References of "Baurain, Denis"
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See detailVertebrate origins: does the tunic make the man?
Delsuc, Frédéric; Baurain, Denis ULg; Philippe, Hervé

in Medecine Sciences : M/S (2006), 22(8-9, AUG-SEP), 688-690

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See detailAssessing the effects of compositional heterogeneity on phylogenomic analyses
Baurain, Denis ULg; Beiko, Robert G.; Ragan, Mark A.

Conference (2005, November 04)

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See detailApplication of the Lempel-Ziv complexity to the alignment-free sequence comparison of protein families
Bacha, Sofiène; Baurain, Denis ULg

Scientific conference (2005, August 26)

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See detailLe darwinisme peut-il tout expliquer ?
Baurain, Denis ULg

Conference given outside the academic context (2005)

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 ... [more ▼]

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. [less ▲]

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See detailApplication of Lempel-Ziv complexity to alignment-free sequence comparison of protein families
Bacha, Sofiène; Baurain, Denis ULg

Poster (2005, April)

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See detailWhy does the red algal plastid lineage lack plastocyanin?
Baurain, Denis ULg; Demoulin, Vincent ULg

Conference (2005, February 03)

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See detailThe mitochondrial oxidative phosphorylation proteome of Chlamydomonas reinhardtii deduced from the genome sequencing project
Cardol, Pierre ULg; Gonzalez-Halphen, Diego; Reyes-Prieto, Adrian et al

in Plant Physiology (2005), 137(2), 447-459

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See detailCondensé de biologie moléculaire à l'usage des biomathématiques et de la bioinformatique
Baurain, Denis ULg

Scientific conference (2004, October 26)

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See detailLa recherche appliquée privilégiée
Baurain, Denis ULg

Article for general public (2003)

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See detailRegulation of the alternative oxidase Aox1 gene in Chlamydomonas reinhardtii. Role of the nitrogen source on the expression of a reporter gene under the control of the Aox1 promoter
Baurain, Denis ULg; Dinant, Monique; Coosemans, Nadine ULg et al

in Plant Physiology (2003), 131(3), 1418-1430

In higher plants, various developmental and environmental conditions enhance expression of the alternative oxidase (AOX), whereas its induction in fungi is mainly dependent on cytochrome pathway ... [more ▼]

In higher plants, various developmental and environmental conditions enhance expression of the alternative oxidase (AOX), whereas its induction in fungi is mainly dependent on cytochrome pathway restriction and triggering by reactive oxygen species. The AOX of the unicellular green alga Chlamydomonas reinhardtii is encoded by two different genes, the Aox1 gene being much more transcribed than Aox2. To analyze the transcriptional regulation of Aox1, we have fused its 1.4-kb promoter region to the promoterless arylsulfatase (Ars) reporter gene and measured ARS enzyme activities in transformants carrying the chimeric construct. We show that the Aox1 promoter is generally unresponsive to a number of known AOX inducers, including stress agents, respiratory inhibitors, and metabolites, possibly because the AOX activity is constitutively high in the alga. In contrast, the Aox1 expression is strongly dependent on the nitrogen source, being down-regulated by ammonium and stimulated by nitrate. Inactivation of nitrate reductase leads to a further increase of expression. The stimulation by nitrate also occurs at the AOX protein and respiratory levels. A deletion analysis of the Aox1 promoter region demonstrates that a short upstream segment (-253 to +59 with respect to the transcription start site) is sufficient to ensure gene expression and regulation, but that distal elements are required for full gene expression. The observed pattern of AOX regulation points to the possible interaction between chloroplast and mitochondria in relation to a potential increase of photogenerated ATP when nitrate is used as a nitrogen source. [less ▲]

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See detailClonage, caractérisation et étude de la régulation transcriptionnelle du gène Aox1 encodant l'oxydase alternative chez Chlamydomonas reinhardtii
Baurain, Denis ULg

Doctoral thesis (2003)

Au sein de la membrane interne des mitochondries, quatre complexes multiprotéiques sont impliqués dans le transfert des électrons depuis les équivalents réducteurs jusqu'à l'oxygène moléculaire. L'énergie ... [more ▼]

