Oskar Bordeaux
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Generation of metabolomic-informed models of metabolism in complex microbial communities
No full textLa génération de réseaux métaboliques à l'échelle du génome est devenue une analyse de routine pour des organismes individuels ou des communautés. Cependant, ces réseaux métaboliques générés automatiquement sont incomplets car ils sont construits sur la base de la combinaison de l'annotation des gènes et des réactions disponibles dans des bases de données génériques (Metacyc, BIGG, ModelSEED...). Ces bases de données sont orientées vers des organismes bien connus ou des organismes modèles et passent à côté de fonctions importantes du métabolisme secondaire. Nous proposons de combiner l'analyse de données métabolomiques, la modélisation métabolique et l'annotation métabolique et la modélisation métabolique et l'annotation minière pour construire des modèles de haute qualité du métabolisme microbien avec l'objectif à long terme d'une meilleure compréhension des communautés microbiennes. En termes d'application des méthodes aux communautés microbiennes végétales, nous espérons que les modèles nouvellement développés permettront de mieux comprendre le processus de recrutement microbien par la plante : fonctions métaboliques impliquées, micro-organismes associés à ces fonctions.The generation of genome-wide metabolic networks has become a routine analysis for individual organisms or communities communities. However, these automatically generated metabolic networks are incomplete because they are constructed by based on the combination of gene annotation and reactions available in generic available in generic databases (Metacyc, BIGG, ModelSEED...). These are oriented towards well-known organisms or organisms or model organisms and miss out on important functions secondary metabolism. We propose to combine metabolomic data analysis, metabolic modelling and annotation metabolic modelling and annotation mining to build high-quality models of high quality models of microbial metabolism with the long-term aim of better understanding of microbial communities. In terms of application of the methods to plant microbial communities, we hope that the plant microbial communities, we hope that the newly developed models will provide a better understanding of the process of microbial recruitment by the plant: metabolic functions involved, micro-organisms associated with these functions.Computationel models of crop plant microbial biodiversit
Crop versus Wild : the two faces of the same coin for addressing global challenges of a sustainable fruit production
No full textWild plant relatives of cultivated crops (here called CWR) are now seen as crucial tools for tackling problems like climate change and food shortages. These wild counterparts hold a massive, largely unexplored wealth of genetic and physical traits. This diversity is essential for making crops more resilient to climate hazards and biotic stresses. This is especially true for wild fruit trees, which still exist in their original locations or in areas where they survived the last ice age. These wild fruit trees possess genes for traits like pest and disease resistance, and tolerance to harsh conditions. They can handle high salt levels, severe droughts, and adapt to poor soils or changing weather, all of which impact fruit quality and yield. Modern genomic tools and "omics" technologies, such as pangenomics and high-throughput metabolomics, allow scientists to understand the molecular basis of complex traits. This helps unravel how these wild trees adapt. This presentation will focus on wild relatives of stone fruit trees as examples. It will demonstrate how advanced "omics" data can be used to understand the molecular roots of important traits for fruit tree adaptation. By utilizing this genetic diversity and employing cutting-edge technologies, collaborative projects like the Horizon Europe FRUITDIV are vital. Such efforts have the potential to create fruit crops that can withstand climate change thus securing future fruit production.ADAPTATION DES CULTURES FRUITIÈRES AU CHANGEMENT CLIMATIQUE DANS LE BASSIN MÉDITERRANÉENExploiting the Untapped potential of Fruit tree Wild DIVersity for Sustainable Agricultur
Early Middle Palaeolithic occupations dated to MIS 7 at the Abri du Maras (Ardèche, Southeast France)
