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One of the fundamental techniques of biology is sequence alignment, namely transforming one sequence into another with minimal change. Sequence alignment is essential for evolutionary studies and is a source of information for the analysis of the physico-chemical mechanisms which are at the heart of protein activity. Biologists almost exclusively use methods based on a very simple model, although they are aware that this can be quite removed from reality. In fact, the more complex models involve so many variables that they cannot be calculated in practice. This paper presents a method to estimate the quality of the approximation made using simple models, giving a measure of the deviation from reality. It is exclusively based on the analysis of pairwise alignments, without resorting to multiple alignments, and therefore without requiring the construction of trees and the problems associated with it. The paper also describes an approach that allows building trees and clusters from sequences without strongly relying on the choice of a dissimilarity measure. It illustrates the interest and effectiveness of the point of view promoted by Alex: assume as little as possible and try to gather information from the data, before turning to explicit modeling if necessary., L'une des techniques fondamentales de la biologie est l'alignement de séquences, c'est-à-dire la transformation d'une séquence en une autre avec un minimum de changement. L'alignement de séquences est essentiel pour les études évolutives et constitue une source d'information pour l'analyse des mécanismes physico-chimiques qui sont au cœur de l'activité des protéines. Les biologistes utilisent presque exclusivement des méthodes basées sur un modèle très simple, même s'ils sont conscients que cela peut être assez éloigné de la réalité. En fait, les modèles les plus complexes impliquent tellement de variables qu'elles ne peuvent pas être calculées en pratique. Cet article présente une méthode pour estimer la qualité de l'approximation faite à l'aide de modèles simples, donnant une mesure de l'écart par rapport à la réalité. Elle repose exclusivement sur l'analyse d'alignements par paires, sans recourir à des alignements multiples, et donc sans nécessiter la construction d'arbres et les problèmes qui y sont associés. L'article décrit également une approche qui permet de construire des arbres et des clusters à partir de séquences sans dépendre fortement du choix d'une mesure de dissimilarité. Elle illustre l'intérêt et l'efficacité du point de vue promu par Alex : supposer le moins possible et essayer de recueillir des informations à partir des données, avant de se tourner si nécessaire vers une modélisation explicite.

Summer mortality of the Pacific oyster Crassostrea gigas is the result of a complex interaction between oysters, their environment, and pathogens. Heredity appears to be a major factor determining the sensitivity of oysters to summer mortality, allowing resistant (R) and susceptible (S) lines to be produced. We conducted genome-wide expression profiling of R and S gonads during the 3-month period preceding a summer mortality event, using a cDNA microarray that we designed. ANOVA analysis revealed that 34 genes were differentially expressed between R and S lines on four dates preceding the mortality event. Annotation of some of these genes highlights reproduction and its allocation and antioxidant defenses as the main pathways that operate differentially between R and S lines. This transcriptional analysis provides new indications to define markers for quantitative trait loci searches and functional studies and evaluate the potential role of each gene in the resistance to summer mortality.

Web geometry is devoted to the study of families of foliations which are in general position. We restrict ourselves to the local situation, in the neighborhood of the origin in C2, with d > 1 complex analytic foliations of curves in general position. We are interested in the geometry of such configurations, that is, properties of planar d-webs which are invariant with respect to analytic local isomorphisms of C2. The initiators of the subject are W. Blaschke, G. Thomsen and G. Bol

