C. André, P. Vincens, J.F. Boisvieux and S. Hazout (2001). - Une nouvelle méthode d'analyse de séquences similaires par découpage en zones évolutivement homogènes. Application à l'étude des régions subtélomériques de la levure. - Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), Montpellier, France (3-5 Mai 2000).
La redondance mise en évidence dans le génome de la levure Saccharomyces cerevisiae est un matériel particulièrement intéressant pour étudier l'évolution intra-génomique des chromosomes. Jusqu'à présent, les travaux réalisés se focalisaient sur les ORFs homologues, du fait de leur fonctionnalité et de leur densité (70% du génome). Cependant, les 30% restants du génome, en particulier les régions subtélomériques, présentent également des similitudes issues de processus d'évolution variés. Nous avons entrepris d'étudier la structure complexe et l'évolution de ces régions constituées d'une mosaïque d'éléments dupliqués. À cette fin, nous avons adopté une stratégie en 3 étapes : (i) une recherche "en aveugle" des séquences similaires, (ii) la constitution de groupes de séquences similaires et l'étude de leur agencement dans les subtélomères, (iii) une analyse détaillée des groupes par à un découpage des séquences composites en zones évolutivement homogènes. Cette approche constitue une première étape dans l'étude de l'évolution des chromosomes et permet de proposer des hypothèses sur les réarrangements des régions subtélomériques.
C. André, P. Vincens, J.F. Boisvieux and S. Hazout (2001). - MOSAIC: segmenting multiple aligned DNA sequences - Bioinformatics 17-2: 196-197.
MOSAIC is a set of tools for the segmentation of multiple aligned DNA sequences into homogeneous zones. The segmentation is based on the distribution of mutational events along the alignment. As an example, the analysis of one repeated sequence belonging to the subtelomeric regions of the yeast genome is presented. (Free access from ftp://ftp.biomath.jussieu.fr/pub/papers/MOSAIC).
M. Cabane, P. Calvet, P. Vincens and A.M. Boudet (1993). - Characterization of chilling-acclimation-related proteins in soybean and identification of one as a member of the heat shock protein (HSP 70) family. - Planta 190: 346-353.
Through a 5-d exposure at 14 degrees C/8 degrees C (day/night), soybean (Glycine max [L.] Merr.) was acclimated to a lower temperature of 8 degrees C. In order to assess changes in protein synthesis related to chilling acclimation, proteins were labeled in vivo with [35S]methionine, separated by two-dimensional gel electrophoresis, and the derived autoradiograms were subjected to computer analysis. Two sets of chilling-acclimation-related proteins were characterized following exposure and labeling at 8 degrees C. One set corresponded to proteins whose synthesis was stimulated in acclimated plants in comparison with non-acclimated plants after transfer to 8 degrees C for 2 d. The other set also displayed an enhanced synthesis in the acclimated plants versus the non-acclimated plants but after 7 d of exposure at 8 degrees C. Most of these chilling-acclimation-related proteins were not increased during the acclimation period at 14 degrees C. Using microsequence analysis, one of these proteins was shown to have a high sequence homology with members of the heat-shock protein (HSP 70) family.
M.N. Chobert, P. Vincens, G. Guellaen, R. Barouki, Y. Laperche, M. Aggerbeck, T. Aissani, A. Pawlak, P. Tarroux and J. Hanoune (1988) - Specific modulation by ethanol of the protein synthesis pattern in the C2 rat Hepatoma cell line. - J. Hepatology 6: 85-93.
The effect of ethanol on protein synthesis in the C2 rat hepatoma cell line was analyzed by two-dimensional gel electrophoresis after the labeling with [35S]methionine of cells that were untreated or had been treated with 180 mM ethanol. In this cell line, this concentration of ethanol is known to induce gamma-glutamyl transpeptidase, a marker of alcoholism in man (Barouki et al., Hepatology 1983; 3: 323-329). In the present work we demonstrate that ethanol, besides causing a slight decrease in overall protein synthesis (less than 25%), primarily regulates the expression of two unique proteins among 1500 labeled products that were analyzed: one of these was induced and did not correspond to gamma-glutamyl transpeptidase, and one was repressed after 20 h of ethanol treatment. We conclude that the set of hepatic proteins altered by ethanol is likely to be very limited in number, which reflects the specificity of alcohol action on protein synthesis in the C2 cell line.