No full textNew excavations at the Abri du Maras have yielded remains of hitherto unknown deposits (layer 6) from the base of the sequence, with a small lithic and faunal series dated to MIS 7. In this paper, we investigate this occupation, undoubtedly in a cave context, before the cave gradually gave way to a shelter where the last occupations took place. The faunal assemblage was accumulated by anthropic activities, and cervids are the dominant species. There are no traces of carnivores at the site. The material indicates anthropogenic bone breakage and the use of fire, among other activities. The lithic series comprises flint gathered in the south (Cenozoic formations), on the plateau and in the northwest (Cretaceous formations) along the Rhône Valley. This raw material procurement suggests a restricted logistical zone, in an area between one and three days' walk from the site. The degree of reduction of cores and products (including some Levallois), the high rate of resharpening for retouched tools, evidence of recycling and the significant fragmentation of operating chains, tend to illustrate a pattern of consumption. The management and transport of Cretaceous raw materials from the north of the site could represent a residue of individual equipment consumed and reused on site, and/or correspond to a possible leftover stockpile. Despite the limited material, the strategies observed in layer 6 at the Abri du Maras can be compared to the MIS 8-6 phase in Western Europe described as the Early Middle Palaeolithic
J Neurol Neurosurg Psychiatry
No full textEffectiveness of disease-modifying treatment (DMT) in people affected by primary progressive multiple sclerosis (PPMS) is limited. Whether specific subgroups may benefit more from DMT in a real-world setting remains unclear. Our aim was to investigate the potential effect of DMT on disability worsening among patients with PPMS stratified by different disability trajectories. Within the framework of the Big MS Data network, we merged data from the Observatoire Français de la Sclérose en Plaques, the Swedish and Italian MS registries, and MSBase. We identified patients with PPMS that started DMT or were never treated during the observed period. Subpopulations with comparable baseline characteristics were selected by propensity score matching. Disability outcomes were analysed in time-to-recurrent event analyses, which were repeated in subclasses with different disability trajectories determined by latent class mixed models. Of the 3243 included patients, we matched 739 treated and 1330 untreated patients with a median follow-up of 3 years after pairwise censoring. No difference in the risk of confirmed disability worsening (CDW) was observed between the groups in the fully matched dataset (HR 1.11, 95% CI 0.97 to 1.23, p=0.127). However, we found a lower risk for CDW among the class of treated patients with an aggressive disability trajectory (n=360, HR 0.68, 95% CI 0.50 to 0.92, p=0.014). In line with previous studies, our data suggest that DMT does not ameliorate disability worsening in PPMS, in general. However, we observed a beneficial effect of DMT on disability worsening in patients with aggressive predicted disability trajectories
Am J Epidemiol
No full textStudies on the relationship between smoking and cognition yield conflicting results, potentially from survival bias. We examined the effect of smoking status on cognitive evolution, accounting for potential bias in attrition. We analyzed 21 216 Black and White participants from the REGARDS cohort study. In order to account for potential differential attrition, a sensitivity analysis compared the association between smoking status and age-sex-specific composite cognitive trajectories using linear mixed models, robust under missing at random assumption, and joint models, robust under the extended missing at random assumptions. Linear mixed model results indicated current smokers had lower overall composite cognitive scores compared to never smokers at baseline (-0.20, 95% confidence interval (CI): -0.23, -0.16) and at 14-years duration in the study (-0.26, 95% CI: -0.33, -0.20), also apparent when comparing current smokers to past smokers, and memory and verbal fluency composite scores. Joint modeling estimates yielded results similar to results from linear mixed models. Joint models are recommended as a potential means to investigate concerns about attrition, particularly in studies of factors associated with both cognition and mortality. This study provides further support that smoking is likely to have negative impacts on cognition
Comparison of predictive ability between genomic and phenomic predictions for flowering date in sweet cherry Prunus avium L.
