The root transcriptome dynamics reveals new valuable insights in the salt-resilience mechanism of wild grapevine (Vitis vinifera subsp. sylvestris)

Introduction: Most of elite cultivated grapevine varieties (Vitis vinifera L.), conventionally grafted on rootstocks, are becoming more and more affected by climate changes, such as increase of salinity. Therefore, we revisited the valuable genetic resources of wild grapevines (V. sylvestris) to elaborate strategies for a sustainable viticulture. Methods: Here, we compared physiological and biochemical responses of two salt-tolerant species: a wild grapevine genotype “Tebaba” from our previous studies and the conventional rootstock “1103 Paulsen”. Interestingly, our physio-biochemical results showed that under 150mM NaCl, “Tebaba” maintains higher leaf osmotic potential, lower Na+/K+ ratio and a significant peaked increase of polyphenol content at the first 8h of salinity stress. This behavior allowed to hypothesis a drastic repatterning of metabolism in “Tebaba’s” roots following a biphasic response. In order to deepen our understanding on the “Tebaba” salt tolerance mechanism, we investigated a time-dependent transcriptomic analysis covering three sampling times, 8h, 24h and 48h. Results: The dynamic analysis indicated that “Tebaba” root cells detect and respond on a large scale within 8h to an accumulation of ROS by enhancing a translational reprogramming process and inducing the transcripts of glycolytic metabolism and flavonoids biosynthesis as a predominate non-enzymatic scavenging process. Afterwards, there is a transition to a largely gluconeogenic stage followed by a combined response mechanism based on cell wall remodeling and lignin biosynthesis with an efficient osmoregulation between 24 and 48 h. Discussion: This investigation explored for the first time in depth the established cross-talk between the physiological, biochemical and transcriptional regulators contributing to propose a hypothetical model of the dynamic salt mechanism tolerance of wild grapevines. In summary, these findings allowed further understanding of the genetic regulation mechanism of salt-tolerance in V. sylvestris and identified specific candidate genes valuable for appropriate breeding strategies

Climatic Aridity Gradient Modulates the Diversity of the Rhizosphere and Endosphere Bacterial Microbiomes of Opuntia ficus-indica

© Copyright © 2020 Karray, Gargouri, Chebaane, Mhiri, Mliki and Sayadi. Recent microbiome research has shown that soil fertility, plant-associated microbiome, and crop production can be affected by abiotic environmental parameters. The effect of aridity gradient on rhizosphere-soil (rhizosphere) and endosphere-root (endosphere) prokaryotic structure and diversity associated with cacti remain poorly investigated and understood. In the current study, next-generation sequencing approaches were used to characterize the diversity and composition of bacteria and archaea associated with the rhizosphere and endosphere of Opuntia ficus-indica spineless cacti in four bioclimatic zones (humid, semi-arid, upper-arid, and lower-arid) in Tunisia. Our findings showed that bacterial and archaeal cactus microbiomes changed in inside and outside roots and along the aridity gradient. Plant compartment and aridity gradient were the influencing factors on the differentiation of microbial communities in rhizosphere and endosphere samples. The co-occurrence correlations between increased and decreased OTUs in rhizosphere and endosphere samples and soil parameters were determined according to the aridity gradient. Blastococcus, Geodermatophilus, Pseudonocardia, Promicromonospora, and Sphingomonas were identified as prevailing hubs and were considered as specific biomarkers taxa, which could play a crucial role on the aridity stress. Overall, our findings highlighted the prominence of the climatic aridity gradient on the equilibrium and diversity of microbial community composition in the rhizosphere and endosphere of cactus.We thank the Tunisian authorities for the support in prickly pear tree sampling and also Dr. Fabrice Armougoum from the Mediterranean Institute of Oceanography (MIO, IRD, UM 110, 13288, Marseille, France) for his great help on microbiome analysis