G. Claros and P. Vincens (1996). - Computational method to predict mitochondrially imported proteins and their targeting sequences. - Eur. J. Biochem. 241: 779-786.
Most of the proteins that are used in mitochondria are imported through the double membrane of the organelle. The information that guides the protein to mitochondria is contained in its sequence and structure, although no direct evidence can be obtained. In this article, discriminant analysis has been performed with 47 parameters and a large set of mitochondrial proteins extracted from the SwissProt database. A computational method that facilitates the analysis and objective prediction of mitochondrially imported proteins has been developed. If only the amino acid sequence is considered, 75-97% of the mitochondrial proteins studied have been predicted to be imported into mitochondria. Moreover, the existence of mitochondrial-targeting sequences is predicted in 76-94% of the analyzed mitochondrial precursor proteins. As a practical application, the number of unknown yeast open reading frames that might be mitochondrial proteins has been predicted, which revealed that many of them are clustered.
A. de Brevern, F. Loirat, A. Badel-Chagnon, P. Vincens and S. Hazout (2002). - Genome compartimentation by a Hybrid Chromosome Model (HXM). Application to Saccharomyces cerevisae subtelomeres - Comp. Chem. In press
The aim of this paper is to present a new approach, called "Hybrid Chromosome Model" (HcM), which allows both the extraction of regions of similarity between two sequences, and the compartimentation of a set of DNA sequences. The principle of the method consists in compacting a set of sequences (split into fragments of fixed length) into a "hybrid chromosome", which results from the stacking of the whole sequence fragments. We have illustrated our approach on the 32 subtelomeres of Saccharomyces cerevisae. The compartimentation of these chromosome extremities into common regions of similarity have been carried out. The approach HcM is a fast and efficient tool for mapping entire genomes and for extracting ancient duplications within or between genomes.
E. Krejci, N. Duval, A. Chatonnet, P. Vincens and J. Massoulie (1991). - Cholinesterase-like domains in enzymes and structural proteins: Functional and evolutionary relationships and identification of a catalytically essential aspartic acid. - Proc. Natl. Acad. Sci.USA 88: 6647-6651.
Primary sequences of cholinesterases and related proteins have been systematically compared. The cholinesterase-like domain of these proteins, about 500 amino acids, may fulfill a catalytic and a structural function. We identified an aspartic acid residue that is conserved among esterases and lipases (Asp-397 in Torpedo acetylcholinesterase) but that had not been considered to be involved in the catalytic mechanism. Site-directed mutagenesis demonstrated that this residue is necessary for activity. Analysis of evolutionary relationships shows that the noncatalytic members of the family do not constitute a separate subgroup, suggesting that loss of catalytic activity occurred independently on several occasions, probably from bifunctional molecules. Cholinesterases may thus be involved in cell- cell interactions in addition to the hydrolysis of acetylcholine. This would explain their specific expression in well-defined territories during embryogenesis before the formation of cholinergic synapses and their presence in noncholinergic tissues.
T. Rabilloud, P. Vincens, M. Hubert, J.-L. Pennetier and P. Tarroux (1985). - Changes in nuclear proteins induced by heat shock in Drosophila culture cells. - FEBS letters 184: 278-284.
Nuclear proteins of normal and heat-shocked Drosophila cells were analysed by two-dimensional electrophoresis. The computerized processing of the gels allowed us to detect 6 proteins strongly induced by the heat treatment, but which were different from the usually described heat-shock proteins. The possible role of these proteins in genetic regulation is discussed, as is the value of this type of approach for the study of other genetic regulation phenomena.
T. Rabilloud, J.L. Pennetier, U. Hibner, P. Vincens, P. Tarroux and F. Rougeon (1991). - Stage transitions in B-lymphocyte differentiation correlate with limited variations in nuclear proteins. - Proc. Natl. Acad. Sci.USA 88: 1830-1834.
