Innovative Biological Solutions to Challenges in Sustainable Biofuels Production

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Plant biosystems design research roadmap 1.0

Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they are still not able to meet the ever-increasing needs, in terms of both quantity and quality, resulting from the rapid increase in world population and expected standards of living. A step change that may address these challenges would be to expand the potential of plants using biosystems design approaches. This represents a shift in plant science research from relatively simple trial-and-error approaches to innovative strategies based on predictive models of biological systems. Plant biosystems design seeks to accelerate plant genetic improvement using genome editing and genetic circuit engineering or create novel plant systems through de novo synthesis of plant genomes. From this perspective, we present a comprehensive roadmap of plant biosystems design covering theories, principles, and technical methods, along with potential applications in basic and applied plant biology research. We highlight current challenges, future opportunities, and research priorities, along with a framework for international collaboration, towards rapid advancement of this emerging interdisciplinary area of research. Finally, we discuss the importance of social responsibility in utilizing plant biosystems design and suggest strategies for improving public perception, trust, and acceptance

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Contribution à l'étude de la structure et du polymorphisme du génome du basidiomycète ectomycorhizien "Laccaria bicolor" (Maire) Orton et identification de QTLs de mycorhization chez les peupliers, "Populus trichocarpa Torr. & A. Gray ex Hook. et "Populus deltoides (Bartr.) Marsh

Les symbioses mycorhiziennes, entre champignons et racines de plantes, concernent 95 % des espèces végétales. Les arbres sociaux des forêts boréales et tempérées forment avec les champignons un type particulier d association : la symbiose ectomycorrhizienne. Les ectomycorrhizes jouent un rôle essentiel dans la nutrition hydrominérale des arbres, le cycle des éléments minéraux et la production primaire. Cependant, leur complexité n a pas permis à ce jour de déchiffrer leurs rôles et leurs fonctions précises. La récente disponibilité du génome du champignon ectomycorhizien Laccaria bicolor et de celui de l'arbre hôte Populus trichocarpa fournit une occasion inégalée d approfondir nos connaissances du développement et du fonctionnement de cette symbiose. Les objectifs de cette étude ont donc été de participer à la caractérisation et au décryptage du génome de L. bicolor puis à la recherche des gènes impliqués dans la formation des ectomycorhizes chez les deux partenaires. Dans un premier temps et afin d aider à l assemblage de la séquence génomique de L. bicolor, nous avons identifié les séquences répétées et construit une carte génétique. Sur les 60 Mb de ce génome, nous avons mis en évidence 8 % de séquences microsatellitaires et 24 % d éléments transposables. Une carte génétique a été construite à partir de 111 monocaryons issus de L. bicolor S238N. Cette carte comprend 326 marqueurs (8 RAPD, 243 AFLP, 59 SSR et 14 SNP) répartis sur 10 groupes de liaison ancrés à la séquence génomique de L. bicolor. Dans un second temps, nous avons tenté d identifier les gènes impliqués dans l établissement des ectomycorhizes chez le peuplier en combinant une approche de détection par QTLs et par puces à ADN. Nous avons ciblé 81 gènes potentiellement impliqués dans l établissement et/ou le fonctionnement de la symbiose.The mycorrhizal symbioses between fungi and roots concern 95 % of the plant species. Social trees of boreal and temperate forests form a particular type of root association with fungi: the ectomycorrhizal symbiosis. Ectomycorrhizas play a major role in tree hydromineral nutrition, nutrient cycles and primary production. However, their complexity have so far prevented from deciphering their precise function and role. The recent availability of the genome of the ectomycorrhizal fungus Laccaria bicolor and that of the host-tree Populus trichocarpa provides an unprecedented opportunity to decipher the key components of development and functioning of this symbiosis. The aims of this study were to participate to the characterization and deciphering of the genome of L. bicolor, and to determine the genes involved in the formation of ectomycorrhizas in both partners. Firstly, in order to facilitate the assembly of the genomic sequence of L. bicolor, we have identified the repeated sequences and generated a genetic map. On the 60 Mb of this genome, 8 % are microsatellite sequences and 24 % transposable elements. A genetic map was built from 111 monokaryons issued from L. bicolor S238N. This map includes 326 markers (8 RAPD, 243 AFLP, 59 SSR and 14 SNP) distributed on 10 linkage groups anchored onto the genomic sequence of L. bicolor. Secondly, we have identified the genes involved in the establishment of ectomycorrhizas in poplar by combining QTL detection and DNA microarrays. We targeted 81 genes which can be involved in the establishment and/or the functioning of the symbiosis.NANCY1-Bib. numérique (543959902) / SudocSudocFranceF