Aspects electroneuromyographiques des traumatismes du plexus brachial

Introduction: L’électroneuromyogramme (ENMG) garde une place cruciale dans l’exploration du plexus brachial. L’objectif de cette étude était d’étudier les caractéristiques électroneuromyographiques des atteintes plexiques brachiales post-traumatiques et de déterminer les facteurs associés à la topographie et à la sévérité des lésions. Patients et méthodes: Une étude rétrospective a été réalisée dans le service de Neurologie du CHU RAZI incluant les patients adressés à l’unité d’électroneurophysiologie pour une atteinte traumatique du plexus brachial durant la période allant de janvier 2003 à juin 2018. Les données démographiques, cliniques et les résultats de l’ENMG ont été recueillis et analysés. La sévérité de la lésion a été évaluée selon la version modifiée de l’échelle de Dumitru et Wilbourn. Résultats: Nous avons colligé 36 plexopathies brachiales post traumatiques chez 35 patients (H/F = 30/5, âge moyen = 39,3 ans). L’ENMG a été réalisé 3 semaines après le traumatisme chez 91,3% des patients. Il a montré une conduction nerveuse altérée (97,2 %), un tracé neurogène (91,7 %) et des signes de dénervation (55,6 %). Le niveau lésionnel concernait les troncs primaires (66,7 %) et les troncs secondaires (33,3 %). Il était sans lien significatif avec la cause (p>0,05). La lésion était sévère (61,1 %), modérée (36,1 %) et légère (2,8 %) sans association significative ni avec la cause ni avec le site lésionnel (p>0,05). Conclusion: Notre étude a permis d’appuyer le rôle de l’ENMG dans l’étude de la plexopathie brachiale post traumatique. Elle a démontré que la topographie et la sévérité des lésions étaient indépendantes des étiologies du traumatisme.   English title: Electroneuromyogram findings of traumatic brachial plexus injuries Background: Electroneuromyogram (ENMG) plays a crucial role in the exploration of the brachial plexus. The purpose of this study was to investigate the electroneuromyographic characteristics of posttraumatic plexus brachial damage and to determine the factors associated with the topography and severity of the lesions. Patients and methods:  A retrospective study was carried out in the Neurology Department of the RAZI University Hospital including patients referred to the electroneurophysiology unit for traumatic brachial plexus damage during the period from January 2003 to June 2018. Demographic, clinical and ENMG’s data results were collected and analyzed. The severity of the lesion was evaluated according to the modified version of the Dumitru and Wilbourn scale. Results:  We collected 36 post-traumatic brachial plexopathies in 35 patients (M / F = 30/5, mean age = 39.3 years). ENMG was performed 3 weeks after trauma in 91.3% of patients. He showed impaired nerve conduction (97.2%), a neurogenic trace (91.7%) and signs of denervation (55.6%). The lesion level concerned the primary trunks (66.7%) and the secondary trunks (33.3%). It was not significantly related to the cause (p> 0.05). The lesion was severe (61.1%), moderate (36.1%) and mild (2.8%) with no significant association with either the cause or the site of injury (p> 0.05). Conclusion:  Our study supported the role of ENMG in the study of post-traumatic brachial plexopathy. It demonstrated that the topography and the severity of the lesions were independent of the etiologies of the trauma. &nbsp

Olive agroforestry shapes rhizosphere microbiome networks associated with annual crops and impacts the biomass production under low-rainfed conditions

Agroforestry (AF) is a promising land-use system to mitigate water deficiency, particularly in semi-arid areas. However, the belowground microbes associated with crops below trees remain seldom addressed. This study aimed at elucidating the effects of olive AF system intercropped with durum wheat (Dw), barely (Ba), chickpea (Cp), or faba bean (Fb) on crops biomass and their soil-rhizosphere microbial networks as compared to conventional full sun cropping (SC) under rainfed conditions. To test the hypothesis, we compared the prokaryotic and the fungal communities inhabiting the rhizosphere of two cereals and legumes grown either in AF or SC. We determined the most suitable annual crop species in AF under low-rainfed conditions. Moreover, to deepen our understanding of the rhizosphere network dynamics of annual crops under AF and SC systems, we characterized the microbial hubs that are most likely responsible for modifying the microbial community structure and the variability of crop biomass of each species. Herein, we found that cereals produced significantly more above-ground biomass than legumes following in descending order: Ba > Dw > Cp > Fb, suggesting that crop species play a significant role in improving soil water use and that cereals are well-suited to rainfed conditions within both types of agrosystems. The type of agrosystem shapes crop microbiomes with the only marginal influence of host selection. However, more relevant was to unveil those crops recruits specific bacterial and fungal taxa from the olive-belowground communities. Of the selected soil physicochemical properties, organic matter was the principal driver in shaping the soil microbial structure in the AF system. The co-occurrence network analyses indicated that the AF system generates higher ecological stability than the SC system under stressful climate conditions. Furthermore, legumes’ rhizosphere microbiome possessed a higher resilient capacity than cereals. We also identified different fungal keystones involved in litter decomposition and drought tolerance within AF systems facing the water-scarce condition and promoting crop production within the SC system. Overall, we showed that AF reduces cereal and legume rhizosphere microbial diversity, enhances network complexity, and leads to more stable beneficial microbial communities, especially in severe drought, thus providing more accurate predictions to preserve soil diversity under unfavorable environmental conditions.This research was carried out as part of the D4DECLIC Project, ARIMNet 2 Young Scientists Call 2017 (ERA-NET program), and Grant agreement no. 618127