A $d$-web ${\Cal W}(d)$ is given by $d$ complex analytic foliations of codimension $n$ in $({\sumbbb C}^N,0)$ such that the leaves are in general position. We are interested in the geometry of such configurations. A complex $({\Cal A}^{\bullet},\delta)$ of ${\sumbbb C}$-vector spaces is defined in which ${\Cal A}^0$ corresponds to functions and ${\Cal A}^p$ to $p$-forms of the web ${\Cal W}(d)$ for $1\leq p\leq n$. If $N=kn$ with $k\geq 2$, it is proved that $r_p:=\dim_{\,\sumbbb C}{\Cal A}^p$ is a finite analytic invariant of ${\Cal W}(d)$ with an optimal upper bound $\pi_{p}(d,k,n)$ for $0\leq p\leq n$. These bounds generalize the Castelnuovo’s ones for genus of curves in ${\sumbbb P}^{k}$ with degree $d$. Some characterization of the the space $H^0(V_n,\omega^p_{V_n})$ of abelian differentials to an algebraic variety $V_n$ in ${\sumbbb P}^{n+k-1}$ of pure dimension $n$ with degree $d$ is given. Moreover, using duality and Abel’s theorem, we investigate how for suitable $V_n$ the natural complex $\bigr(H^0(V_n,\omega^{\bullet}_{V_n}),d\,\bigr)$ and the abelian relation complex $({\Cal A}^{\bullet},\delta)$ of the linear web associated to $V_n$ in $({\sumbbb C}^{kn},0)$ are related.

An analytic \(d\)-web \(\mathcal{W}(d)\) in a neighborhood of \(0\in {\mathbb C}^2\) with \(d\ge 4\) and maximum rank \(\pi _d:={1\over 2}(d-1)(d-2)\) gives rise to an analytic map \({\mathfrak u}:({\mathbb C}^2,0)\longrightarrow \check{\mathbb P}^{\,\pi _d-1}\) through an abelian basis. Classic and new properties of the resulting projective surface, smooth but transcendental in general, are presented. Modeled on the previous \(\mathfrak u\), special maps \(f:({\mathbb C}^2,0)\longrightarrow \check{\mathbb P}^{\,\pi _d-1}\) induce Bompiani webs \(\mathcal{W}_f(d)\) through their \((d-4)\)-principal curves that we define. It is proved in particular that those Bompiani webs \(\mathcal{W}_f(d)\) of maximum rank are characterized only by a vanishing curvature.

In this paper, the relationship between codon usage and the physiological pattern of expression of a gene is investigated while considering a dataset of 815 nuclear genes of Arabidopsis thaliana. Factorial Correspondence Analysis, a commonly used multivariate statistical approach in codon usage analysis, was used in order to analyse codon usage bias gene by gene. The analysis reveals a single major trend in codon usage among genes in Arabidopsis. At one end of the trend lie genes with a highly G/C biased codon usage. This group contains mainly photosynthetic and housekeeping genes which are known to encode the most abundant proteins of the vegetal cell. At the other extreme lie genes with a weaker A/T-biased codon usage. This group contain genes with various functions which exhibits most of the time a strong tissue-specific pattern of expression in relation, for example, to stress conditions. These observations were confirmed by the detailed analysis of codon usage in the multigene family of tubulins and appear to be general in plant species, even as distant from Arabidopsis thaliana as a monocotyledonous plant such as maize.

A computer-assisted analysis was made of 24 complete nucleotide sequences selected from the vertebrate retroviruses to represent the ten viral groups. The conclusions of this analysis extend and strengthen the previously made hypothesis on the Moloney murine leukemia virus: The evolution of the nucleotide sequence appears to have occurred mainly through at least three overlapping levels of duplication: (1) The distributions of overrepresented (3-6)-mers are consistent with the universal rule of a trend toward TG/CT excess and with the persistence of a certain degree of symmetry between the two strands of DNA. This suggests one or several original tandemly repeated sequences and some inverted duplications. (2) The existence of two general core consensuses at the level of these (3-6)-mers supports the hypothesis of a common evolutionary origin of vertebrate retroviruses. Consensuses more specific to certain sequences are compatible with phylogenetic trees established independently. The consensuses could correspond to intermediary evolutionary stages. (3) Most of the (3-6)-mers with a significantly higher than average frequency appear to be internally repeated (with monomeric or oligomeric internal iterations) and seem to be at least partly the cause of the bias observed by other researchers at the level of retroviral nucleotide composition. They suggest a third evolutionary stage by slippage-like stepwise local duplications.