No full textIn plant breeding, genomic selection is a powerful tool allowing for early and accurate selection of complex traits, reducing the time and resources required for breeding cycles. However, in the quest for alternatives to genotyping, it has been proposed recently a low-cost and efficient alternative, called phenomic selection, in which genotyping is replaced by endophenotypes such as near-infrared spectra (NIRS).At INRAE Bordeaux, the PrADAM team working on Prunus aims at predict complex traits related to phenology in sweet cherry to facilitate the early selection of interesting hybrids in breeding programs. Therefore, a comparison of the predictive ability between genomic and phenomic predictions would represent a step forward in sweet cherry breeding. Using sweet cherry germplasm collection of INRAE Prunus-Juglans Biological Resources Center, we investigated both approaches: (i) genomic prediction based on 115 accessions phenotyped for beginning, full and end flowering dates, and genotyped using the 6K SNP Illumina Infinium® array, and (ii) phenomic prediction based on 98 accessions phenotyped for the same traits using Bruker® NIRS equipment.Preliminary results gave satisfying predictive ability for both approaches. Indeed, using rrBLUP model, 1,294 SNPs and BLUPs over 7 years of phenotyping, we obtained genomic predictive abilities (PA) of 0.61 to 0.66 depending on the trait, using a training set size of 80%. Using NIRS data as phenomic tool, we observed an effect of the preprocessing method on PA such as Savitzky–Golay (SG) derivatives, standard normal variate (SNV) or multiplicative scatter correction (MSC). Using rrBLUP and one single year of phenotyping, the best PA of 0.52 was obtained for full flowering date with the combination of SNV and first SG derivative, using a training set size of 80% as well. This study highlights the promising opportunity in the use of such new omics-based breeding approaches for complex traits in sweet cherry
Study of the effect of an Aqua-Stand-Up Paddle programme on cardiorespiratory capacity during exercise and lower limb muscle strength in patients with idiopathic Parkinson's disease
No full textIntroduction : l’activité physique régulière est recommandée dans la prise en charge des patients atteints de la maladie de Parkinson idiopathique (MPI). Ils présentent une perte des capacités cardio-respiratoires d’effort du fait de la baisse d’activité physique, mais aussi une faiblesse musculaire des membres inférieurs source de chutes. Afin d’élargir le choix des activités à proposer aux patients, il est nécessaire de tester l’efficacité de nouveaux programmes de rééducation. Méthode : nous avons réalisé une étude prospective, contrôlée, randomisée, visant à évaluer l’effet d’un programme d’aqua-stand-up paddle (Aqua-SUP) sur l’instabilité posturale dans la MPI. Les patients inclus présentaient un stade modéré à sévère (2,5 à 4 sur l’échelle de Hoehn & Yahr) et étaient répartis en deux groupes : un groupe bénéficiant d’un programme d’Aqua-SUP et un groupe contrôle de kinésithérapie conventionnelle. Tous les patients participaient à 2 sessions de 60 minutes/semaine, durant 2 mois. Au sein d’Aqua-SUP PARK, nous nous sommes intéressés à deux critères secondaires : l’évolution à 2 mois des capacités cardio-respiratoires à l’effort et de la force musculaire isocinétique des muscles quadriceps (Q) et ischio-jambiers (IJ) à 3 vitesses (60°/s, 180°/s et 240°/s). Résultats : 73 patients ont été inclus. À 2mois, la consommation maximale d’oxygène (V02max) moyenne gagnait 0,8 m1.min-1.kg-1 dans les deux groupes. La tendance était à l’amélioration de la force musculaire. Conclusion : les résultats étaient encourageants quant à l’amélioration des capacités cardio-respiratoires d’effort des patients parkinsoniens grâce à la pratique de l’Aqua-SUP. Les deux programmes semblaient avoir un effet positif sur la force musculaire des membres inférieurs. Néanmoins le gain paraissait plus important pour le programme kinésithérapie.Introduction: regular physical activity is recommended in the management of patients with idiopathic Parkinson's disease (IPD). These patients suffer from a loss of cardiorespiratory effort capacity as a result of reduced physical activity, as well as muscular weakness in the lower limbs, which can lead