Identification of regulatory network hubs that control lipid metabolism in Chlamydomonas reinhardtii

HighlightCharacterization of regulatory networks in Chlamydomonas reinhardtii led to the identification of regulatory hubs that control the repatterning of cellular metabolism that leads to triacylglycerol accumulation in microalgae.Microalgae-based biofuels are promising sources of alternative energy, but improvements throughout the production process are required to establish them as economically feasible. One of the most influential improvements would be a significant increase in lipid yields, which could be achieved by altering the regulation of lipid biosynthesis and accumulation. Chlamydomonas reinhardtii accumulates oil (triacylglycerols, TAG) in response to nitrogen (N) deprivation. Although a few important regulatory genes have been identified that are involved in controlling this process, a global understanding of the larger regulatory network has not been developed. In order to uncover this network in this species, a combined omics (transcriptomic, proteomic and metabolomic) analysis was applied to cells grown in a time course experiment after a shift from N-replete to N-depleted conditions. Changes in transcript and protein levels of 414 predicted transcription factors (TFs) and transcriptional regulators (TRs) were monitored relative to other genes. The TF and TR genes were thus classified by two separate measures: up-regulated versus down-regulated and early response versus late response relative to two phases of polar lipid synthesis (before and after TAG biosynthesis initiation). Lipidomic and primary metabolite profiling generated compound accumulation levels that were integrated with the transcript dataset and TF profiling to produce a transcriptional regulatory network. Evaluation of this proposed regulatory network led to the identification of several regulatory hubs that control many aspects of cellular metabolism, from N assimilation and metabolism, to central metabolism, photosynthesis and lipid metabolism

The Regulation of Photosynthetic Structure and Function during Nitrogen Deprivation in Chlamydomonas reinhardtii

The accumulation of carbon storage compounds by many unicellular algae after nutrient deprivation occurs despite declines in their photosynthetic apparatus. To understand the regulation and roles of photosynthesis during this potentially bioenergetically valuable process, we analyzed photosynthetic structure and function after nitrogen deprivation in the model alga Chlamydomonas reinhardtii. Transcriptomic, proteomic, metabolite, and lipid profiling and microscopic time course data were combined with multiple measures of photosynthetic function. Levels of transcripts and proteins of photosystems I and II and most antenna genes fell with differing trajectories; thylakoid membrane lipid levels decreased, while their proportions remained similar and thylakoid membrane organization appeared to be preserved. Cellular chlorophyll (Chl) content decreased more than 2-fold within 24 h, and we conclude from transcript protein and 13C labeling rates that Chl synthesis was down-regulated both pre- and posttranslationally and that Chl levels fell because of a rapid cessation in synthesis and dilution by cellular growth rather than because of degradation. Photosynthetically driven oxygen production and the efficiency of photosystem II as well as P700+ reduction and electrochromic shift kinetics all decreased over the time course, without evidence of substantial energy overflow. The results also indicate that linear electron flow fell approximately 15% more than cyclic flow over the first 24 h. Comparing Calvin-Benson cycle transcript and enzyme levels with changes in photosynthetic 13CO2 incorporation rates also pointed to a coordinated multilevel down-regulation of photosynthetic fluxes during starch synthesis before the induction of high triacylglycerol accumulation rates

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

A new approach based on learning services to generate appropriate learning paths

International audienceThis article presents a new approach to provide learners learning paths adapted to their profiles. These courses are generated as the automatic composition of learning services. It is made up of three modules: search module, matching module and composition module. Our approach is based on new model of learningservice (SWAP) that extends semantic web service (OWL-S) to describe the semantics of learning modules and facilitated the discovery of learning paths adapted to each learner