Au sein de la membrane interne des mitochondries, quatre complexes multiprotéiques sont impliqués dans le transfert des électrons depuis les équivalents réducteurs jusqu'à l'oxygène moléculaire. L'énergie associée à ce transport au travers des complexes I, III et IV est couplée à la synthèse d'ATP par l'intermédiaire d'un gradient de protons. Chez les plantes supérieures, de nombreux champignons et quelques protistes, une seconde voie de transfert diverge de la voie principale au niveau du pool d'ubiquinone, celui-ci étant alors oxydé directement par l'oxygène moléculaire. Lorsque les électrons empruntent cette voie alternative, deux sites d'éjection de protons sont court-circuités et l'énergie produite est dissipée sous forme de chaleur. Cette réaction est catalysée par une enzyme unique, l'oxydase alternative (AOX), souvent encodée par une petite famille multigénique chez les plantes supérieures. Une activité accrue de la voie alternative est observée suite à divers stimuli développementaux et environnementaux, en particulier en conditions de stress. Cette augmentation d'activité résulte d'une activation transcriptionnelle du gène Aox et/ou de modifications post-traductionnelles de la protéine mature. L'AOX de l'algue verte unicellulaire Chlamydomonas reinhardtii est encodée par deux gènes différents, Aox1 et Aox2, le premier étant beaucoup plus transcrit que le second. Les cDNAs Aox1 et Aox2, de même que la séquence génomique Aox2, ont été isolés et caractérisés dans notre laboratoire. Dans un premier temps, nous avons entrepris le clonage et la caractérisation de la séquence génomique Aox1, ce qui nous a permis de comparer sa structure avec celle de son homologue Aox2. Ensuite, afin d'étudier sa régulation transcriptionnelle, nous avons fusionné un segment de 1,4 kb contenant la région promotrice Aox1 à la région codante du gène (Ars) de l'arylsulfatase et mesuré les activités ARS dans des transformants porteurs de la construction chimérique. Nous avons ainsi montré que le promoteur Aox1 est insensible à la plupart des inducteurs classiques de l'AOX, parmi lesquels des agents de stress, des inhibiteurs respiratoires et des métabolites. En revanche, l'expression du gène Aox1 répond à la nature de la source d'azote, sa transcription étant réprimée par l'ammonium et stimulée par le nitrate. De plus, en milieu contenant du nitrate, l'inactivation de la nitrate réductase (première enzyme de la voie d'assimilation du nitrate) conduit à une expression du gène Aox1 encore plus importante. Nous avons en outre observé que cette stimulation par le nitrate se répercute aux niveaux protéique et respiratoire. Une étude de délétion de la région promotrice Aox1 indique qu'un segment court (de −253 à +59 par rapport à l'origine de transcription) est suffisant pour assurer la transcription et la régulation du gène, mais que son expression maximale requiert également des éléments distaux. Aucun motif nucléotidique susceptible d'intervenir dans l'expression du gène Aox1 n'a été identifié à l'issue d'une analyse bioinformatique du promoteur. L'effet de la nature de la source d'azote sur l'expression de l'AOX est interprété sous l'angle d'une optimisation de la synthèse d'ATP mitochondrial sans modification de l'activité respiratoire, en relation avec un possible accroissement de la production d'ATP photosynthétique lorsque le nitrate est utilisé comme source d'azote. [less ▲]

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See detailRemarkable conservation of internally transcribed spacer sequences of Arthrospira ("Spirulina") (Cyanophyceae, Cyanobacteria) strains from four continents and of recent and 30-year-old dried samples from Africa
Baurain, Denis ULg; Renquin, Laurent; Grubisic, Stana ULg et al

in Journal of Phycology (2002), 38(2), 384-393

The internally transcribed spacer (ITS) sequences of 21 Arthrospira clonal strains from four continents and assigned to four different species (A. platensis, A. maxima, A. fusiformis, A. indica) in the ... [more ▼]