to falls. In order to broaden the choice of activities available to patients, it is necessary to test the effectiveness of new rehabilitation programmes. Method: we conducted a prospective, randomised controlled trial to evaluate the effect of an Aqua-SUP programme on postural instability in IPD. The patients included had a moderate to severe stage (2.5 to 4 on the Hoehn & Yahr scale) and were divided into two groups: one group receiving an aqua-stand-up paddle (Aqua-SUP) programme and a control group receiving conventional physiotherapy. All patients participated in 2 sessions of 60 minutes/week for 2 months. Within Aqua-SUP PARK, we were interested in two secondary criteria: changes at 2 months in cardiorespiratory capacity during exercise and isokinetic muscle strength of the quadriceps (Q) and hamstring (IJ) muscles at 3 speeds (60°/s, 180°/s and 240°/s). Results:73 patients were included. At 2 months, mean V02max had increased by 0.8 m1.min-1.kg-1 in both groups. The trend was towards an improvement in muscle strength. Conclusion: the results were encouraging in terms of the improvement in the cardiorespiratory effort capacity of Parkinson's patients thanks to Aqua-SUP. Both programmes seemed to have a positive effect on lower limb muscle strength. However, the gain appeared to be greater for the physiotherapy programme
PLoS Biol
No full textUnderstanding how cells assemble internal structures is central to cell biology. In Trypanosoma brucei, the flagellar pocket (FP) is essential for nutrient uptake, and immune evasion, and its formation depends on a cytoskeletal structure called the flagellar pocket collar (FPC). However, the mechanisms underlying FPC assembly remain poorly understood. In this study, we used cutting-edge ultrastructure expansion microscopy (U-ExM) to investigate FPC biogenesis in T. brucei. We mapped the formation of the proximal part of the new microtubule quartet (nMtQ) alongside flagellum growth, providing new insights into its assembly. Additionally, we tracked the localization dynamics of key structural proteins-BILBO1, MORN1, and BILBO2-during the biogenesis of the FPC and the hook complex (HC). Notably, we identified two previously undetected structures: the proFPC and the transient FPC-interconnecting fiber (FPC-IF), both of which appear to play crucial roles in linking and organizing cellular components during cell division. By uncovering these novel aspects of FPC biogenesis, our study significantly advances the understanding of cytoskeletal organization in trypanosomes and opens new avenues for exploring the functional significance of these structures
Neuroepidemiology
No full textEpidemiological studies on peripheral neuropathy (PN) in sub-Saharan Africa (SSA) have been conducted out in various target populations. This systematic review and meta-analysis aim to present and update available descriptive data on PN in SSA from 2000 to 2020. Research was performed in indexed databases PubMed (MEDLINE), Web of Science, Google Scholar, Scopus, African Journals Online, and grey literature databases. Studies were selected according to the PRISMA methodology and data were extracted using a collection grid. A meta-analysis with a random-effects model was performed to determine the pooled frequency measures of PNs. Overall, 116 studies were included in this review, comprising 75,227 subjects (59.71% male, mean age range 9-68.8 years). The highest number of studies were conducted in East Africa (n = 47; 40.5%). The pooled hospital frequency of PN was 39.6% ([95% CI: 34.2-45.2], I2 = 99.32%), the pooled prevalence was 4.30% ([95% CI: 2.50-6.50], I2 = 97.52%), and the pooled hospital incidence was 15.60% per year ([95% CI: 5.10-29.70], I2 = 98.78%). Pooled hospital frequency of PN was higher in diabetic patients (50.30% [95% CI: 28.30-66.70], I2 = 99%) and in Southern Africa (44.30% [95% CI: 27.80-61.10], I2 = 99%). For using electroneuromyogram as a diagnostic tool, the pooled hospital frequency of PN was 76.80% ([95% CI: 67.30-85.40], I2 = 67%). The frequency of polyneuropathy subgroup was 34.40% ([95% CI: 29.90-46.90], I2 = 99.20%). PNs are frequent in SSA and particularly in certain target groups. It is important to improve preventive measures for HIV and diabetes and increase the understanding of risk factors associated with PN