Effet des coupes partielles sur les propriétés mécaniques du bois de l’épinette noire (Picea Mariana)

L’aménagement forestier intensif, dont les coupes partielles, représente une possibilité visant à augmenter la croissance de l’épinette noire. Bien que ces pratiques aient des effets positifs sur la croissance en diamètre, l’impact sur la qualité du bois a été peu étudié. Ainsi, l’objectif de cette étude est d’évaluer l’effet des coupes partielles sur la qualité du bois de l’épinette noire, à savoir les propriétés mécaniques et acoustiques. Des placettes permanentes ont été sélectionnées dans un réseau de coupes partielles mis en place au cours des quinze dernières années. Trois intensités de récolte des coupes ont été étudiées : 0 %, 0-50 % et 75-100 % de la surface terrière. Les arbres sélectionnés ont été divisés en trois classes de diamètre à hauteur de poitrine (DHP) : 10-15 cm, 15-20 cm et > 20 cm. Un échantillonnage destructif a été réalisé dans trois sites et des éprouvettes normalisées ont été prélevées avant et après le traitement pour étudier les propriétés mécaniques (flexion, compression parallèle et perpendiculaire). Le module d’élasticité dynamique a été mesuré de la moelle à l’écorce, au DHP, avec un outil ultrasonique. Les résultats indiquent qu’une croissance accélérée de l’épinette noire après les coupes partielles n’a eu des effets négatifs que sur les propriétés mécaniques en flexion trois points et en compression parallèle (MOE, rup, max). Également, il n’y a pas de différence significative entre les intensités de traitement. Une réponse différente a été observée pour les propriétés mécaniques en compression perpendiculaire à la suite d’une coupe partielle. La variation du module d’élasticité est reliée seulement à sa valeur avant le traitement. Quant à la contrainte de rupture, un changement négatif est observé, causé par un traitement de prélèvement d’intensité modérée; cependant, un traitement de prélèvement d’intensité forte n’avait aucun effet nuisible sur cette propriété. Une forte corrélation existe entre le module d’élasticité dynamique mesuré dans le sens longitudinal et le module d’élasticité statique, déterminée par un test de flexion trois points et un test de compression parallèle. Toutefois, aucune bonne corrélation n’a été trouvée en compression perpendiculaire. Cette étude suggère que l’efficacité de l’outil ultrason pour l’évaluation non destructive des propriétés mécaniques de l’épinette noire varie selon la direction des fibres du bois

Management of pulpal floor perforation using BiodentineTM : Case report

During endodontic treatment in multi-rooted teeth, furcation perforation refers to an opening in the pulpal floor, leading to a communication with the periodontal ligament space. A three-dimensional hermetic seal, with a biocompatible material, is a key point for the success of pulp floor perforation repair. MTA® has been considered, for a long time, as a gold standard in furcation perforation repair. Besides, BiodentineTM, when used for the same purpose, showed considerable performance and good results. The purpose of this paper was to report the management of an iatrogenic perforation of pulpal floor in the maxillary right first molar, using BiodentineTM

High-throughput functional metagenomics for the discovery of glycan metabolizing pathways

Glycans are widely distributed in nature. Produced by almost all organisms, they are involved in numerous cellular processes, such as energy supply and storage, cell structuration, protein maturation and signalling, and cell recognition. Glycans are thus key elements mediating the interactions between mammals, plants, bacteria, fungi and even viruses. They also represent a reliable source of carbon for microbes, which have developed complex strategies to face their structural diversity and to harvest them. However between 70 and 99% of these microorganisms are still uncultured, while they represent a goldmine for the discovery of new enzymes. In order to boost their identification and characterization, a functional metagenomic approach was developed, based on the design of various high-throughput, robust and sensitive screening strategies. The functional potential of Gbp of metagenomic DNA from various origins was explored, revealing dozens of novel enzyme families and functions. Integration of biochemical, structural, meta-omic and omic data allowed us to decipher, from the molecular to the ecosystemic scale, novel mechanisms of plant, microbial and mammal glycan metabolization. These new metabolic pathways involve batteries of glycoside-hydrolases, glycoside-phosphorylases and sugar transporters. These fascinating proteins appear as new targets to control host-microbe interactions. They also constitute very efficient biotechnological tools for biorefineries and synthetic biology

