Le darwinisme peut-il tout expliquer ?

Vus d'Europe, les procès opposant les farouches défenseurs du darwinisme à leurs pugnaces détracteurs ont de quoi faire sourire. Certes, il n'y a pas qu'aux Etats-Unis que l'on puisse encore trouver des Chrétiens fondamentalistes persuadés que Dieu a créé la Terre en six jours. En revanche, aucun gouvernement de nos contrées n'aurait l'idée saugrenue de faire interdire l'enseignement de la théorie de l'évolution dans nos écoles, ni même de l'autoriser à la condition expresse de la traiter sur le même pied que le créationnisme inspiré d'une lecture littérale de la Genèse. Cela dit, croire que le refus de l'évolution par "sélection naturelle des mutations favorables" se limite aux couches populaires de l'Amérique conservatrice serait inexact. En réalité, les plus acharnés des tenants du créationnisme pur et dur -- ou de son avatar à peine plus subtil, l'Intelligent Design -- sont généralement des intellectuels, voire dans certains cas des biologistes qui ont renoncé à toute carrière dans l'orthodoxie académique. Faut-il n'y voir qu'aveuglement religieux ? Sans doute, mais pas seulement... Originellement proposée en 1859, la théorie de l'évolution de Charles Darwin a profondément bouleversé la science et la société toute entière. Débarrassé de ses relents lamarckiens par August Weismann entre 1883 et 1888, le darwinisme, désormais qualifié de "néo-", s'est enrichi de la génétique de Gregor Mendel pour donner naissance en 1937, sous l'impulsion de Theodosius Dobzhansky, à la théorie synthétique de l'évolution. C'est dans cette incarnation "moderne" qu'il est devenu l'unique paradigme de la biologie contemporaine. Pourtant, loin des feux de la rampe, le couple infernal mutation/sélection ne satisfait pas tous les spécialistes. A quel point sa toute puissance peut-elle être mise en doute ? Dispose-t-on réellement de preuves de son efficacité, ou même tout simplement de son existence ? La diversité de la Vie sur Terre peut-elle s'expliquer par un principe aussi naïvement libéral ? C'est à ces questions et à quelques autres que nous tenterons de répondre au cours de cette conférence-débat, tout en tâchant de rester prudemment en dehors de toute considération métaphysique. Docteur en Sciences (Génétique Moléculaire Végétale), Denis BAURAIN est bioinformaticien à l'Université de Liège. Financées par le FNRS, ses recherches portent essentiellement sur l'histoire évolutive des premières cellules à noyau telle qu'on peut l'inférer à partir des séquences de gènes

Denis BAURAIN – Portfolio pédagogique

Ce portfolio reprend des considérations pédagogiques générales s’appliquent à l’ensemble de mes enseignements. Les parties plus réflexives sont centrées sur les cours où les populations étudiantes ne se comptent pas sur les doigts d’une seule main : Microbiologie (partim 1 : Algologie et mycologie), Bioinformatique et Méthodes de phylogénie. J’ai par ailleurs réservé une large place à mon cours de Compléments de microbiologie : Protistologie, puisque c’est celui pour lequel j’ai mené une « vraie » réflexion pédagogique avec l’aide de l’IFRES (séminaire de mise en œuvre personnalisé). Enfin, j’ai inclus une série de commentaires sur la nécessité de former les biologistes à la bioinformatique, ainsi que sur la mise en pratique de cette conviction : la finalité spécialisée en Bioinformatique et Modélisation et la formation FOREM sur les Outils de la Bioinformatique

Gram-Negative Bacteria: "Inner" vs. "Cytoplasmic" or "Plasma Membrane": A Question of Clarity rather than Vocabulary

In this short commentary, we show that the utilisation of the term “inner membrane” to characterize the cytoplasmic or plasma membrane of Gram-negative bacteria can be a source of confusion and we propose that it should be completely abandoned

Contamination detection in genomic data: more is not enough

The decreasing cost of sequencing and concomitant augmentation of publicly available genomes have created an acute need for automated software to assess genomic contamination. During the last six years, 18 programs have been pub-lished, each with its own strengths and weaknesses. Deciding which tools to use becomes more and more difficult without an understanding of the underlying algo-rithms. We review these programs, benchmarking six of them, and present their main operating principles. This article is intended to guide researchers in the selec-tion of appropriate tools for specific applications. Finally, we present future chal-lenges in the developing field of contamination detection.BCCM GEN-ER

