’ and ‘qF17’ inherited from the cultivar ‘Fiesta’ have a broader spectrum of action. To further understand the molecular mechanisms underlying these rQTL, we studied the metabolome of this progeny before or after inoculation with two different isolates including one known to overcome ‘qT1’. Depending on the experiment, 1,500 to 3,000 metabolic features were detected using an untargeted metabolomic approach. In addition, their genetic determinism was characterized using metabolic QTL (mQTL) mapping. We then focused on resistance-associated metabolites controlled by mQTL co-localizing with previously identified rQTL. We identified up to 20 mQTL co-localizing with ‘qF11/qF17’ rQTL and a hot-spot of 200 mQTL co-localizing with ‘qT1’ in one of the two Vi-infected conditions. Out of these 200 metabolic features, 30 were annotated as triterpenoids and their potential antifungal roles will be further explored through in vitro bioassays. Our results show that investigating the genetic architecture of specialized metabolism may help characterise the biochemical pathways involved in apple resistance to scab. This knowledge will shed light on the most efficient combination of mechanisms to breed new durably-resistant apple varieties
Identifying pleiotropic alleles in biotic stress resistance and exploring underlying molecular mechanisms for apple orchard durability
No full textInternational audienceTo address environmental and human health challenges, agroecological apple orchards have to be more resistant to a wide range of pests and pathogens while using sustainable alternatives to replace phytosanitary chemicals. So far, most resistant commercial varieties harbor only one major favorable allele for the most common disease, that can be easily eroded over time. Thus, to ensure durable resistance over time, it is essential to combine multiple resistances with pleiotropic effects, involving complementary molecular pathways that can be mobilized against multiple pests.To achieve this goal, we propose to: (i) design and phenotype a new core-collection focused on cider varieties and crop wild relative (CWR) species, (ii) use association studies to identify resistance alleles to fire blight and apple scab and (iii) use a combinatory approach of genomics and metabolomics to determine the molecular actors of apple resistance.Recently, we focused our studies on CWR and cider varieties, that supposedly, have retained unexplored resistance alleles that were less shaped by human selection. In addition, we gathered a decade of phenotyping results on fire blight and apple scab resistance in more than 400 Malus accessions. Contrasting phenotypic responses for the different cultivar groups and wild relatives were found. This variability was then associated with SNP polymorphisms and new favorable alleles were discovered. In order to test the diversification of molecular mechanisms along with presence of various resistance alleles, we performed targeted metabolic analyses of several biphenyl compounds on a set of 20 genotypes. We also aim to detect genomic regions harboring key enzymes of the biphenyl pathway and compare their synteny and polymorphisms within Malus sp.This project will deliver innovative and timely results on the molecular determinants of biotic stress resistance. These findings will directly support breeding programs by establishing ideotypes, identifying progenitors and developing genetic and biochemical markers
Development and preliminary analysis of a new multispecies genotyping array including apple and pear SNPs
No full textInternational audienceAs domestication and selection have only exploited a small fraction of the existing genetic diversity, reintroducing rare, ancient or wild diversity in breeding schemes is becoming a necessity to face climate change and agroecological constraints. Towards this objective, new multi-species genotyping arrays have been developed and used to characterize genetic diversity available in collections of 4 botanical families in the frame of the AgroDiv project (https://anr.fr/ProjetIA-22-PEAE-0005). One of these arrays includes SNPs for apple and pear, together with SNPs for garden pea, faba bean and white lupin. For apple, SNPs were mostly chosen from previous arrays, i.e. the Illumina 20K and the Axiom 480K and JKI-50K arrays. The choice was based on marker performance in previous genotyping experiments and positions on a genetic map enriched by alignment to the HFTH1 whole genome sequence. The initial choice included the markers from the core 20K-480K compatibility set, known markers targeting traits of interest and markers from the Apple ID SNP set. Markers were then added to fill gaps larger than 1 cM and chosen for high minor allele frequency in available genotypic data. Additional markers were added to potentially fill gaps in a few biparental progenies where genetic mapping for QTL analysis is intended. For pear, SNPs were chosen from the Axiom 70K array in an approach similar to apple. After accommodating for replicates needed for the probesets chosen for each of the five species of the array, a total of 9533 SNPs were tiled for apple and 7663 SNPs for pear. Diversity analysis for 384 apple or pear accessions from the INRAE collection (CRB RosePom) and preliminary genetic mapping results for biparental progenies will be presented
Monde rural, une cohabitation impossible ?
