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Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of and , references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative (\"evo-devo\") approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.

Abstract For successful infection of host cells and virion production, enveloped viruses, including Zika virus (ZIKV), extensively rely on cellular lipids. However, how virus protein–lipid interactions contribute to the viral life cycle remains unclear. Here, we employ a chemo-proteomics approach with a bifunctional cholesterol probe and show that cholesterol is closely associated with the ZIKV structural protein prM. Bioinformatic analyses, reverse genetics alongside with photoaffinity labeling assays, and atomistic molecular dynamics simulations identified two functional cholesterol binding motifs within the prM transmembrane domain. Loss of prM–cholesterol association has a bipartite effect reducing ZIKV entry and leading to assembly defects. We propose a model in which membrane-resident M facilitates cholesterol-supported lipid exchange during endosomal entry and, together with cholesterol, creates a platform promoting virion assembly. In summary, we identify a bifunctional role of prM in the ZIKV life cycle by mediating viral entry and virus assembly in a cholesterol-dependent manner.

Large dsDNA viruses from the Naldaviricetes class are currently composed of four viral families infecting insects and/or crustaceans. Since the 1970s, particles described as filamentous viruses (FVs) have been observed by electronic microscopy in several species of Hymenoptera parasitoids but until recently, no genomic data was available. This study provides the first comparative morphological and genomic analysis of these FVs. We analyzed the genomes of seven FVs, six of which were newly obtained, to gain a better understanding of their evolutionary history. We show that these FVs share all genomic features of the Naldaviricetes while encoding five specific core genes that distinguish them from their closest relatives, the Hytrosaviruses. By mining public databases, we show that FVs preferentially infect Hymenoptera with parasitoid lifestyle and that these viruses have been repeatedly integrated into the genome of many insects, particularly Hymenoptera parasitoids, overall suggesting a long-standing specialization of these viruses to parasitic wasps. Finally, we propose a taxonomical revision of the class Naldaviricetes in which FVs related to the Leptopilina boulardi FV constitute a fifth family. We propose to name this new family, Filamentoviridae.

Meloidogyne incognita is a plant-parasitic root-knot nematode (RKN, PPN) responsible for causing damage to several crops worldwide. In Caenorhabditis elegans , the DAF-16 and SKN-1 transcription factors (TFs) orchestrate aging, longevity, and defense responses to several stresses. Here, we report that MiDaf16-like1 and MiSkn1-like1 , which are orthologous to DAF-16 and SKN-1 in C. elegans , and some of their targets, are modulated in M. incognita J2 during oxidative stress or plant parasitism. We used RNAi technology for the stable production of siRNAs in planta to downregulate the MiDaf16-like1 and MiSkn1-like1 genes of M. incognita during host plant parasitism. Arabidopsis thaliana and Nicotiana tabacum overexpressing a hairpin-derived dsRNA targeting these genes individually (single-gene silencing) or simultaneously (double-gene silencing) were generated. T 2 plants were challenged with M. incognita and the number of eggs, galls, and J2, and the nematode reproduction factor (NRF) were evaluated. Our data indicate that MiDaf16-like1 , MiSkn1-like1 and some genes from their networks are modulated in M. incognita J2 during oxidative stress or plant parasitism. Transgenic A. thaliana and N. tabacum plants with single- or double-gene silencing showed significant reductions in the numbers of eggs, J2, and galls, and in NRF. Additionally, the double-gene silencing plants had the highest resistance level. Gene expression assays confirmed the downregulation of the MiDaf16-like1 and MiSkn1-like1 TFs and defense genes in their networks during nematode parasitism in the transgenic plants. All these findings demonstrate that these two TFs are potential targets for the development of biotechnological tools for nematode control and management in economically important crops.

