Oskar Bordeaux
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Developing a microfluidic qPCR chip to quantify microbial taxa with a potential biocontrol activity against grapevine downy mildew
No full textGrapevine downy mildew, caused by the oomycete Plasmopara viticola, is responsible for significant economic losses each year and for a large proportion of the fungicides used in viticulture. In order to limit the use of these chemical pesticides, which are incompatible with the development of sustainable viticulture, biocontrol solutions based on cultivated simplified communities of microorganisms (SimComs) are gradually emerging. In the present study, we designed several SimComs for the control of downy mildew, using a collection of microorganisms isolated from grapevine leaves by a culturomic approach. The SynComs composed of bacteria, yeasts and filamentous fungi, either described to have either a biocontrol activity against plant pathogens or abundant on grapevine leaves. We tested the hypothesis that including abundant species in the SimComs would help the microbial community colonize the leaves.Materials and methods A quantitative PCR microfluidic chip (Fluidigm Biomark) was developed to monitor the establishment of SinComs on grapevine leaves. Larger number of reaction are allowed by microfluidic PCR compared to classical qPCR, resulting in quicker and cheaper price per sample. It also has the advantage of providing absolute abundance data compared to metabarcoding approaches that only estimate the relative abundance of microbial taxa.ResultsSo far, specific primers for 34 microbial taxa (out of the 42 selected for inclusion in the SimComs) have been designed in single-copy housekeeping genes. We are currently sequencing the genomes of the remaining microbial taxa to complete the primer design. We applied the microfluidic chip to DNA samples extracted from grapevine leaf discs inoculated with SimComs and were able to detect most of the inoculated microorganisms, including some microbial taxa that significantly reduced the intensity of downy mildew symptoms under laboratory conditions. The microfluidic chip was then applied to environmental DNA collected in vineyard from spore sensor, in order to detect and quantify the targeted protective microorganisms. By doing so, we were able to detect the presence of several microorganisms, including some microbial taxa with proven biocontrol activity against plant pathogens such as Bacillus pumilus, Aureobasidium pullulans and Epicoccum nigrum.Conclusion : These preliminary results shed light on the potential of microfluidic chip as a new molecular diagnostic tool to monitor specific microbial communities present naturally or artificially after SimCom inoculation in the field.Cultivating the grapevine without pesticides : towards agroecological wine-producing socio-ecosystemsComputationel models of crop plant microbial biodiversit
Sediments accumulated in sewer settling basins as recorders of historical use of drugs: potential and limitations
No full textThis study assesses the occurrence of various types of drugs in a sedimentary archive cored in a sewer settling basin with a depth of 14 m. The coring operations were conducted before the basin was drained. A 2.2-m long sedimentary core was recovered. The sediments consisted of successions of coarse minerals and coarse or fine organic layers. One of the main challenges is to be able to date such a very recent archive. This was realized by using an event-based approach with nineteen 14C Carbon dating out of the rising and decay phase of atmospheric 14C content linked to the aerial explosion of thermonuclear bombs (bomb peak). The first results revealed the potential of these sediments to record diverse contaminants. Eighteen of the 20 molecules targeted were quantified at least once. The potential of such archives to record the first use of each drug in the city is questioned, as well as the potential of back-calculated drug consumption on the basis of sedimentary occurrences. The estimated wastewater concentrations fit quite well for some molecules, whereas further work remains necessary for other drug values, especially concerning the back-calculation parameters.Observations Géochimiques des Trajectoires UrbainesGeofluids and Volatil elements – Earth, Atmosphere, Interfaces – Resources and Environmen
Multiscale entropy rates: a study on different stochastic processes
No full textIn this paper, we propose to analyze the behavior of the entropy rate (ER) when applied to a signal and its coarse-grained versions. The “multiscale entropy rate” (MSER) is deduced by storing in a vector the resulting ERs. Our contribution consists in studying the MSER calculated on different stochastic processes. When dealing with Gaussian complex or real moving average (MA) processes or autoregressive (AR) processes, which can be seen as the filtering of a white Gaussian driving process, the MSER depends on the variances of the driving processes of the corresponding minimum-phase ARMA process at each scale. More particularly, we derive the analytical expression of the MSER for -order MA or AR processes using different approaches. This study allows us to better understand what each scale brings in and to describe the behavior of the MSER for these types of processes. We also show that there is a mapping between the stochastic-process parameters and the ER computed at different scales. Finally, we show that the multiscale procedure is not relevant for a sum of complex exponentials disturbed by an additive white Gaussian noise
Agriculture, aquaculture et pêche : impacts des modes de production labellisés sur la biodiversité. Rapport scientifique de l'étude