Total nuclear proteins extracted from cell lines representing various stages of differentiation of mouse B lymphocytes were studied by computer analysis of two-dimensional gels. Of the 1438 spots present on the gels, 55 varied significantly in intensity during differentiation. The variations occurred most often in steps correlating with those classically defined for B-cell differentiation. Seventeen spots were not detectable in at least one of the stages (qualitative variations) and could represent switching on or off of genes coding for nuclear proteins. Detailed analysis of the 55 variable spots showed that they fall into small sets characterized by similar expression profiles, which argues for a combinatorial, multistep control mechanism of gene expression. In addition, analysis of the expression of all the nuclear proteins resolved on the gels clearly differentiated B-lineage cells from myeloid cells and suggested that the most important transition in B-cell differentiation occurs between the resting B cell and plasmocyte stages.
T. Rabilloud, P. Vincens, D. Asselineau, J.-L. Pennetier, M. Darmon and P. Tarroux (1994). - Computer analysis of two-dimensional electrophoresis gels as a tool in cell biology: study of the protein expression of human keratinocytes from normal to tumor cells. - Cell. Mol. Biol. 40: 17-27.
The usefulness of computer analysis of two-dimensional electrophoresis gels has been investigated on the example of human keratinocytes transformation. For this purpose, the protein expression of various keratinocytes strains from normal to tumor cells has been analysed by two-dimensional electrophoresis. The resulting gels have been submitted to computer analysis, including various data analysis techniques allowing to select spots on the gels or to classify the gels themselves. The latter techniques appeared very useful, since they demonstrated that the major transition in words of variation of the protein expression lies at the normal cell/transformed cell transition rather than at the transformed cell/tumorigenic cell transition.
P. Tarroux, P. Vincens and T. Rabilloud (1987) - HERMeS: a second generation approach to the automatic analysis of two-dimensional electrophoresis gels. Part V: data analysis. - Electrophoresis 8: 187-199.
Data analysis programs are essential tools for processing the large quantity of data produced by two-dimensional gel electrophoris computerized analysis. Global handling of two-dimensional gel information can be achieved using both analysis programs and artificial intelligence techniques. First, a statistical multivariate approach is presented, used to sort gels and to obtain a gel classification according to protein patterns. Both clustering and multivariate techniques are used and the results show that a classification of protein expression patterns according to effector action can be achieved. Spots can also be sorted and compared according to their expression under effector action. Each spot is thus described using a set of variables (its intensity for each gel pattern) and its description is essentially given in a multivariate way. Therefore, each facet of the regulation of a particular protein according to the action of several effectors can easilybe taken into account. Spot sets containing spots having common regulation characteristics are obtained using principal component analysis. We show that each group corresponds to a functional aspect of the regulation in a given cell line. The map obtained describes the organization of cell functions and the interactions of these functions. Another approach employs artificial intelligence techniques. Since the rules available for describing some aspects of knowledge in the field of two-dimensional electrophoresis remain unknown, learning techniques are suitable for defining them. Their use for the automatic recognition of spot groups belonging to the same entity on a gel is illustrated. Our learning program is applied to the determination of glycosylation groups and to the identification of relevant spot patterns.
P. Vincens, N. Paris, J.L. Pujol, C. Gaboriaud, T. Rabilloud, J.L. Pennetier, P. Matherat, P. and P. Tarroux (1986) - HERMeS: a second generation approach to the automatic analysis of two-dimensional electrophoresis gels. Part I: Data acquisition. - Electrophoresis 7: 347-356.
In this series of papers, we describe the computer system we have
developed for two-dimensional (2-D) gel analysis. Here the acquisition part of the system is described and a set of criteria able to measure the overall performance of the system is presented. These criteria are essentially based on frequency domain considerations using Fourier transforms. We show that the transfer function characteristics of the input system must be carrefully checked to avoid any image distorsion; we propose an easily computed criterion to obtain setting conditions giving a correct system response. These features are discussed considering the specificity of the 2-D gel images that can be well modeled by a multi-Gaussian surface. Then the visualization device and its main abilities to treat and modify the aspect of the images are presented. Statistical functions using second-order image histograms are introduced. They can be used to look at the general aspect of the image, as a global and accurate criterion for quality checking. For this purpose, covariance, entropy and inertia have been found to be most suitable. Second order histograms give additional information on image anisotropy and can direct the user towards the convenient values of the parameters for the subsequent treatments. Coding is considered from both the point of view of image compression and image sending throughout a computer network. An efficient code protecting all the image information is suggested and discussed.