Soil organic carbon storage is a well-identified climate change mitigation solution. Quantification of the soil carbon storage in cropland for agricultural policy and offset carbon markets using in situ sampling would be excessively costly, especially at the intrafield scale. For this reason, comprehensive monitoring, reporting, and verification (MRV) of soil carbon and its explanatory variables at a large scale need to rely on hybrid approaches that combine remote sensing and modelling tools to provide the carbon budget components with their associated uncertainties at intrafield scale. Here, we present AgriCarbon-EO v1.0.1: an end-to-end processing chain that enables the estimation of carbon budget components for major and cover crops at intrafield resolution (10 m) and regional extents (e.g. 10 000 km2) by assimilating remote sensing data (e.g. Sentinel-2 and Landsat8) in a physically based radiative transfer (PROSAIL) and agronomic models (SAFYE-CO2). The data assimilation in AgriCarbon-EO is based on a novel Bayesian approach that combines normalized importance sampling and look-up table generation. This approach propagates the uncertainties across the processing chain from the reflectances to the output variables. After a presentation of the chain, we demonstrate the accuracy of the estimates of AgriCarbon-EO through an application over winter wheat in the southwest of France during the cropping seasons from 2017 to 2019. We validate the outputs with flux tower data for net ecosystem exchange, biomass destructive samples, and combined harvester yield maps. Our results show that the scalability and uncertainty estimates proposed by the approach do not hinder the accuracy of the estimates (net ecosystem exchange, NEE: RMSE =1.68–2.38 gC m-2, R2=0.87–0.77; biomass: RMSE =11.34 g m-2, R2=0.94). We also show the added value of intrafield simulations for the carbon components through scenario testing of pixel and field simulations (biomass: bias =-47 g m-2, -39 % variability). Our overall analysis shows satisfying accuracy, but it also points out the need to represent more soil processes and include synthetic aperture radar data that would enable a larger coverage of AgriCarbon-EO. The paper's findings confirm the suitability of the choices made in building AgriCarbon-EO as a hybrid solution for an MRV scheme to diagnose agro-ecosystem carbon fluxes.

Difference in dispersal ability is a key driver of species coexistence in metacommunities. However, the available frameworks for interpreting species diversity patterns in natura often overlook trade-offs and evolutionary constraints associated with dispersal. Here,we build a metacommunity model accounting for dispersal evolution and a competition-dispersal trade-off. Depending on the distribution of carrying capacities among communities, species dispersal values are distributed either around a single strategy (evolutionarily stable strategy, ESS), or around distinct strategies (evolutionary branching, EB). We show that limited dispersal generates spatial aggregation of dispersal traits in ESS and EB scenarios, and that the competition-dispersal trade-off strengthens the pattern in the EB scenario. Importantly, individuals in larger (respectively (resp.) smaller) communities tend to harbour lower (resp. higher) dispersal, especially under the EB scenario.We explore how dispersal evolution affects species diversity patterns by comparing those from our model to the predictions of a neutral metacommunity model. The most marked difference is detected under EB, with distinctive values of both alpha and beta diversity (e.g. the dissimilarity in species composition between small and large communities was significantly larger than neutral predictions). We conclude that, from an empirical perspective, jointly assessing community carrying capacity with species dispersal strategies should improve our understanding of diversity patterns in metacommunities.

Abstract Active-desks are emerging strategies aiming at reducing sedentary time while working. A large inter-individual variability in energy expenditure (EE) profile has been identified and has to be explored to better optimize and individualize those strategies. Thus the present study aimed at comparing the metabolic and physical profile of individuals characterized as high spenders (H-Spenders) versus low spenders (L-Spenders) based on EE during a cycle-desk low intensity exercise. 28 healthy women working in administrative positions were enrolled. Anthropometric, body composition and fasting metabolic profile parameters were assessed. EE was determined by indirect calorimetry, at rest and during a 30-min cycle-desk use. Participants were categorized as H-Spenders and L-Spenders using the median of the difference between EE at rest and during the 30-min exercise. H-Spenders had higher mean EE ( p < 0.001) and carbohydrate oxidation ( p = 0.009) during exercise. H-Spenders displayed higher values for fasting plasma insulin ( p = 0.002) and HOMA-IR ( p = 0.002) and lower values for HDL-cholesterol ( p = 0.014) than L-Spenders. The percentage of body fat mass was significantly higher in H-Spenders ( p = 0.034). Individuals expending more energy during a low intensity cycling exercise presented a less healthy metabolic profile compared with L-Spenders. Future studies will have to explore whether the chronic use of cycle-desks during work time can improve energy profile regarding metabolic parameters.