The internally transcribed spacer (ITS) sequences of 21 Arthrospira clonal strains from four continents and assigned to four different species (A. platensis, A. maxima, A. fusiformis, A. indica) in the culture collections were determined. Two main clusters, I and H, were differentiated by 49 positions out of 475 nt or 477 nt, respectively. Each cluster was further subdivided into two subclusters. Subclusters LA and I.B were separated by two substitutions, whereas subclusters II.A, and II.B were distinguished by four substitutions. After direct sequencing of the PCR products, three dried samples from Chad aged between 3 months and 35 years yielded a sequence belonging to subcluster I.A, as did a recent commercial product. The strains grown in production plants belonged to the same (sub)clusters as strains from culture collections, mainly LA and II. PCR primers specific for each cluster and subcluster were designed and tested with crude cell lysates of Arthrospira strains. One dried sample ("dihe' 1) and a herbarium sample from Lake Sonachi (Kenya) only contained I.A sequences, whereas the commercial product was a mixture of the four genotypes and the other two dried samples contained minor polymorphisms characteristic of different clusters. Five clonal Arthrospira strains, thought to be duplicates, showed the simultaneous presence of the two :Forms of the four diagnostic positions that distinguish subclusters genotype H.A and genotype II.B. This is likely to be caused by multiple copies of the rDNA operon, in a intermediate stage of homogenization between subcluster II.A and subcluster II.B. The high conservation of ITS sequences is in contrast with the assignment to four different species, the great morphological variability of the strains, and their wide geographic distribution. [less ▲]

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See detailA mutation in the GTPase domain of the large subunit rRNA is involved in the suppression of a -1T frameshift mutation affecting a mitochondrial gene in Chlamydomonas reinhardtii
Matagne, René-Fernand ULg; Baurain, Denis ULg

in Molecular Genetics & Genomics (2001), 266(1), 103-108

The dum19 mutation isolated in Chlamydomonas reinhardtii is due to the deletion of one T at codon 152 of the mitochondrial cox1 gene sequence. Phenotypically, the dum19 mutant is characterized by a lack ... [more ▼]

The dum19 mutation isolated in Chlamydomonas reinhardtii is due to the deletion of one T at codon 152 of the mitochondrial cox1 gene sequence. Phenotypically, the dum19 mutant is characterized by a lack of cytochrome c oxidase activity and is unable to grow under heterotrophic conditions. A spontaneous pseudo-revertant that grows slowly in the dark was isolated from the dum19 mutant strain. A genetic and molecular analysis allowed us to demonstrate that the revertant phenotype is the consequence of two additional mutations that together act as a frameshift suppressor: an m mutation affecting a mitochondrial gene other than cox1 and an n mutation affecting a nuclear gene. On its own the n mutation does not act as a suppressor, whereas the m mutation very slightly compensates for the effect of the -1T mutation. Sequencing analysis showed that the m mutation affects the GTPase-associated domain of the large subunit (LSU) ofmitochondrial rRNA. Surprisingly, two substitutions, A1090 to G and A1098 to C, were found in the LSU rRNA of the revertant, the latter one being already present in the dum19 mutant strain itself. The A1090 to G substitution is thus involved in the suppression of the frameshift mutation, but it is not clear whether the change at position 1098 is also required for the expression of the suppressed phenotype. To our knowledge, this is the first example of a mutation in the GTPase-associated domain acting as a suppressor of a frameshift mutation. [less ▲]

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See detailMutants of Chlamydomonas reinhardtii deficient in mitochondrial complex I: Characterization of two mutations affecting the nd1 coding sequence
Remacle, Claire ULg; Baurain, Denis ULg; Cardol, Pierre ULg et al

in Genetics (2001), 158(3), 1051-60

The mitochondrial rotenone-sensitive NADH:ubiquinone oxidoreductase (complex I) comprises more than 30 subunits, the majority of which are encoded by the nucleus. In Chlamydomonas reinhardtii, only five ... [more ▼]

The mitochondrial rotenone-sensitive NADH:ubiquinone oxidoreductase (complex I) comprises more than 30 subunits, the majority of which are encoded by the nucleus. In Chlamydomonas reinhardtii, only five components of complex I are coded for by mitochondrial genes. Three mutants deprived of complex I activity and displaying slow growth in the dark were isolated after mutagenic treatment with acriflavine. A genetical analysis demonstrated that two mutations (dum20 and dum25) affect the mitochondrial genome whereas the third mutation (dn26) is of nuclear origin. Recombinational analyses showed that dum20 and dum25 are closely linked on the genetic map of the mitochondrial genome and could affect the nd1 gene. A sequencing analysis confirmed this conclusion: dum20 is a deletion of one T at codon 243 of nd1; dum25 corresponds to a 6-bp deletion that eliminates two amino acids located in a very conserved hydrophilic segment of the protein. [less ▲]

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See detailTranscriptional regulation of the Chlamydomonas alternative oxidase (Aox1) gene studied with a reporter gene construct
Baurain, Denis ULg; Dinant, Monique; Matagne, René-Fernand ULg