P. Vincens (1986) - HERMeS: a second generation approach to the automatic analysis of two-dimensional electrophoresis gels. Part II: Spot detection and integration. - Electrophoresis 6: 357-367.
This work describes the techniques used to detect the presence of a spot at a given place in a two-dimensional gel and to compute its volume. This is done using filtering techniques to extract significant information from rough images. Four types of treatments were applied to images in order to improve the detection of spots belonging to different categories. Mathematical techniques of morphology were used to lower the effect of spot overlapping, while histogram modifications using power functions were used to improve the detection of major and minor spots, respectively, thereby generating four processed images. On each generated image, spot detection is computed by looking at the local maxima. Then the four spots lists are gathered and the volume is computed according to a spot model. To improve the accuracy of volume detection, a spot model constituted by two half-Gaussian curves in each space direction is used. The pitch of each spot according to the horizontal direction is also computed. A total of 8 parameters, including spot position, shape parameters, surface intensity and volume, is gathered into a spot list which constitutes the reduced information which will be handled subsequently. the choice of a model allow us to get a round the improper volume calculations caused by spot overlapping. The mutual penetration of spot into another is thus automatically taken into account. A set of statistical considerations is computed from these data in order to validate our spot model, to check for parameter independence, to obtain quality criteria which may be used to judge gel quality, to propose different diagnoses for the observed defaults and to lead to a self-adaptation process of treatment parameters. These statistical considerations can be used to study the effect of each type of treatment to compare the effect of each filter on the final result.
P. Vincens and P. Tarroux, P. (1987) - HERMeS: a second generation approach to the automatic analysis of two-dimensional electrophoresis gels. Part III: Spot list matching. - Electrophoresis 8: 100-107.
One of the most critical steps in two-dimensional gel analysis in the comparison of spot lists. In this paper, we describe our approach to the matching problem. We propose a method based on syntactic pattern recognition techniques, which differs from previously used methods and offers a major improvment to cope with discontinuous geometric distorsions. The method is based on non-metric considerations and describes the pattern observed on a given gel in a non-geometric way. This aproach leads to the definition of finite automatons which can be used to automatically find the presence of a given pattern on a gel. The program uses a technique of clause generation related to artificial intelligence techniques. A set of rules is applied to the definition of homologous spots, and probability coefficients are computed to compare and to chose between different pairing hypetheses. Once matching has been achieved between a set of gels, the construction of a master gel which summarizes the information obtained is allowed. Two types of master can be used. The first one summarizes the information between spots lists belonging to the same experiment and includes intensity considerations, while the second one summarizes the information resulting from different gels and does not include spot intensity and volume. Masters are written and known by the system as a spot list. This ability allows them to be handled just like spot lists and, using them, to perform all the actions available to the system. This approach is compared with a more classical one based on geometric corrections. The use of probability coefficients is also discussed and extended to their application to multiple matching and further uses of masters.
P. Vincens and P. Tarroux (1987) - HERMeS: a second generation approach to the automatic analysis of two-dimensional electrophoresis gels. Part IV: Database organization and management. - Electrophoresis 8: 173-186.
A database structure is needed for easy handling of the large quantity of data obtained from a series of gel electrophoresis experiments and also for defining the firts statements of a standard between experiments from different origins. This paper describes the database concept and the database interrogation strategies in the field of two-dimensional electrophoresis and protein expression data. First, the main characteristics of our database structure and the main capabilities offered to the user to handle and interrogate the structure, as well as to retrieve his information are described. gel standardization and protein identification are the examined. A relational database, associated with the description of each spot according to internal and external (physicochemical) descriptors, provides a suitable structure for a standardization procedure. A dynamic updating of the actual position of each spot, each time new positional information is entered in the system, allows the encoding of standardized positions. A database structure can also be used to establish a link between different kinds of information from different areas required for a correct interpretation of two-dimensional gel data. Particularly, information from the gene sequence of a givent protein may offer insights into the regulation of this protein. Thus a link between the two-dimensional gel database and sequences databases is implemented in our system. The information available from sequence data may help to interpret electrophoresis data. Furthermore, a formal presentation of the database structure is achieved in order to propose a standardized description of the database structure and concept used. This feature allows comparisons between different databases and frees the user from a specific configuration. Logical formulations are introduced using predicate calculus and then lead to a description of manipulation tools in terms of a declarative programming language.