Clinically used botulinum neurotoxins (BoNTs) are natural products of Clostridium botulinum. A novel, recombinant BoNT type A1 (rBoNT/A1; IPN10260) has been synthesized using the native amino acid sequence expressed in Escherichia coli and has previously been characterized in vitro and ex vivo. Here, we aimed to characterize rBoNT/A1 in vivo and evaluate its effects on skeletal muscle. The properties of rBoNT/A1 following single, intramuscular administration were evaluated in the mouse and rat digit abduction score (DAS) assays and compared with those of natural BoNT/A1 (nBoNT/A1). rBoNT/A1‐injected tibialis anterior was assessed in the in situ muscle force test in rats. rBoNT/A1‐injected gastrocnemius lateralis (GL) muscle was assessed in the compound muscle action potential (CMAP) test in rats. The rBoNT/A1‐injected GL muscle was evaluated for muscle weight, volume, myofiber composition and immunohistochemical detection of cleaved SNAP25 (c‐SNAP25). Results showed that rBoNT/A1 and nBoNT/A1 were equipotent and had similar onset and duration of action in both mouse and rat DAS assays. rBoNT/A1 caused a dose‐dependent inhibition of muscle force and a rapid long‐lasting reduction in CMAP amplitude that lasted for at least 30 days. Dose‐dependent reductions in GL weight and volume and increases in myofiber atrophy were accompanied by immunohistochemical detection of c‐SNAP25. Overall, rBoNT/A1 and nBoNT/A1 exhibited similar properties following intramuscular administration. rBoNT/A1 inhibited motoneurons neurotransmitter release, which was robust, long‐lasting, and accompanied by cleavage of SNAP25. rBoNT/A1 is a useful tool molecule for comparison with current natural and future modified recombinant neurotoxins products.

Non-timber forest products (NTFPs) are important components of rural people’s livelihood, being used notably for food and medicine. Given their socio-economic importance, NTFP species are often integrated in farmers’ fields using wild seed material from adjacent forests. In sub-Saharan Africa, the evolutionary history, and more specifically, the cultivation history of these species (geographical origin, dating), is still largely unknown. This study focuses on an African medicinal tree species, originating from the Guineo-Congolian rain forests and commonly known as the bitter kola tree (Garcinia kola, Clusiaceae). We estimated species genome size and chromosome number. We developed eleven highly polymorphic nuclear microsatellite markers and used seven of them to characterize patterns of distribution of genetic diversity within populations of G. kola in the forest (161 wild individuals coming from nine different populations from Cameroon, Gabon, and the Republic of Congo) and on-farm (82 cultivated individuals from five populations from Cameroon). The species is most probably hexaploid, with a relatively large genome size (2C = 25.5 to 28.5 picogram) and ca. 170 chromosomes. Three intra-specific gene pools were observed along a north–south axis within wild populations. This genetic differentiation pattern presents some similarities with patterns already observed in other tree species from the region, suggesting that a common factor, potentially past-climatic oscillations, has affected the demography of forest trees in the same way. Cultivated populations were not spatially structured, and the genetic differentiation between wild and cultivated populations was low (GST = 0.017). The cultivation history of the species was difficult to interpret. It is actually unclear if cultivated populations from Cameroon are derived from wild Cameroonian populations or if they originate from wild populations of West African countries, notably Nigeria.

Human exposure to foodborne inorganic nanoparticles (NPs) is a growing concern. However, identifying potential hazards linked to NP ingestion often requires long-term exposure in animals. Owing these constraints, intestinal organoids are a promising alternative to in vivo experiments; as such, an in vitro approach should enable a rapid and reliable assessment of the effects of ingested chemicals on the gut. However, this remains to be validated for inorganic substances. In our study, a transcriptomic analysis and immunofluorescence staining were performed to compare the effects of food-grade TiO2 (fg-TiO2) on enteroid-derived monolayers (EDMs) from murine intestinal organoids to the known impacts of TiO2 on intestinal epithelium. After their ability to respond to a pro-inflammatory cytokine cocktail was validated, EDMs were exposed to 0, 0.1, 1, or 10 µg fg-TiO2/mL for 24 h. A dose-related increase of the muc2, vilin 1, and chromogranin A gene markers of cell differentiation was observed. In addition, fg-TiO2 induced apoptosis and dose-dependent genotoxicity, while a decreased expression of genes encoding for antimicrobial peptides, and of genes related to tight junction function, was observed. These results validated the use of EDMs as a reliable model for the toxicity testing of foodborne NPs likely to affect the intestinal barrier.