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

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

A Fast-Growing Oleaginous Strain of Coelastrella Capable of Astaxanthin and Canthaxanthin Accumulation in Phototrophy and Heterotrophy.

peer reviewedConsidering the importance of microalgae as a promising feedstock for the production of both low- and high-value products, such as lipids and pigments, it is desirable to isolate strains which simultaneously accumulate these two types of products and grow in various conditions in order to widen their biotechnological applicability. A novel freshwater strain from the genus Coelastrella was isolated in Belgium. Compared to other Coelastrella species, the isolate presented rapid growth in phototrophy, dividing 3.5 times per day at a light intensity of 400 µmol·m-2·s-1 and 5% CO2. In addition, nitrogen depletion was associated with the accumulation of astaxanthin, canthaxanthin, and fatty acids, which reached ~30% of dry weight, and a majority of SFAs and MUFAs, which are good precursors for biodiesel. This strain also accumulated astaxanthin and canthaxanthin in heterotrophy. Although the content was very low in this latter condition, it is an interesting feature considering the biotechnological potential of the microalgal heterotrophic growth. Thus, due to its rapid growth in the light, its carotenogenesis, and its fatty acids characteristics, the newly identified Coelastrella strain could be considered as a potential candidate for biorefinery purposes of both low- and high-values products

Phylogenomic Analyses of Snodgrassella Isolates from Honeybees and Bumblebees Reveal Taxonomic and Functional Diversity.

peer reviewedSnodgrassella is a genus of Betaproteobacteria that lives in the gut of honeybees (Apis spp.) and bumblebees (Bombus spp). It is part of a conserved microbiome that is composed of a few core phylotypes and is essential for bee health and metabolism. Phylogenomic analyses using whole-genome sequences of 75 Snodgrassella strains from 4 species of honeybees and 14 species of bumblebees showed that these strains formed a monophyletic lineage within the Neisseriaceae family, that Snodgrassella isolates from Asian honeybees diverged early from the other species in their evolution, that isolates from honeybees and bumblebees were well separated, and that this genus consists of at least seven species. We propose to formally name two new Snodgrassella species that were isolated from bumblebees: i.e., Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov. Possible evolutionary scenarios for 107 species- or group-specific genes revealed very limited evidence for horizontal gene transfer. Functional analyses revealed the importance of small proteins, defense mechanisms, amino acid transport and metabolism, inorganic ion transport and metabolism and carbohydrate transport and metabolism among these 107 specific genes. IMPORTANCE The microbiome of honeybees (Apis spp.) and bumblebees (Bombus spp.) is highly conserved and represented by few phylotypes. This simplicity in taxon composition makes the bee's microbiome an emergent model organism for the study of gut microbial communities. Since the description of the Snodgrassella genus, which was isolated from the gut of honeybees and bumblebees in 2013, a single species (i.e., Snodgrassella alvi), has been named. Here, we demonstrate that this genus is actually composed of at least seven species, two of which (Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov.) are formally described and named in the present publication. We also report the presence of 107 genes specific to Snodgrassella species, showing notably the importance of small proteins and defense mechanisms in this genus