Characterization of two genes encoding the mitochondrial alternative oxidase in Chlamydomonas reinhardtii

peer reviewedTwo cDNA clones (AOX1 and AOX2) and the corresponding genes encoding the alternative oxidases (AOXs) from Chlamydomonas reinhardtii were isolated and sequenced. The cDNAs, AOX1 and AOX2, contained open reading frames (ORFs) encoding putative proteins of 360 amino acids and 347 amino acids, respectively. For each of the ORFs, a potential mitochondrial-targeting sequence was found in the 5'-end regions. In comparison to AOX enzymes from plants and fungi, the predicted amino acid sequences of the ORFs showed their highest degree of identity with proteins from Aspergillus niger (38.1% and 37.2%) and Ajellomyces capsulatus (37% and 34.9%). Several residues supposed either to be Fe ligands or to be involved in the ubiquinol-binding site were fully conserved in both C. reinhardtii putative AOX proteins. In contrast, a cysteine residue conserved in the sequences of all higher plants and probably involved in the regulation of the enzyme activity was missing both from the AOX1 and AOX2 amino acid sequences and from protein sequences from various other microorganisms. The transcriptional expression of the AOX1 and AOX2 genes in wild-type cells and in mutant cells deficient in mitochondrial complex III activity was also investigated

AMAW: automated gene annotation for non-model eukaryotic genomes

peer reviewedBackground: The annotation of genomes is a crucial step regarding the analysis of new genomic data and resulting insights, and this especially for emerging organisms which allow researchers to access unexplored lineages, so as to expand our knowledge of poorly represented taxonomic groups. Complete pipelines for eukaryotic genome annotation have been proposed for more than a decade, but the issue is still challenging. One of the most widely used tools in the field is MAKER2, an annotation pipeline using experimental evidence (mRNA-seq and proteins) and combining different gene prediction tools. MAKER2 enables individual laboratories and small-scale projects to annotate non-model organisms for which pre-existing gene models are not available. The optimal use of MAKER2 requires gathering evidence data (by searching and assembling transcripts, and/or collecting homologous proteins from related organisms), elaborating the best annotation strategy (training of gene models) and efficiently orchestrating the different steps of the software in a grid computing environment, which is tedious, time-consuming and requires a great deal of bioinformatic skills. Methods: To address these issues, we present AMAW (Automated MAKER2 Annotation Wrapper), a wrapper pipeline for MAKER2 that automates the above-mentioned tasks. Importantly, AMAW also exists as a Singularity container recipe easy to deploy on a grid computer, thereby overcoming the tricky installation of MAKER2. Use case: The performance of AMAW is illustrated through the annotation of a selection of 32 protist genomes, for which we compared its annotations with those produced with gene models directly available in AUGUSTUS. Conclusions: Importantly, AMAW also exists as a Singularity container recipe easy to deploy on a grid computer, thereby overcoming the tricky installation of MAKER

The rhizosphere microbiota of the zinc and cadmium hyperaccumulators Arabidopsis halleri and Noccaea caerulescens is highly convergent in Prayon (Belgium)

The Prayon site is known as a zinc-polluted area where two zinc and cadmium hyperaccumulator plant species currently coexist, although Arabidopsis halleri was introduced more recently than Noccaea caerulescens . While soil microorganisms may influence metal uptake, the microbial community present in the rhizosphere of hyperaccumulators remains poorly known. Plants of both species were sampled with their bulk and rhizosphere soil from different plots of the Prayon site. Soil components (ionome, pH, water composition, temperature) were analyzed, as well as shoot ionome and expression levels of metal transporter genes ( HMA3 , HMA4 , ZIP4 / ZNT1 , ZIP6 , MTP1 ). The taxonomic diversity of the microorganisms in soil samples was then determined by 16S rRNA metabarcoding and compared at the Operational Taxonomy Unit (OTU) level and across different taxonomic levels. Our elemental analyses confirmed that the site is still highly contaminated with zinc and cadmium and that both plant species indeed hyperaccumulate these elements in situ . Although the pollution is overall high, it is heterogenous at the site scale and correlates with the expression of some metal transporter genes. Metabarcoding analyses revealed a decreasing gradient of microbial diversity, with more OTUs discovered in the rhizosphere than in the soil bulk, especially at the bottom of the cores. However, the variability gradient increases with the distance from roots. Using an ad hoc pseudo-taxonomy to bypass the biases caused by a high proportion of unclassified and unknown OTUs, we identified Chloroflexi, Armatimonadetes, Pirellulaceae, Gemmatimonadetes and Chitinophagaceae as the drivers of the differences in the gradient along the cores. In contrast, no significant difference was identified between the rhizosphere composition of A. halleri and N. caerulescens . This suggests that, despite their distinct colonization history in Prayon, the two plant species have now recruited highly convergent microbial communities in the rhizosphere