Poster (2001, May)

Beside the cytochrome pathway of respiration, mitochondria of higher plants and many microeukaryotes possess an alternative pathway that bypasses complexes III and IV to directly catalyze the oxidation of ... [more ▼]

Beside the cytochrome pathway of respiration, mitochondria of higher plants and many microeukaryotes possess an alternative pathway that bypasses complexes III and IV to directly catalyze the oxidation of the ubiquinol pool by molecular oxygen. No proton motive force is generated during this reaction and free energy is thus lost as heat. The alternative oxidase (AOX), which is the sole enzyme implicated in this wasteful process, is generally subject to both transcriptional and post-translational regulation. — Recently, we have cloned and characterized two cDNAs and the corresponding gene sequences (AOX1 and AOX2) encoding the alternative oxidase in the green alga Chlamydomonas reinhardtii (1). In order to investigate the transcriptional regulation of the AOX1 gene (which is more strongly expressed than AOX2), we fused the AOX1 promoter to the arylsulfatase-encoding ARS reporter gene. Several transformants expressing the ARS protein were selected and characterized at the molecular level. While AOX transcription is induced or at least enhanced by cytochrome pathway inhibitors in fungi and higher plants, our results indicate that the expression of the AOX1:ARS construct remains unchanged following inhibitor addition in Chlamydomonas. Moreover, its expression was not affected by light, acetate as a carbon source and osmotic stress. A five-to-ten-fold stimulation was however achieved by using nitrate instead of ammonium as a nitrogen source. Effects of toxic compounds (oxidative stress agents and heavy metals) are currently investigated. This work was supported by grants from the Belgian FRFC (2.4527.97) and Fonds Spéciaux pour la Recherche dans les Universités. D. Baurain is a FNRS Research Fellow. (1) Dinant, M., Baurain, D., Coosemans, N., Joris, B. and Matagne, R. F. (2001) Characterization of two genes encoding the mitochondrial alternative oxidase in Chlamydomonas reinhardtii. Curr. Genet. (in press) [less ▲]

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See detailCharacterization of two genes encoding the mitochondrial alternative oxidase in Chlamydomonas reinhardtii
Dinant, Monique; Baurain, Denis ULg; Coosemans, Nadine ULg et al

in Current Genetics (2001), 39(2), 101-108

Two 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 ... [more ▼]

Two 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. [less ▲]

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See detailAnalyse de séquences d'ITS de souches d'Arthrospira provenant de quatre continents
Baurain, Denis ULg; Wilmotte, Annick ULg

Scientific conference (2001, March 13)

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See detailThe alternative oxidase genes and their expression in Chlamydomonas
Baurain, Denis ULg; Matagne, René-Fernand ULg; Dinant, Monique

Poster (2000, May)

Mitochondria of Chlamydomonas possess a terminal cyanide-resistant alternative oxidase (AOX) that reduces oxygen to water with electrons derived from the ubiquinone pool. Mutants inactivated in the ... [more ▼]

Mitochondria of Chlamydomonas possess a terminal cyanide-resistant alternative oxidase (AOX) that reduces oxygen to water with electrons derived from the ubiquinone pool. Mutants inactivated in the cytochrome pathway of respiration are still able to consume oxygen via the alternative oxidase pathway. – By combining PCR, RT-PCR and screening of a Chlamydomonas cDNA library, two genes, AOX1 and AOX2, were identified. The cDNAs from AOX1 and AOX2 contain ORFs encoding predicted proteins of 360 and 347 amino acids, respectively. In both cases, a potential targeting presequence was identified in the protein sequence. The two AOX proteins have only 57.6% identity. Compared to AOX proteins from plants and fungi, the highest degree of identity (35-38%) was found with proteins from Aspergillus niger and Ajellomyces capsulatus. – The expression of AOX1 and AOX2 was analyzed at transcriptional level in wild-type and in dum19 mutant cells deprived of cytochrome c oxidase activity. Very low amounts of the 1.9-kb AOX2 transcript were present compared to the 2.3-kb AOX1 transcript. The expression of AOX1 was 2-6 times higher in the mutant than in wild-type, indicating that the absence of the cytochrome pathway of respiration enhances the transcriptional activity of the gene. Supported by FRFC grant 2.4527.97. [less ▲]

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