No full textEmission radiophoniqueThis radio interview sweeps away a number of preconceived ideas about the countryside and contemporary rural areas. On their little-known economic activities (industry, the residential economy), on their dependence on the automobile (but less so on the airplane), on the causes and effects of the rural exodus and neo-rurality, on contemporary forms of village solidarity (with a focus on popular education), on the respective potential of the law and the market to regulate relations between inhabitants who have different or even opposing perspectives (pesticides, hunting, nuisances...). In the end, the most important thing is undoubtedly to recognize that rural dwellers have something to offer an urban society: the ability to live frugally, to practice a complex relationship with wild/commensal/domestic nature, to value the bottom-up approach, to roll up their sleeves to make life beautiful... Renan Volclair illustrates this exchange with a column on recent conflicts surrounding agricultural nuisances, based on the testimony of Vincent Verschuere, convicted of abnormal neighborhood disturbance following the construction of his farm buildings in the village.Cet entretien radiophonique balaye un certain nombre d’idées reçues sur la campagne et les territoires ruraux aujourd’hui. Sur leurs activités économiques méconnues (l’industrie, l’économie résidentielle), sur la dépendance à l’automobile (mais moins à l’avion), sur les causes et les effets de l’exode rural et de la néo-ruralité, sur les formes contemporaine de la socidarité villageoise (avec un focus sur l’éducation populaire), sur les potentialités respectives de la loi et du marché pour réguler les relations entre des habitants qui ont des perspectives différentes voire opposées (pesticides, chasse, nuisances…). Finalement, l’essentiel est sans doute de reconnaître que les ruraux ont des choses à faire valoir dans une société urbaine : savoir vivre la sobriété, pratiquer un rapport complexe à la nature sauvage/commensale/domestique, valoriser le bottom-up, se retrousser les manches pour que la vie soit belle… Renan Volclair illustre cet échange avec une chronique sur les conflits récents autour de nuisances agricoles, appuyée sur le témoignage de Vincent Verschuere, condamné pour trouble anormal de voisinage suite à la construction de ses bâtiments d’élevage dans le bourg
Effect of a ceruminolytic ear cleaner on clinical, microbiological and ear canal microbiome evolution in canine erythemato‐ceruminous otitis externa associated with proliferation of Malassezia yeasts
No full textInternational audienceZusammenfassung Hintergrund Eine erythematös‐ceruminöse Otitis externa (ECOE) wird häufig mit Malassezia spp. und einer mikrobiellen Imbalance in Zusammenhang gesehen. Hypothese/Ziele Eine Untersuchung der klinischen Leistung eines Ohrreinigers bei Hunden, die eine ECOE mit einem Malassezia spp. Überwachstum haben und eine Messung dieses Einflusses auf die Mikrobiota. Tiere Dreißig Hunde in Privatbesitz mit einer mild‐bis‐moderaten ECOE im Zusammenhang mit einem Malassezia spp. Überwachstum. Materialien und Methoden Pruritus Wert (PS), klinischer Wert (0‐3 Otitis Index Score [OTIS3]: basierend auf Sekretion, Erythem, Hyperplasie und Ulzeration) und zytologischer Wert (CS) wurden am Tag (D)0, D7 und D14 erfasst. Es wurden am D0 und D14 sterile Ohrtupfer verwendet, um eine Pilzkultur durchzuführen. DNA‐Extraktion und PCR‐Amplifizierung des 18 ITS und 16S rRNA‐Gens wurden durchgeführt, um die Zusammensetzung und die Veränderungen im otischen Mikrobiom zu evaluieren. Die Ohren wurden je nach Sekretionswert täglich, jeden zweiten Tag oder zweimal wöchentlich mit einem ceruminolytischen Ohrreiniger gereinigt. Ergebnisse Siebenundfünfzig Ohren (30 Hunde) beendeten die Studie. PS, OTIS‐3 und CS waren am D7 bzw D14 (‐45%, ‐43%, ‐60% bzw ‐77%, ‐66%, ‐76%; p < 0,0001 Wilcoxon Test) signifikant vermindert. Die Pilzkulturen waren am D0 nur bei 34 Ohren positiv ( Malassezia spp.) und bei allen Ohren am D14 negativ. Die Mykobiota Zusammensetzung war vor und nach der Behandlung signifikant verschieden, wobei die Diversität der Pilze am D14 im Vergleich zu D0 zunahm (Shannon Index; p < 0,003 Wilcoxon Test). Bei der bakteriellen Zusammensetzung gab es keine