Motivation: Compression algorithms can be used to analyse genetic sequences. A compression algorithm tests a given property on the sequence and uses it to encode the sequence: if the property is true, it reveals some structure of the sequence which can be described briefly, this yields a description of the sequence which is shorter than the sequence of nucleotides given in extenso. The more a sequence is compressed by the algorithm, the more significant is the property for that sequence. Results: We present a compression algorithm that tests the presence of a particular type of dosDNA (defined ordered sequence-DNA): approximate tandem repeats of small motifs (i.e. of lengths

International audience; Leukodystrophies (LD) are rare inherited disorders that primarily affect the white matter (WM) of the central nervous system. The large heterogeneity of LD results from the diversity of the genetically determined defects that interfere with glial cells functions. Astrocytes have been identified as the primary target of LD with cystic myelin breakdown including those related to mutations in the ubiquitous translation initiation factor eIF2B. EIF2B is involved in global protein synthesis and its regulation under normal and stress conditions. Little is known about how eIF2B mutations have a major effect on WM. We performed a transcriptomic analysis using fibroblasts of 10 eIF2B-mutated patients with a severe phenotype and 10 age matched patients with other types of LD in comparison to control fibroblasts. ANOVA was used to identify genes that were statistically significantly differentially expressed at basal state and after ER-stress. The pattern of differentially expressed genes between basal state and ER-stress did not differ significantly among each of the three conditions. However, 70 genes were specifically differentially expressed in eIF2B-mutated fibroblasts whatever the stress conditions tested compared to controls, 96% being under-expressed. Most of these genes were involved in mRNA regulation and mitochondrial metabolism. The 13 most representative genes, including genes belonging to the Heterogeneous Nuclear Ribonucleoprotein (HNRNP) family, described as regulators of splicing events and stability of mRNA, were dysregulated during the development of eIF2B-mutated brains. HNRNPH1, F and C mRNA were over-expressed in foetus but under-expressed in children and adult brains. The abnormal regulation of HNRNP expression in the brain of eIF2B-mutated patients was concomitant with splicing dysregulation of the main genes involved in glial maturation such as PLP1 for oligodendrocytes and GFAP in astrocytes. These findings demonstrate a developmental deregulation of splicing events in glial cells that is related to abnormal production of HNRNP, in eIF2B-mutated brains.

A method aimed at classifying protein sequences withoutresorting to pairwise alignment is presented. Called DOCMA(DOt-plot Comparisons by Multivariate Analysis), it is basedon a multivariate analysis of the pairwise dot-plots between allthe sequences in the set. The dot-plots are first simplified byconsidering only the projections of the 'diagonal' segments ofsimilarity onto the axes. From these projections a data matrixis built, in which each column is representative of thecomparisons of one given sequence with all the other ones. Thisdata matrix is then transformed into a distance matrix by achi-squared analysis, from which the coordinates of thesequences in an orthonormal Euclidean space are obtained. Thesequences are finally classified by a dynamic clusteringprocedure followed by a search for strong clusters. Applicationof this method to protein families such as the globins, thecytochromes c and the aminoacyl-tRNA synthetases shows thatit is quite effective in delineating subgroups that contain evendistantly related sequences.IntroductionAs more and more amino acid sequences of proteins becomeavailable, there has been a growing number of studies aimedat establishing the evolutionary relationships between membersof one given set of proteins, or, less ambitiously, at classifyingthe sequences as a function of their similarities. In the first case,the problem is to find the tree(s) in which the lengths of thebranches reflect at best the pairwise distances between thesequences—assuming that these distances are directly relatedto evolutionary times. The search for such a tree is generallyextremely time consuming, even if efficient heuristics are usedto speed up the process. For instance, the determination of themost parsimonious tree for 245 globin sequences (Goodmanet al., 1988) required the use of a Cray-2 supercomputer. In thesecond case, the problem is rather to delineate the groups, orclusters, of the most closely related sequences. The informationthus gained can be used, for instance, as a guideline forperforming a multiple alignment of the sequences, i.e. thosethat are most alike will be aligned first (e.g. Corpet, 1988; Fengand Doolittle, 1987; Taylor, 1988), or to select those sequences

