In Organic Agriculture, cultivation environments and agronomic practices are very diverse. This diversity can be handled with decentralized selection based on the knowledge of farmers and scientists. ...A collaborative work between associations from Réseau Semences Paysannes and the DEAP team from INRA du Moulon set up an innovative breeding approach on farm based on decentralization and participation of farmers. This approach makes it possible to (i) create new population varieties of bread wheat locally adapted (genetic innovation) (ii) set up an organizational scheme based on decentralization and co construction between actors (societal innovation) and (iii) develop experimental designs, create statistical and data management tools which stimulate these genetic and societal innovations.
En Agriculture Biologique, les environnements des cultures et les pratiques agronomiques sont très diversifiés. Cette diversité peut être prise en compte par une sélection décentralisée associant le savoirfaire des agriculteurs et les connaissances scientifiques des chercheurs. Un travail co-construit entre associations et paysans du Réseau Semences Paysannes et l'équipe de recherche DEAP de l'INRA du Moulon a permis d'élaborer une approche innovante de sélection décentralisée et participative à la ferme. Cette approche permet de (i) créer de nouvelles variétés populations de blé tendre adaptées localement (innovation génétique) (ii) mettre en place un mode d'organisation basé sur la co-construction entre acteurs et la décentralisation (innovation organisationnelle) et (iii) développer des dispositifs expérimentaux, créer des outils statistiques et de gestion de données qui favorisent ces innovations génétique et sociétale
The burden of antibiotic resistance is currently estimated by mathematical modeling, without real count of resistance to key antibiotics. Here we report the real rate of resistance to key antibiotics ...in bacteria isolated from humans during a 5 years period in a large area in southeast in France. We conducted a retrospective study on antibiotic susceptibility of 539,107 clinical strains isolated from hospital and private laboratories in south of France area from January 2014 to January 2019. The resistance rate to key antibiotics as well as the proportion of bacteria classified as Difficult-to-Treat (DTR) were determined and compared with the Mann-Whitney U test, the χ
test or the Fisher's exact test. Among 539,037 isolates, we did not observe any significant increase or decrease in resistance to key antibiotics for 5 years, (oxacillin resistance in Staphylococcus aureus, carbapenem resistance in enterobacteria and Pseudomonas aeruginosa and 3rd generation cephalosporin resistance in Escherichia coli and Klebsiella pneumoniae). However, we observed a significant decrease in imipenem resistance for Acinetobacter baumannii from 2014 to 2018 (24.19-12.27%; p = 0.005) and a significant increase of ceftriaxone resistance in Klebsiella pneumoniae (9.9-24.03%; p = 0.001) and Enterobacter cloacae (24.05-42.05%; p = 0.004). Of these 539,037 isolates, 1604 (0.3%) had a DTR phenotype. Over a 5-year period, we did not observe a burden of AR in our region despite a high rate of antibiotic consumption in our country. These results highlight the need for implementation of real-time AR surveillance systems which use factual data.
The hepatitis C virus (HCV) life cycle is closely associated with lipid metabolism. In particular, HCV assembly initiates at the surface of lipid droplets. To further understand the role of lipid ...droplets in HCV life cycle, we assessed the relationship between HCV and the adipose differentiation-related protein (ADRP), a lipid droplet-associated protein. Different steps of HCV life cycle were assessed in HCV-infected human Huh-7 hepatoma cells overexpressing ADRP upon transduction with a lentiviral vector. HCV infection increased ADRP mRNA and protein expression levels by 2- and 1.5-fold, respectively. The overexpression of ADRP led to an increase of (i) the surface of lipid droplets, (ii) the total cellular neutral lipid content (2.5- and 5-fold increase of triglycerides and cholesterol esters, respectively), (iii) the cellular free cholesterol level (5-fold) and (iv) the HCV particle production and infectivity (by 2- and 3.5-fold, respectively). The investigation of different steps of the HCV life cycle indicated that the ADRP overexpression, while not affecting the viral replication, promoted both virion egress and entry (~12-fold), the latter possibly via an increase of its receptor occludin. Moreover, HCV infection induces an increase of both ADRP and occludin expression. In HCV infected cells, the occludin upregulation was fully prevented by the ADRP silencing, suggesting a specific, ADRP-dependent mechanism. Finally, in HCV-infected human livers, occludin and ADRP mRNA expression levels correlated with each other. Alltogether, these findings show that HCV induces ADRP, which in turns appears to confer a favorable environment to viral spread.