Fungal biology : compiling genomes and exploiting them

The 12th European Conference on Fungal Genetics (ECFG12) took place in March 2014. Every 2 years a European country welcomes this meeting, which is held in coordination with the Fungal Genetics Conferences that take place every 2 years in Asilomar (USA). This year over 700 participants from40 countries gathered in Seville (Spain) to exchange ideas on the central theme of fungal genetics and general fungal biology including molecular and cell biology, genomics, evolution and biotechnology. The conference included plenary sessions in honor of three prominent fungal geneticists (Charles Yanofsky, John Clutterbuck and Claudio Sccazocchio), concurrent sessions such as the tremendous ‘Fungal genomes: now what?’, and six satellite meetings including the 4th Mycorrhizal Genomics Initiative Workshop (MGIW4). In the latter meeting, coordinated by Francis Martin (INRA, Nancy, France), approx. 30 junior and senior scientists discussed progress made on exploring the genome diversity of mycorrhizal fungi and debated future directions on how to use the current data sets to bridge mycorrhizal genomics, metagenomics and forest ecology. In this meeting report, we focus on the engaging discussions surrounding fungal genomes and their utilization

Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

International audienceIt is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in the L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. In the L. bicolor genome, most of the SSRs were located in intergenic regions (73.3%) and the highest SSR density was observed in transposable elements (TEs; 6,706 SSRs/Mb). However, 81% of the protein-coding genes contained SSRs in their exons, suggesting that SSR polymorphism may alter gene phenotypes. Within a L. bicolor offspring, sequence polymorphism of 78 SSRs was mainly detected in non-TE intergenic regions. Unlike previously developed microsatellite markers, these new ones are spread throughout the genome; these markers could have immediate applications in population genetics

Laccaria amethystina, modèle d’étude multi-échelles de la structure génétique spatiale des populations de Basidiomycètes ectomycorhiziens tempérés

International audienc

Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor

Background: The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TE-specific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome. [br/] Methodology/Principal Findings: TEs occupy 24% of the 60 Mb L. bicolor genome and represent 25,787 full-length and partial copy elements distributed within 171 families. The most abundant elements were the Copia-like. TEs are not randomly distributed across the genome, but are tightly nested or clustered. The majority of TEs exhibits signs of ancient transposition except some intact copies of terminal inverted repeats (TIRS), long terminal repeats (LTRs) and a large retrotransposon derivative (LARD) element. There were three main periods of TE expansion in L. bicolor: the first from 57 to 10 Mya, the second from 5 to 1 Mya and the most recent from 0.5 Mya ago until now. LTR retrotransposons are closely related to retrotransposons found in another basidiomycete, Coprinopsis cinerea. [br/] Conclusions: This analysis 1) represents an initial characterization of TEs in the L. bicolor genome, 2) contributes to improve genome annotation and a greater understanding of the role TEs played in genome organization and evolution and 3) provides a valuable resource for future research on the genome evolution within the Laccaria genus

Laccaria amethystina, modèle d’étude multi-échelles de la structure génétique spatiale des populations de Basidiomycètes ectomycorhiziens tempérés

International audienc

Extensive gene flow over Europe and possible speciation over Eurasia in the ectomycorrhizal basidiomycete Laccaria amethystina complex

Biogeographical patterns and large-scale genetic structure have been little studied in ectomycorrhizal (EM) fungi, despite the ecological and economic importance of EM symbioses. We coupled population genetics and phylogenetic approaches to understand spatial structure in fungal populations on a continental scale. Using nine microsatellite markers, we characterized gene flow among 16 populations of the widespread EM basidiomycete Laccaria amethystina over Europe (i.e. over 2900 km). We also widened our scope to two additional populations from Japan (104 km away) and compared them with European populations through microsatellite markers and multilocus phylogenies, using three nuclear genes (NAR, G6PD and ribosomal DNA) and two mitochondrial ribosomal genes. European L. amethystina populations displayed limited differentiation (average FST = 0.041) and very weak isolation by distance (IBD). This panmictic European pattern may result from effective aerial dispersal of spores, high genetic diversity in populations and mutualistic interactions with multiple hosts that all facilitate migration. The multilocus phylogeny based on nuclear genes confirmed that Japanese and European specimens were closely related but clustered on a geographical basis. By using microsatellite markers, we found that Japanese populations were strongly differentiated from the European populations (FST = 0.416), more than expected by extrapolating the European pattern of IBD. Population structure analyses clearly separated the populations into two clusters, i.e. European and Japanese clusters. We discuss the possibility of IBD in a continuous population (considering some evidence for a ring species over the Northern Hemisphere) vs. an allopatric speciation over Eurasia, making L. amethystina a promising model of intercontinental species for future studies