P. Vincens and P. Tarroux (1988) - Two-dimensional electrophoresis computerized processing. - International Journal of Biochemistry 20: 499-509.
This paper describes various methods suitable for implementation of two-dimensional processing software. The different steps leading to a complete processing are described, from the digitalization of the image to the processing of the resulting data. The characteristics of a convenient digitalization system are discussed. The different software devoted to spot detection is reviewed with respect to the presence or otherwise of a spot model and its characteristics. The major techniques for gel matching are compared as are designs for database structures suitable for tabulation of measurements. Finally, the need for a sophisticated system of data processing is stressed and its main requirements are described.
P. Vincens, L. Buffat, C. André, J.P. Chevrolat, J.F. Boisvieux and S. Hazout (1998) - A strategy for finding regions of similarity in complete genome sequences. - Bioinformatics 14-8: 715-725.
Motivation : Complete genomic sequences will become available in the future. New methods to deal with very large sequences (sizes beyond 100 kb) efficiently are required. One of the main aims of such work is to increase our understanding of genome organization and evolution. This requires studies of the locations of regions of similarity.
Results : We present here a new tool, ASSIRC ('Accelerated Search for SImilarity Regions in Chromosomes'), for finding regions of similarity in genomic sequences. The method involves three steps: (i) identification of short exact chains of fixed size, called 'seeds', common to both sequences, using hashing functions; (ii) extension of these seeds into putative regions of similarity by a 'random walk' procedure; (iii) final selection of regions of similarity by assessing alignments of the putative sequences. We used simulations to estimate the proportion of regions of similarity not detected for particular region sizes, base identity proportions and seed sizes . This approach can be tailored to the user's specifications. We looked for regions of similarity between two yeast chromosomes (V and IX). The efficiency of the approach was compared to those of conventional programs BLAST and FASTA, by assessing CPU time required and the regions of similarity found for the same data set .
Availability : Source programs are freely available at the following address: ftp://ftp.biologie.ens.fr/pub/molbio/assirc.tar.gz
Contact :
vincens@biologie.ens.fr,
hazout@urbb.jussieu.fr.
P. Vincens, C. André, A. Badel-Chagnon, F. Guyon and S. Hazout (2001) - SIMCOGEN : une base de données recensant les régions de similitudes dans les génomes complets - Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), Toulouse, France (30 Mai - 1 Juin 2001) (Affiche - Poster) (Transparents - Slides).
La localisation des régions dupliquées au sein des génomes compl ets est une source importante d'informations que ce soit pour la compréhension des mécanismes évolutifs ayant abouti à leurs structures actuelles ou pour l'étude de leurs fonctionnements. La base de données SIMCOGEN recense les régions présentant des similitudes de séquences identifiées au sein de génomes complets procaryotes et eucaryotes. Un ensemble d'outils associés accessible à travers une interface web (http://www.simcogen.ens.fr) facilite l'accès aux informations à l'utilisateur.
P. Vincens, A. Badel-Chagnon, C. André and S. Hazout (2002) - D-ASSIRC: Distributed program for finding sequence similarities in genomes - Bioinformatics 18 (3), 246-251.
Motivation : Locating the regions of similarity in a genome requires the availability of appropriate tools such as 'Accelerated Search for Similar Regions in Chromosomes' (ASSIRC: Vincens et al., Bioinformatics, 14, 715-725, 1998). The aim of this paper is to present different strategies for improving this program by distributing the operations and data to multiple processing units and to assess the efficiency of the different implementations in terms of running time as a function of the number of processing units.
Results : The new version D-ASSIRC is based on three alternative strategies of task sharing: (1) a distributed search using the splitting of studied sequences into large overlapping subsequence (strategy ASS); (2) two distributed searches for repeated exact motis of fixed size either managed by a central processor (strategy AGD) or locally managed by numerous processors (strategy ALD). The result is that the strategy ASS is suitable for a large number of processing units (the time was divided by a factor of 12 when the number of processing units was increased from 1 to 16) whereas the strategy ALD is better for a small set of processors (typically for four or six). The different proposed strategies are efficient for various applications in genomic research, particularly for locating similarities of nucleic sequences in large genomes.