The high organic pollutant concentration of aged polycyclic aromatic hydrocarbon (PAH)-contaminated wasteland soils is highly recalcitrant to biodegradation due to its very low bioavailability. In ...such soils, the microbial community is well adapted to the pollution, but the microbial activity is limited by nutrient availability. Management strategies could be applied to modify the soil microbial functioning as well as the PAH contamination through various amendment types. The impact of amendment with clay minerals (montmorillonite), wood sawdust and organic matter plant roots on microbial community structure was investigated on two aged PAH-contaminated soils both in laboratory and 1-year on-site pot experiments. Total PAH content (sum of 16 PAHs of the US-EPA list) and polar polycyclic aromatic compounds (pPAC) were monitored as well as the available PAH fraction using the Tenax method. The bacterial and fungal community structures were monitored using fingerprinting thermal gradient gel electrophoresis (TTGE) method. The abundance of bacteria (16S rRNA genes), fungi (18S rRNA genes) and PAH degraders (PAH-ring hydroxylating dioxygenase and catechol dioxygenase genes) was followed through qPCR assays. Although the treatments did not modify the total and available PAH content, the microbial community density, structure and the PAH degradation potential changed when fresh organic matter was provided as sawdust and under rhizosphere influence, while the clay mineral only increased the percentage of catechol-1,2-dioxygenase genes. The abundance of bacteria and fungi and the percentage of fungi relative to bacteria were enhanced in soil samples supplemented with wood sawdust and in the plant rhizospheric soils. Two distinct fungal populations developed in the two soils supplemented with sawdust, i.e. fungi related to
Chaetomium
and
Neurospora
genera and
Brachyconidiellopsis
and
Pseudallescheria
genera, in H and NM soils respectively. Wood sawdust amendment favoured the development of PAH-degrading bacteria holding Gram-negative PAH-ring hydroxylating dioxygenase, catechol-1,2-dioxygenase and catechol-2,3-dioxygenase genes. Regarding the total community structure, bacteria closely related to
Thiobacillus
(β-Proteobacteria) and
Steroidobacter
(γ-Proteobacteria) genera were favoured by wood sawdust amendment. In both soils, plant rhizospheres induced the development of fungi belonging to Ascomycota and related to
Alternaria
and
Fusarium
genera. Bacteria closely related to
Luteolibacter
(Verrucomicrobia) and
Microbacterium
(Actinobacteria) were favoured in alfalfa and ryegrass rhizosphere.
To prospectively assess the efficiency of a standardized diagnostic approach, compared to an open strategy, for the etiologic diagnosis of uveitis.
Noninferiority, prospective, multicenter, clustered ...randomized controlled trial.
Consecutive patients with uveitis, who visited 1 of the participating departments of ophthalmology, were included. In the standardized group, all patients had a minimal evaluation regardless of the type of uveitis (complete blood count, erythrocyte sedimentation rate, C-reactive protein, tuberculin skin test, syphilis serology, and chest radiograph) followed by more complex investigations according to ophthalmologic findings. In the open group, the ophthalmologist could order any type of investigation. Main outcome was the percentage of etiologic diagnoses at 6 months.
Nine hundred and three patients with uveitis were included from January 2010 to May 2013 and the per-protocol population comprised 676 patients (open 373; standardized 303). Mean age at diagnosis was 46 years. Anatomic distribution of uveitis was as follows: anterior (60.8% and 72.3%, P = .0017), intermediate (11.7% and 12.3%, P = .8028), posterior (17.8% and 8.2%, P = .0004), and panuveitis (15.3% and 15.2%, P = .9596). An etiologic diagnosis was established in 54.4% of cases in the open group and 49.5% in the standardized group (P = .2029). The difference between both strategies (standardized minus open) was −4.9% (95% CI −12.5%; 2.6%). There were more investigations in the open group than in the standardized group (5371 vs 3759, P < .0001).
The standardized strategy appears to be an efficient diagnostic approach for the etiologic diagnosis of uveitis, although its noninferiority cannot be proved.
Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, ...viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the insect genetics resulted in successive outbreaks across the globe when rootstocks failed. Here we report the 294-Mb genome of D. vitifoliae as a basic tool to understand host plant manipulation, nutritional endosymbiosis, and enhance global viticulture.
Using a combination of genome, RNA, and population resequencing, we found grape phylloxera showed high duplication rates since its common ancestor with aphids, but similarity in most metabolic genes, despite lacking obligate nutritional symbioses and feeding from parenchyma. Similarly, no enrichment occurred in development genes in relation to viviparity. However, phylloxera evolved > 2700 unique genes that resemble putative effectors and are active during feeding. Population sequencing revealed the global invasion began from the upper Mississippi River in North America, spread to Europe and from there to the rest of the world.
The grape phylloxera genome reveals genetic architecture relative to the evolution of nutritional endosymbiosis, viviparity, and herbivory. The extraordinary expansion in effector genes also suggests novel adaptations to plant feeding and how insects induce complex plant phenotypes, for instance galls. Finally, our understanding of the origin of this invasive species and its genome provide genetics resources to alleviate rootstock bottlenecks restricting the advancement of viticulture.