Veränderung. Schlussfolgerungen und klinische Bedeutung Im Falle einer ECOE mit Malassezia spp. Überwachstum zeigte der getestete Ohrreiniger einen positiven Einfluss auf die Dysbiose der Pilze und das Überwachstum der Malassezia spp.Abstract Background Erythemato‐ceruminous otitis externa (ECOE) is commonly associated with Malassezia spp. and microbial imbalance. Hypothesis/Objective To assess the clinical performance of an ear cleaner in dogs suffering from ECOE associated with Malassezia spp. overgrowth and to measure its impact on the microbiota. Animals Thirty privately owned dogs suffering from mild‐to‐moderate ECOE associated with Malassezia spp. overgrowth. Materials and Methods Pruritus score (PS), clinical score (0–3 Otitis Index Score [OTIS3]: based on secretions, erythema, hyperplasia and ulceration) and cytological score (CS) were assessed on Day (D)0, D7, and D14. Sterile ear swabs were used on D0 and D14 to perform fungal culture DNA extraction, and PCR amplification of the 18 ITS and 16S rRNA gene was carried out to evaluate the composition and changes of the otic microbiome. Ears were cleaned with a cerumenolytic ear cleanser daily, every other day, or twice a week depending on the secretion score. Results Fifty‐seven ears (30 dogs) completed the study. PS, OTIS‐3, and CS were significantly decreased at D7 and D14 (−45%, −43%, −60% and −77%, −66%, −76%, respectively; p < 0.0001 Wilcoxon test). Fungal culture was positive ( Malassezia spp. ) in only 34 ears at D0 and was negative in all ears at D14. Mycobiota composition was significantly different before and after treatment with an increase of fungal diversity (Shannon index; p < 0.003 Wilcoxon test) at D14 compared to D0. There was no change in bacterial composition. Conclusions and Clinical Relevance In case of ECOE associated with Malassezia spp. overgrowth, the use of the tested ear cleaner showed a positive impact on the fungal dysbiosis and Malassezia spp. overgrowth.RESUMEN Introducción La otitis externa eritematoceruminosa (ECOE) se asocia comúnmente con Malassezia spp . y desequilibrio microbiano. Hipótesis/Objetivo Evaluar el rendimiento clínico de un limpiador de oídos en perros con ECOE asociada a un sobrecrecimiento de Malassezia spp . y medir su impacto en la microbiota. Animales Treinta perros de propiedad privada con ECOE leve a moderada asociada a un sobrecrecimiento de Malassezia spp . Materiales y métodos Se evaluaron la puntuación de prurito (PS), la puntuación clínica (puntuación del índice de otitis [OTIS3] de 0 a 3 : basada en secreciones, eritema, hiperplasia y ulceración) y la puntuación citológica (CS) los días 0, 7 y 14. Se utilizaron hisopos óticos estériles los días D0 y D14 para extraer DNA del cultivo fúngico, y se realizó la amplificación por PCR de los genes 18 ITS y 16S rRNA para evaluar la composición y los cambios en el microbioma ótico. Los oídos se limpiaron con un limpiador cerumenolítico diariamente, cada dos días o dos veces por semana, según el nivel de secreción. Resultados Cincuenta y siete oídos (30 perros) completaron el estudio. PS, OTIS‐3 y CS disminuyeron significativamente los días D7 y D14 (–45 %, –43 %, –60 % y –77 %, –66 %, –76 %, respectivamente ; p < 0,0001 prueba de Wilcoxon). El cultivo fúngico fue positivo ( Malassezia spp .) solo en 34 oídos el día D0 y negativo en todos los oídos el día D14. La composición de la micobiota fue significativamente diferente antes y después del tratamiento, con un aumento de la diversidad fúngica (índice de Shannon ; p < 0,003 prueba de Wilcoxon) en el día 14 en comparación con el día 0. No se observaron cambios en la composición bacteriana. Conclusiones y relevancia clínica En el caso de ECOE asociada con sobrecrecimiento de Malassezia spp ., el uso del limpiador ótico evaluado mostró un impacto positivo en la disbiosis fúngica y el sobrecrecimiento de Malassezia spp .Résumé Contexte L'otite externe érythémato‐cérumineuse ( OEEC) est souvent associée à Malassezia spp. et à un déséquilibre microbien. Hypothèse/Objectif Evaluer la performance clinique d'un nettoyant auriculaire chez des chiens souffrant d'une OEEC associée à une prolifération de Malassezia spp. et mesurer son impact sur le microbiote. Animaux Trente chiens privés souffrant d'une OEEC légère à modérée