The present work describes an attempt to identify reliable criteria which could be used as distance indices between protein sequences. Seven different criteria have been tested: i and ii) the scores of the alignments as given by the BESTFIT and the FASTA programs; iii) the ratio parameter, i.e. the BESTFIT score divided by the length of the aligned peptides; iv and v) the statistical significance (Z-scores) of the scores calculated by BESTFIT and FASTA, as obtained by comparison with shuffled sequences; vi) the Z-scores provided by the program RELATE which performs a segment-by-segment comparison of 2 sequences, and vii) an original distance index calculated by the program DOCMA from all the pairwise dotplots between the sequences. These 7 criteria have been tested against the aminoacid sequences of 39 globins and those of the 20 aminoacyl-tRNA synthetases from E. coli. The distances between the sequences were analyzed by the multivariate analysis techniques. The results show that the distances calculated from the scores of the pairwise alignments are not adequately sensitive. The Z-score from RELATE is not selective enough and too demanding in computer time. Three criteria gave a classification consistent with the known similarities between the sequences in the sets, namely the Z-scores from BESTFIT and FASTA and the multiple dotplot comparison distance index from DOCMA.

The information collected in national and international libraries on nucleotide and protein sequences cannot be directly treated for proper handling by existing software. Therefore we evaluated the feasibility of constructing a data base for Escherichia coli using the data present in the banks. The knowhow thus acquired was applied to Bacillus subtilis. Specific examples of the general procedure are given.

Yarrowia lipolytica is one of the yeasts most frequently isolated from the surface of ripened cheeses. In previous work, it has been shown that this yeast is able to convert l -methionine into various volatile sulfur compounds (VSCs) that may contribute to the typical flavors of several cheeses. In the present study, we show that Y. lipolytica does not assimilate lactate in the presence of l -methionine in a cheeselike medium. Nineteen presumptive genes associated with l -methionine catabolism or pyruvate metabolism in Y. lipolytica were transcriptionally studied in relation to l -methionine degradation. The expression levels of the Yl ARO8 (YALI0E20977g), Yl BAT1 (YALI0D01265g), and Yl BAT2 (YALI0F19910g) genes (confirmed by real-time PCR experiments) were found to be strongly up-regulated by l -methionine, and a greater variety and larger amounts of VSCs, such as methanethiol and its autooxidation products (dimethyl disulfide and dimethyl trisulfide), were released in the medium when Y. lipolytica was grown in the presence of a high concentration of l -methionine. In contrast, other genes related to pyruvate metabolism were found to be down-regulated in the presence of l -methionine; two exceptions were the Yl PDB1 (YALI0E27005g) and Yl PDC6 (YALI0D06930g) genes, which encode a pyruvate dehydrogenase and a pyruvate decarboxylase, respectively. Both transcriptional and biochemical results corroborate the view that transamination is the first step of the enzymatic conversion of l -methionine to VSCs in Y. lipolytica and that the Yl ARO8 , Yl BAT1 , and Yl BAT2 genes could play a key role in this process.

Background The processes of gene transcription, translation, as well as the reactions taking place between gene products, are subject to stochastic fluctuations. These stochastic events are being increasingly examined as it emerges that they can be crucial in the cell's survival. In a previous study we had examined the transcription patterns of two bacterial species (Escherichia coli and Bacillus subtilis) to elucidate the nucleoid's organization. The basic idea is that genes that share transcription patterns, must share some sort of spatial relationship, even if they are not close to each other on the chromosome. We had found that picking any gene at random, its transcription will be correlated with genes at well-defined short – as well as long-range distances, leaving the explanation of the latter an open question. In this paper we study the transcription correlations when the only transcription taking place is stochastic, in other words, no active or "deterministic" transcription takes place. To this purpose we use transcription data of Sinorhizobium meliloti. Results Even when only stochastic transcription takes place, the co-expression of genes varies as a function of the distance between genes: we observe again the short-range as well as the regular, long-range correlation patterns. Conclusion We explain these latter with a model based on the physical constraints acting on the DNA, forcing it into a conformation of groups of a few successive large and transcribed loops, which are evenly spaced along the chromosome and separated by small, non-transcribed loops. We discuss the question about the link between shared transcription patterns and physiological relationship and come to the conclusion that when genes are distantly placed along the chromosome, the transcription correlation does not imply a physiological relationship.