Availability : D-ASSIRC is freely available by anonymous FTP at ftp://ftp.biologie.ens.fr/pub/molbio/dassirc.tar.gz. Sources and binaries for Solaris and Linux are included in the distribution.
Contact :
vincens@biologie.ens.fr,
M. Vuillaume, Y. Decroix, R. Calvayrac, J.B. Truc, B.J. Paniel, P. Vincens, P. Tarroux and P. Poitout (1991). - Catalase-associated abnormalities and H2O2 increase in pre-neoplastic and neoplastic lesions of the human lower female genital tract and their near adjacent epithelia. - Biomed. Pharmacother. 45: 435-444.
We report that an internal and non-UV-dependent type of neoplasia, the human cervical intraepithelial neoplasia (SIL), is also deficient in catalase activity, like the UV-induced tumors in the autosomal recessive human epithelial disease, xeroderma pigmentosum (XP). Whether or not the lesions are papillomavirus (HPV) positive in the different categories of preneoplastic and neoplastic extracts, the following parameters are affected: i), catalase activity level; ii), kinetic profile of catalase activity; iii), H2O2 increase. Mathematical treatment of these parameters (CONSTEL-Program), unambiguously distinguishes between normal and pathological cases. Such analyses make it possible to grade the pathological samples into 4 classes, depending on their deviance from normality. These classes may be correlated with the gradual steps in the process of malignant transformation defined by histological and clinical diagnosis. We found conformity between catalase activity and histological analyses in 66 biopsies, out of a total of 100 biopsies (35 patients). Moreover, 23 patients presenting decreased catalase activities in 31 biopsies showed disease progression after 3 to 6 months contrary to surgery histological data. We show that ATP synthesis in the presence of catalase and H2O2 (further aspect of catalase function), may occur in neoplastic extracts at much lower concentrations of H2O2 than in normal extracts. Thus, the catalase abnormality seems to be a good tool to study pre-neoplastic to neoplastic evolution of lesions and their adjacent tissues of the lower female genital tract; furthermore, i) it provides an earlier, more powerful means of detecting micro-SIL in progression to squamous cell carcinoma, than combined clinical and histological examinations; ii) model for investigating drugs such as in situ H2O2 scavengers or agents increasing glutathione peroxidase activity (GSH).
M. Vuillaume, L. Daya-Grosjean, P. Vincens, J.L. Pennetier, P. Tarroux, A. Baret, R. Calvayrac, A. Taieb and A. Sarasin (1992). - Striking differences in cellular catalase activity between two DNA repair-deficient diseases: Xeroderma pigmentosum and trichothiodystrophy. - Carcinogenesis 13: 321-328.
Xeroderma pigmentosum (XP) and trichothiodystrophy (TTD) are two recessively transmitted human diseases characterized by DNA repair deficiency. While XP is associated with a very high incidence of cancer on skin exposed to sunlight, TTD is not a cancer-prone disease. Therefore, unrepaired UV-induced DNA lesions do not appear to be enough to give rise to tumors. In order to understand the differences between these two syndromes, we measured catalase activity in cellular extracts, UV irradiated or not, and quantified H2O2 production following in vitro UV irradiation. We confirmed on 21 different XP diploid fibroblast lines that catalase activity was decreased on average by a factor of five as compared to controls, while XP heterozygote lines exhibited intermediary responses. All seven TTD lines we tested were deficient in UV-induced lesion repair and exhibited a high level of catalase activity. However, molecular analysis of catalase transcription showed no difference between normal, XP and TTD cell lines. This was confirmed by Western blots where the amount of catalase subunits was identical in all cell lines studied. Finally, UV irradiation induces five and three times more H2O2 production in XP lines compared with TTD or controls respectively. These striking differences between TTD and XP indicate that UV light, directly or indirectly, together with defective oxidative metabolism may increase the initiation and/or the progression steps in the XP environment compared to TTD. This may partly explain the different tumoral phenotype observed between the two diseases.
Date de la dernière mise à jour: 03/04/2002