No full textLa loi Climat et résilience de 2021 a instauré la mise en place d’un affichage environnemental sur les produits alimentaires afin d’informer les consommateurs du coût environnemental de leurs achats. La construction de cet affichage a suscité un important travail méthodologique ouvert aux acteurs. Un bilan intermédiaire a souligné la difficulté à appréhender toutes les dimensions de la biodiversité. C’est dans ce cadre que les ministères en charge de la transition écologique, et de l’agriculture et de l’alimentation, ainsi que l’ADEME, ont sollicité INRAE et l’Ifremer courant 2022 pour mieux documenter ce volet biodiversité, en se focalisant sur les pratiques de production. Afin d’éclairer plus largement les politiques publiques, les pouvoirs publics ont choisi de s’appuyer sur les labels dont les cahiers des charges certifient des pratiques et parce que leur développement les place au cœur de nombreux débats sur les relations entre production et consommation durables. L’étude, intitulée « BiodivLabel », a été menée par un comité pluridisciplinaire d’experts scientifiques issus d’organismes publics de recherche et d’enseignement supérieur
Feathered noses: methodological insights into understanding avian olfaction and foraging
No full textResearch into avian olfactory abilities has so far attracted relatively limited attention due to their complex nature and methodological difficulties. To address the challenges of avian olfactory research, we screened literature spanning four decades by searching publications in the Web of Science and Google Scholar databases. Based on the analyses of 80 experiments that focused on the foraging behaviour of birds, we highlight significant biases in the study of avian olfactory foraging, emphasizing gaps in bird taxa, geographical regions and methodological approaches. While much attention has been paid to the responses of seabirds to dimethyl sulphide (DMS) or of insectivorous birds to herbivore-induced plant volatiles (HIPVs), olfactory responses of frugivorous or nectarivorous birds remain underexplored. The predominance of studies in temperate regions further limits our understanding of bird olfaction in bird species-rich tropical areas. The detection of general traits of bird olfactory behaviour is difficult especially because of varying methodological approaches and lack of detailed information on bird and odour characteristics. Future research should distinguish between innate and learned olfactory behaviours, address the impact of environmental noise and consider individual and sex-specific differences in response to volatile compounds. Intensifying the consideration of these aspects will improve and deepen our knowledge of bird olfactory foraging behaviour and allow for ecological applications for targeted pest management and fruit dispersal strategies
Geroscience
No full textThe cognitive and neuroimaging evolution over the course of dementia with Lewy bodies (DLB) from prodromal stage - Pro-DLB (subjective (SCI) to mild cognitive impairment (MCI)) - is poorly understood. The aim of this study was to analyze from 5-year longitudinal data the trajectories of Pro-DLB patients. The "Lewy- MEMENTO" prospective clinical cohort recruited 773 patients for either SCI or MCI. The Pro-DLB group was compared to a group with prodromal Alzheimer's disease (Pro-AD), a group with "prodromal DLB and AD" (Pro-DLB + AD), and a group without prodromal DLB and AD (no symptom [NS]). We modeled the 5-year evolution of cognitive functions and the 2-year evolution of brain MRI volumetry on MRI and brain metabolism (FDG PET). The Pro-AD and Pro-DLB + AD groups had more cognitive and functional decline than the Pro-DLB and NS groups (P < .001). The Pro-DLB group had more cognitive decline than the NS group (P < .004). Incident dementia during the follow-up was higher in the Pro-AD (13.0 per 100 person-years) and Pro-DLB + AD (10.3) groups than in the Pro-DLB (1.02) and NS (0.44) groups (P < .001). The decline in the metabolism of the left orbitofrontal cortex was greater in the Pro-DLB + AD group. The volume decrease of hippocampi, entorhinal cortices, amygdalae, and left insula was higher in the Pro-AD and the pro-DLB + AD groups. Patients in the pro-DLB group had less cognitive, functional, brain volume, and metabolism decrease than patients in the Pro-AD and pro-DLB + AD groups. DLB would therefore be a less degenerative and more dysfunctional disease at the prodromal stage
Drug Saf
Get PDFSignal management, defined as the set of activities from signal detection to recommendations for action, is conducted using different data sources and leveraging data from spontaneous reporting databases (SRDs), which represent the cornerstone of pharmacovigilance. However, the exponentially increasing generation and availability of real-world data collected in longitudinal healthcare databases (LHDs), along with the rapid evolution of artificial intelligence-based algorithms and other advanced analytical methods, offers a wide range of opportunities to complement SRDs throughout all stages of signal management, especially signal detection. Integrating information derived from SRDs and LHDs may reduce their respective limitations, thus potentially enhancing post-marketing surveillance. The aim of this position statement is to critically evaluate the complementary role of SRDs and LHDs in signal management, exploring the potential benefits and challenges in integrating information coming from these two data sources. Furthermore, we presented successful cases of the interplay between SRDs and LHDs for signal management, along with future opportunities and directions to improve such interplay
Analyzing pollen content to assess honey bee (Apis mellifera Linnaeus, 1758) foraging in an urban area
No full textBees play an essential role as pollinators in both natural and agricultural ecosystems. The Africanized honey bee (Apis mellifera Linnaeus, 1758) is a common species in modified ecosystems being an important pollinator for many crops, such as pepper (Capsicum spp.). In this study, we assessed the individual variation in floral resource foraging by examining the pollen loads in the corbiculae of A. mellifera workers. We sampled the bees in a pepper experimental crop for two months. We found between two and 17 pollen types in the bees' corbiculae, with a high abundance of the Fabaceae, Asteraceae, and Rubiaceae families. The pollen types ranged from 18 to 19 over the months. A. mellifera collected floral resources mainly from arboreal plants providing nectar and pollen. Our findings highlight the importance of understanding the ecological interactions between bee and plant species in agricultural areas to inform management and conservation strategies aimed at sustaining bee populations and enhancing pollination services