DNA microarrays of 86 genes from the yeasts Debaryomyces hansenii , Kluyveromyces marxianus , and Yarrowia lipolytica were developed to determine which genes were expressed in a medium mimicking a cheese-ripening environment. These genes were selected for potential involvement in lactose/lactate catabolism and the biosynthesis of sulfur-flavored compounds. Hybridization conditions to follow specifically the expression of homologous genes belonging to different species were set up. The microarray was first validated on pure cultures of each yeast; no interspecies cross-hybridization was observed. Expression patterns of targeted genes were studied in pure cultures of each yeast, as well as in coculture, and compared to biochemical data. As expected, a high expression of the LAC genes of K. marxianus was observed. This is a yeast that efficiently degrades lactose. Several lactate dehydrogenase-encoding genes were also expressed essentially in D. hansenii and K. marxianus , which are two efficient deacidifying yeasts in cheese ripening. A set of genes possibly involved in l -methionine catabolism was also used on the array. Y. lipolytica , which efficiently assimilates l -methionine, also exhibited a high expression of the Saccharomyces cerevisiae orthologs BAT2 and ARO8 , which are involved in the l -methionine degradation pathway. Our data provide the first evidence that the use of a multispecies microarray could be a powerful tool to investigate targeted metabolism and possible metabolic interactions between species within microbial cocultures.

Background Although the organisation of the bacterial chromosome is an area of active research, little is known yet on that subject. The difficulty lies in the fact that the system is dynamic and difficult to observe directly. The advent of massive hybridisation techniques opens the way to further studies of the chromosomal structure because the genes that are co-expressed, as identified by microarray experiments, probably share some spatial relationship. The use of several independent sets of gene expression data should make it possible to obtain an exhaustive view of the genes co-expression and thus a more accurate image of the structure of the chromosome. Results For both Bacillus subtilis and Escherichia coli the co-expression of genes varies as a function of the distance between the genes along the chromosome. The long-range correlations are surprising: the changes in the level of expression of any gene are correlated (positively or negatively) to the changes in the expression level of other genes located at well-defined long-range distances. This property is true for all the genes, regardless of their localisation on the chromosome. We also found short-range correlations, which suggest that the location of these co-expressed genes corresponds to DNA turns on the nucleoid surface (14–16 genes). Conclusion The long-range correlations do not correspond to the domains so far identified in the nucleoid. We explain our results by a model of the nucleoid solenoid structure based on two types of spirals (short and long). The long spirals are uncoiled expressed DNA while the short ones correspond to coiled unexpressed DNA.

International audience; Microarrays are becoming a ubiquitous tool of research in life sciences. However, the working principles of microarray-based methodologies are often misunderstood or apparently ignored by the researchers who actually perform and interpret experiments. This in turn seems to lead to a common over-expectation regarding the explanatory and/or knowledge-generating power of microarray analyses.In this note we intend to explain basic principles of five (5) major groups of analytical techniques used in studies of microarray data and their interpretation: the principal component analysis (PCA), the independent component analysis (ICA), the t-test, the analysis of variance (ANOVA), and self organizing maps (SOM). We discuss answers to selected practical questions related to the analysis of microarray data. We also take a closer look at the experimental setup and the rules, which have to be observed in order to exploit microarrays efficiently. Finally, we discuss in detail the scope and limitations of microarray-based methods. We emphasize the fact that no amount of statistical analysis can compensate for (or replace) a well thought through experimental setup. We conclude that microarrays are indeed useful tools in life sciences but by no means should they be expected to generate complete answers to complex biological questions. We argue that even well posed questions, formulated within a microarray-specific terminology, cannot be completely answered with the use of microarray analyses alone.