associée à une prolifération de Malassezia spp. Matériels et méthodes Le score de prurit (PS), le score clinique (0‐3 Otitis Index Score [OTIS3] : basé sur les sécrétions, l'érythème, l'hyperplasie et l'ulcération) et le score cytologique (CS) ont été évalués à J0, J7 et J14. Des écouvillons stériles ont été utilisés à J0 et J14 pour extraire l'ADN des cultures fongiques, et l'amplification par PCR du gène 18 ITS et du gène de l'ARNr 16S a été réalisée pour évaluer la composition et les changements du microbiome otique. Les oreilles ont été nettoyées avec un nettoyant auriculaire céruminolytique tous les jours, tous les deux jours ou deux fois par semaine en fonction du score de sécrétion. Résultats Cinquante‐sept oreilles (30 chiens) ont participé à l'étude. Le PS, l'OTIS‐3 et le CS étaient significativement diminués à J7 et J14 (‐45%, ‐43%, ‐60% et ‐77%, ‐66%, ‐76%, respectivement ; p < 0,0001 test de Wilcoxon). La culture fongique était positive (Malassezia spp.) dans seulement 34 oreilles à J0 et était négative dans toutes les oreilles à J14. La composition du mycobiote était significativement différente avant et après le traitement, avec une augmentation de la diversité fongique (indice de Shannon ; p < 0,003 test de Wilcoxon) à J14 par rapport à J0. Il n'y a pas eu de changement dans la composition bactérienne. Conclusions et pertinence clinique En cas d'OEEC associé à une prolifération de Malassezia spp., l'utilisation du nettoyant auriculaire testé a eu un impact positif sur la dysbiose fongique et la prolifération de Malassezia spp.要約 背景 紅斑性耳垢性外耳道炎(ECOE)は一般的にマラセチア属と微生物の不均衡と関連している。 仮説/目的 本研究の目的は、マラセチア属真菌の過剰増殖に関連するECOEに罹患している犬におけるイヤークリーナーの臨床的性能を評価し、微生物叢への影響を測定することであった。 対象動物 マラセチア属真菌の過剰増殖を伴う軽度から中等度のECOEに罹患している30頭のオーナー所有犬。 材料と方法 掻痒スコア(PS)、臨床スコア(0‐3 Otitis Index Score [OTIS3]:分泌物、紅斑、過形成および潰瘍形成に基づく)および細胞学的スコア(CS)をDay(D)0、D7およびD14に評価した。D0およびD14に滅菌耳スワブを用いて真菌培養DNA抽出し、18ITSおよび16S rRNA遺伝子のPCR増幅を実施して、耳微生物叢の構成と変化を評価した。耳は分泌物スコアに応じて、毎日、隔日または週2回、耳垢溶解性イヤークリーナーで洗浄した。 結果 57の耳(30頭)が研究を完了した。PS、OTIS‐3およびCSは、D7およびD14で有意に減少した(それぞれ‐45%、‐43%、‐60%および‐77%、‐66%、‐76%；p<0.0001 Wilcoxon検定)。真菌培養はD0ではわずか34耳で陽性( Malassezia spp.)であったが、D14ではすべての耳で陰性であった。真菌叢の組成は治療前後で有意に異なり、D0と比較してD14では真菌の多様性(Shannon index; p < 0.003ウィルコクソン検定)が増加した。細菌組成に変化はなかった。 結論および臨床的妥当性 マラセチア属真菌の過剰増殖を伴うECOEの場合、試験したイヤークリーナーの使用は、真菌のディスバイオーシスおよびマラセチア属の過剰増殖に好影響を示した。Resumo Contexto A otite externa eritemato‐ceruminosa (OECE) é comumente associada à infecção por Malassezia spp. e ao desequilíbrio microbiano. Hipótese/Objetivo Avaliar o desempenho clínico de uma solução de limpeza auricular em cães com OECE associada ao supercrescimento de Malassezia spp. e mensurar seu impacto na microbiota. Animais Trinta cães de propriedade particular com OECE leve a moderada associada ao crescimento excessivo de Malassezia spp. Materiais e Métodos O escore de prurido (EP), o escore clínico (0‐3, Escore do Índice de Otite [OTIS3]: baseado em secreções, eritema, hiperplasia e ulceração) e o escore citológico (EC) foram avaliados no Dia (D)0, D7 e D14. Swabs auriculares estéreis foram utilizados no D0 e D14 para extração de DNA da cultura fúngica, e amplificação por PCR dos genes 18 ITS e 16S rRNA foi realizada para avaliar a composição e as alterações do microbioma ótico. As orelhas foram limpas com um limpador auricular ceruminolítico diariamente, em dias alternados ou duas vezes por semana, dependendo da do escore de secreção. Resultados Cinquenta e sete orelhas (30 cães) completaram o estudo. EP, OTIS‐3 e EC diminuíram significativamente nos dias 7 e 14 (–45%, –43%, –60% e –77%, –66%, –76%, respectivamente; p < 0,0001 no teste de Wilcoxon). A cultura fúngica foi positiva ( Malassezia spp.) em apenas 34 orelhas no dia 0 e negativa em todas as orelhas no dia 14. A composição da micobiota foi significativamente diferente antes e depois do tratamento, com aumento da diversidade fúngica (índice de Shannon; p < 0,003 no teste de Wilcoxon) no D14 em comparação ao D0. Não houve alteração na composição bacteriana. Conclusões e Relevância Clínica Em caso de OECE associada ao supercrescimento de Malassezia spp., o uso do limpador auricular testado demonstrou um impacto positivo na disbiose fúngica e no supercrescimento de Malassezia spp
Morphological mapping and dating of recent ice-rich deposits on Alba Mons, Mars.