(1) Objectives: French Guiana is the French territory most affected by sickle cell disease (SCD). This study investigates the associations between different environmental factors relative to climate, ...infectious outbreaks, and emergency visits or weekly hospital admissions for vaso-occlusive crisis (VOC). The identification of risk factors would lead to better patient care and patient management, and more targeted prevention and therapeutic education for patients with SCD in French Guiana. (2) Methods: This study was performed using data collected from the medicalized information system and emergency medical records of Cayenne General Hospital, between 1 January 2010 and 31 December 2016. ARIMA models were used to investigate the potential impact of weather conditions and flu epidemics on VOC occurrence. (3) Results: During the study period, 1739 emergency visits were recorded among 384 patients, of which 856 (49.2%) resulted in hospitalization, 811 (46.6%) resulted in hospital discharge, and 72 (4.2%) in another orientation. Decreased temperature and decreased humidity were both independent factors associated with an increase of VOC cases (
= 0.0128 and
= 0.0004, respectively). When studying severe VOC (leading to hospitalization, with or without prior emergency visit), 2104 hospital admissions were recorded for 326 patients. The only factor associated with severe VOC, in the multivariate analysis, was flu epidemics (
= 0.0148). (4) Conclusions: This study shows a link between climate, flu epidemics, and VOC in French Guiana. Patient's awareness of risks related to climate and flu epidemics should be encouraged, as home prevention measures can help avoid painful crises. Moreover, physicians should encourage patients to get immunized for influenza every year.
Hepatitis C virus (HCV) infected patients often develop steatosis and the HCV core protein alone can induce this phenomenon. To gain new insights into the pathways leading to steatosis, we performed ...lipidomic profiling of HCV core protein expressing-Huh-7 cells and also assessed the lipid profile of purified lipid droplets isolated from HCV 3a core expressing cells. Cholesteryl esters, ceramides and glycosylceramides, but not triglycerides, increased specifically in cells expressing the steatogenic HCV 3a core protein. Accordingly, inhibitors of cholesteryl ester biosynthesis such as statins and acyl-CoA cholesterol acyl transferase inhibitors prevented the increase of cholesteryl ester production and the formation of large lipid droplets in HCV core 3a-expressing cells. Furthermore, inhibition of de novo sphingolipid biosynthesis by myriocin - but not of glycosphingolipid biosynthesis by miglustat - affected both lipid droplet size and cholesteryl ester level. The lipid profile of purified lipid droplets, isolated from HCV 3a core-expressing cells, confirmed the particular increase of cholesteryl ester. Thus, both sphingolipid and cholesteryl ester biosynthesis are affected by the steatogenic core protein of HCV genotype 3a. These results may explain the peculiar lipid profile of HCV-infected patients with steatosis.
Variants in the UNC45A cochaperone have been recently associated with a syndrome combining diarrhea, cholestasis, deafness, and bone fragility. Yet the mechanism underlying intestinal failure in ...UNC45A deficiency remains unclear. Here, biallelic variants in UNC45A were identified by next-generation sequencing in 6 patients with congenital diarrhea. Corroborating in silico prediction, variants either abolished UNC45A expression or altered protein conformation. Myosin VB was identified by mass spectrometry as client of the UNC45A chaperone and was found misfolded in UNC45AKO Caco-2 cells. In keeping with impaired myosin VB function, UNC45AKO Caco-2 cells showed abnormal epithelial morphogenesis that was restored by full-length UNC45A, but not by mutant alleles. Patients and UNC45AKO 3D organoids displayed altered luminal development and microvillus inclusions, while 2D cultures revealed Rab11 and apical transporter mislocalization as well as sparse and disorganized microvilli. All those features resembled the subcellular abnormalities observed in duodenal biopsies from patients with microvillus inclusion disease. Finally, microvillus inclusions and shortened microvilli were evidenced in enterocytes from unc45a-deficient zebrafish. Taken together, our results provide evidence that UNC45A plays an essential role in epithelial morphogenesis through its cochaperone function of myosin VB and that UNC45A loss causes a variant of microvillus inclusion disease.
L’important corpus de charbons de bois issus de la fouille des niveaux néolithiques de l’abri Pendimoun, datés de 5 800 à 2 000 ans cal. BCE (Before the Common Era), permet une étude fine de la ...dynamique du paysage végétal, en lien avec l’exploitation agro-sylvo-pastorale du milieu et les variations du climat. Le spectre anthracologique reflète très tôt une végétation en mosaïque, où se côtoient une chênaie caducifoliée, des formations de lisières et des milieux ouverts. Ce paysage végétal contrasté renvoie originellement à des conditions topographiques et édaphiques variées, avant d’être favorisé par les activités humaines. La chênaie caducifoliée domine le spectre jusqu’au Chasséen, mais nous émettons l’hypothèse qu’elle a pu connaitre, au cours de cette période, un changement de physionomie, lié à son exploitation anthropique. Au Chasséen, le chêne sempervirent, plus compétitif en contexte perturbé, connaît une forte augmentation. Celle-ci coïncide avec l’intensification de l’exploitation pastorale de la montagne et avec la montée en puissance de l’utilisation des cavités, dont Pendimoun, comme bergeries. Ces évolutions se produisent au cours d’une période où les sociétés agro-sylvo-pastorales pourraient avoir délibérément choisi de remédier à une moindre disponibilité des basses terres pour les activités pastorales par l’exploitation étagée de la végétation.
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