The number of statistical tools used to analyze transcriptome data is continuously increasing and no one, definitive method has so far emerged. There is a need for comparison and a number of different approaches has been taken to evaluate the effectiveness of the different statistical tools available for microarray analyses. In this paper, we describe a simple and efficient protocol to compare the reliability of different statistical tools available for microarray analyses. It exploits the fact that genes within an operon exhibit the same expression patterns. In order to compare the tools, the genes are ranked according to the most relevant criterion for each tool; for each tool we look at the number of different operons represented within the first twenty genes detected. We then look at the size of the interval within which we find the most significant genes belonging to each operon in question. This allows us to define and estimate the sensitivity and accuracy of each statistical tool. We have compared four statistical tools using Bacillus subtilis expression data: the analysis of variance (ANOVA), the principal component analysis (PCA), the independent component analysis (ICA) and the partial least square regression (PLS). Our results show ICA to be the most sensitive and accurate of the tools tested. In this article, we have used the protocol to compare statistical tools applied to the analysis of differential gene expression. However, it can also be applied without modification to compare the statistical tools developed for other types of transcriptome analyses, like the study of gene co-expression.

International audience; We propose and study a new approach for the analysis of families of protein sequences. This method is related to the LogDet distances used in phylogenetic reconstructions; it can be viewed as an attempt to embed these distances into a multidimensional framework. The proposed method starts by associating a Markov matrix to each pairwise alignment deduced from a given multiple alignment. The central objects under consideration here are matrix-valued logarithms L of these Markov matrices, which exist under conditions that are compatible with fairly large divergence between the sequences. These logarithms allow us to compare data from a family of aligned proteins with simple models (in particular, continuous reversible Markov models) and to test the adequacy of such models. If one neglects fluctuations arising from the finite length of sequences, any continuous reversible Markov model with a single rate matrix Q over an arbitrary tree predicts that all the observed matrices L are multiples of Q. Our method exploits this fact, without relying on any tree estimation. We test this prediction on a family of proteins encoded by the mitochondrial genome of 26 multicellular animals, which include vertebrates, arthropods, echinoderms, molluscs, and nematodes. A principal component analysis of the observed matrices L shows that a single rate model can be used as a rough approximation to the data, but that systematic deviations from any such model are unmistakable and related to the evolutionary history of the species under consideration.

Genomic analyses on part of Escherichia coli's chromosome had suggested the existence of a GATC regulated network. This has recently been confirmed through a transcriptome analysis. Two hypotheses about the molecular control mechanism have been proposed-(i) the GATC network regulation is caused by the presence of GATC clusters within the coding sequences; the regulation is the direct consequence of the clusters' hemi-methylation and therefore their elevated melting temperature, (ii) the regulation is caused by the presence of GATCs in the non-coding 500 bp upstream regions of the affected genes; it is the consequence of an interaction with a regulatory protein like Fnr or CAP. An analysis of the transcriptome data has not allowed us to decide between the two hypotheses. We have therefore taken a classic genomic approach, analyzing the statistical distribution of GATC along the chromosome, using a realistic model of the chromosome as theoretical reference. We observe no particular distribution of GATC in the non-coding upstream regions; however, we confirm the presence of GATC clusters within the genes. In order to verify that the particular distribution observed in E. coli is not a statistical artefact, but has a physiological role, we have carried out the same analysis on Salmonella, making the hypothesis that the genes containing a GATC clusters should be largely the same in the two bacteria. This has been indeed observed, showing that the genes containing a GATC cluster are part of a regulation network. The present is a case study, which demonstrates that the analysis of transcriptome data does not always permit to identify the primary cause of a phenomenon observed; on the other hand, a classic genomic approach linked with a comparative study of related genomes may allow this identification.