Investigating Host Microbiota Relationships Through Functional Metagenomics

The human Intestinal mucus is formed by glycoproteins, the O- and N-linked glycans which constitute a crucial source of carbon for commensal gut bacteria, especially when deprived of dietary glycans of plant origin. In recent years, a dozen carbohydrate-active enzymes from cultivated mucin degraders have been characterized. But yet, considering the fact that uncultured species predominate in the human gut microbiota, these biochemical data are far from exhaustive. In this study, we used functional metagenomics to identify new metabolic pathways in uncultured bacteria involved in harvesting mucin glycans. First, we performed a high-throughput screening of a fosmid metagenomic library constructed from the ileum mucosa microbiota using chromogenic substrates. The screening resulted in the isolation of 124 clones producing activities crucial in the degradation of human O- and N-glycans, namely sialidases, beta-D-N-acetyl-glucosaminidase, beta-D-N-acetyl-galactosaminidase, and/or beta-D-mannosidase. Thirteen of these clones were selected based on their diversified functional profiles and were further analyzed on a secondary screening. This step consisted of lectin binding assays to demonstrate the ability of the clones to degrade human intestinal mucus. In total, the structural modification of several mucin motifs, sialylated mucin ones in particular, was evidenced for nine clones. Sequencing their metagenomic loci highlighted complex catabolic pathways involving the complementary functions of glycan sensing, transport, hydrolysis, deacetylation, and deamination, which were sometimes associated with amino acid metabolism machinery. These loci are assigned to several Bacteroides and Feacalibacterium species highly prevalent and abundant in the gut microbiome and explain the metabolic flexibility of gut bacteria feeding both on dietary and human glycans

Development and application of metagenomic tools for characterization of toluene degradation in hydrocarbon polluted sediments

A metagenomic procedure was developed to assess microbial potential for toluene degradation within the sediment of a polluted aquifer at the tar-oil-contaminated site of Flingern, Germany. We targeted genes encoding the α-subunit of the toluene-4-monooxygenase (tmoA genes) to find new toluene degradation genes and pathways. Good quality and high molecular weight environmental DNA was extracted and cloned in BAC and fosmid vectors in Escherichia coli. The BAC library was transferred to other hosts, Cupriavidus metallidurans (Proteobacteria) and Edaphobacter aggregans (Acidobacteria). The use of an acidobacterial strain for the first time as an alternative host implied further characterization of its interaction with broad host range (BHR) plasmids (pMOL98, pKT230, and RP4). New ecological insight regarding host range of these plasmids was gained, which opened up new perspectives of developing BHR vectors for metagenomic applications. Exploitation of the acidobacterial-hosted BAC library led to the isolation of an as-yet unsequenced fragment from an Acidobacterium source that contains genes involved in aerobic and anaerobic toluene degradation. The functional screening of the BAC library in C. metallidurans CH34 led to the capture of 3 novel toluene monoxygenase-encoding operons located on IncP1 plasmids. The genetic screening using an innovative high throughput hybridization procedure allowed recovery of 16 significantly divergent tmoA-like genes. Their source fragments belonged exclusively to Proteobacteria and more specifically to Acinetobacter species. This unique metagenomic study applied to the Flingern groundwater sediment has opened future horizons for more applications.(AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 201

Metagenomics for bioremediation

info:eu-repo/semantics/publishe

Metagenomics: Probing pollutant fate in natural and engineered ecosystems

Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.SCOPUS: re.jinfo:eu-repo/semantics/publishe

Metagenomics: Probing pollutant fate in natural and engineered ecosystems

Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.SCOPUS: re.jinfo:eu-repo/semantics/publishe

Metagenomics for Bioremediation

Large amounts of toxic contaminants are released in the environment by mining, industrial, agricultural, and urban activities. These are natural compounds (fossil fuels or heavy metals discharged at high concentration) or, more commonly, chemically synthesized compounds (the so-called “xenobiotics”, such as chlorinated, halogenated, or nitroaromatic compounds). Of great concern is also the continuous discharge of various bioactive molecules in the environment (mostly endocrine disruptors and pharmaceutically active compounds), for which there is accumulating evidence of adverse effects on humans and animals. To clean up contaminated sites, one option is to use organisms (mainly bacteria, and also fungi and plants) that can oxidize/ reduce, bind, immobilize, volatize, or transform contaminants