No full textInternational audienceMapping and dating of hummocky ice-rich deposits on Alba Mons in crater pole-facing slopes: these deposits, tied to past obliquity-induced glaciation (4.5–8.8 Ma), show spatial links to erosion and align with ice accumulation zones in climate models
mRNA loaded Lipid Nanocapsule Formulation: a promising therapeutic strategy to treat Pseudoxanthoma elasticum
No full textInternational audiencePseudoxanthoma elasticum (PXE) is a rare genetic disorder characterized by progressive ectopic calcification, which is caused by mutations in the ABCC6 gene. PXE predominantly affects the elastic fibers of the skin, Bruch’s membrane in the retina and the cardiovascular system. Unfortunately, no curative treatment exists. To compensate the deficiency of the protein normally expressed in hepatocytes, the delivery of the corresponding mRNA has emerged as a promising therapeutic strategy. However, this approach requires a nanocarrier to cross the cell membrane, protect the mRNA, and ensure delivery to the targeted tissues.During the Covid-19 pandemic, lipid nanoparticles (LNP) highlighted the huge potential of nanomedicines: they successfully demonstrated their ability to protect and deliver mRNA. Among LNP, lipid nanocapsules (LNC) were designed and patented in 2014 by the MINT laboratory (patent FR 3026009 (A1)) with the goal of protecting genetic material such as DNA, siRNA, and miRNA.The objective of this project is to formulate and characterize mRNA loaded LNC, assessing their in vitro toxicity on the hepatocyte cell lines HepG2 and SNU-387 and to validate the therapeutic strategy in Abcc6−/− mice.As a model to validate the formulation, mRNA encoding Enhanced Green Fluorescent Protein (EGFP) was initially used. In parallel, a total of 948.2 µg of ABCC6 mRNA was produced in Prof. Pichon’s laboratory. Both ABCC6 and EGFP mRNA-loaded LNC were fully characterized. Subsequently, dose-dependent cytotoxicity was assessed using MTT and LDH assays, resulting in the determination of an IC50 that will be utilized in future experiments.Cell internalization studies using flow cytometry revealed an efficient uptake of DiD-labeled EGFP mRNA loaded LNC over time with a 100% internalization after 24 hours. Finally, in vivo studies were conducted in healthy mice by intravenous injection of DiD-labeled LNC. The results showed a significant accumulation of LNC in the liver 24 hours post-injection: ABCC6 being predominantly expressed in the liver, this biodistribution is an important result. Encouragingly, hepatic mRNA expression was also observed 6h post-injection, offering promising prospects for future therapeutic applications in PXE
Ensemble et Fusion d'Agents RL pour la Robustesse aux Attaques Adverses
No full textInternational audienceL'Apprentissage par Renforcement Profond (RL) permet d'entraîner des agents autonomes à prendre des décisions dans des environnements complexes, mais reste sensible aux variations et perturbations des observations. L'entraînement adverse permet d'améliorer la robustesse des agents en les exposant à des attaques adverses. L'association des méthodes adverses avec des méthodes ensemblistes et la fusion de modèles peut permettre de renforcer la généralisation de la robustesse. Cet article compare les méthodes d’attaques et d’entraînement adverses tout en explorant les méthodes ensemblistes et la fusion de modèles en RL
Britannia Rules the Rhine: Die Britische Rheinlandbesatzung 1918–1926
No full textInternational audienc