Background A new variant of Creutzfeldt-Jakob disease was described in the United Kingdom. It is often claimed that it is caused by consumption of food infected with the agent of bovine spongiform encephalopathy. However, this remains open to question because the number of cases of the variant is, at the present time, less than would be expected from a major food-borne source. Discussion The EUROCJD cooperative study presents currently available epidemiological data of Creutzfeldt-Jakob disease and its new variant, for nine European countries plus Australia and Canada. Unexpectedly, for the United Kingdom where all but a few cases of the new variant have been reported, these cases have to be included in the incidence curve of the sporadic forms of the disease in order to obtain the best fit with the median curve from all the countries. This variant could be merely a rare clinical phenotype within the sporadic disease. The published clinical and experimental data which suggest that it is linked with bovine spongiform encephalopathy, lead us to propose that this link could be a common etiological origin other than consumption of bovine infected food. In any case, public health recommendations hold and further investigation is required. Summary The lack of a relative increase of the Creutzfeldt-Jakob-disease mortality rate in the United Kingdom, does not fit well with the new variant being the consequence of consumption of food infected with the agent of bovine spongiform encephalopthy.

Summary: GeneANOVA is an ANOVA-based software devoted to the analysis of gene expression data. Availability: GeneANOVA is freely available on request for non-commercial use. Contact: didier@genopole.cnrs.fr

Previous analyses of retroviral nucleotide sequences, suggest a so-called "scrambled duplicative stepwise molecular evolution" (many sectors with successive duplications/deletions of short and longer motifs) that could have stemmed from one or several starter tandemly repeated short sequence(s). In the present report, we tested this hypothesis by focusing on the long terminal repeats (LTRs) (and flanking sequences) of 24 human and 3 simian immunodeficiency viruses. By using a calculation strategy applicable to short sequences, we found consensus overrepresented motifs (often containing CTG or CAG) that were congruent with the previously defined "retroviral signature." We also show many local repetition patterns that are significant when compared with simply shuffled sequences. First- and second-order Markov chain analyses demonstrate that a major portion of the overrepresented oligonucleotides can be predicted from the dinucleotide compositions of the sequences, but by no means can biological mechanisms be deduced from these results: some of the listed local repetitions remain significant against dinucleotide-conserving shuffled sequences; together with previous results, this suggests that interspersed and/or local mononucleotide and oligonucleotide repetitions could have biased the dinucleotide compositions of the sequences. We searched for suggestive evolutionary patterns by scrutinizing a reliable multiple alignment of the 27 sequences. A manually constructed alignment based on homology blocks was in good agreement with the polypeptide alignment in the coding sectors and has been exhaustively assessed by using a multiplied alphabet obtained by the promising mathematical strategy called the N-block presentation (taking into account the environment of each nucleotide in a sequence). Sector by sector, we hypothesize many successive duplication/deletion scenarios that fit our previous evolutionary hypotheses. This suggests an important duplication/deletion role for the reverse transcriptase, particularly in inducing stuttering cryptic simplicity patterns.

Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.

A program for assembling sequences by using a global approach has been developed. By successive steps, a more and more precise classification of DNA fragments permits the positioning of the sequences on the contig; after having detected the pairs of overlapping sequences, groups are formed such that all sequences in a group overlap. Sequences common to several groups enable the groups to be ordered in a series. Ambiguities in the order of groups can arise at this stage, due to the presence of repeated fragments; different solutions are then proposed. Putting the groups into order leads to a preclassification of sequences. The fragments are then aligned by group, by searching for words common to all sequences in the group, and using an algorithm of dynamic programming. A detailed example on a set of nine sequences accompanies the description of the method.

The table of 'biochemical pathways' published by Boehringer is considered as the most exhaustive document dealing with intermediary metabolism. The present work consisted of constructing a database in which is collected everything known to date about intermediary metabolism: metabolic pathways, bioreactions, metabolites, enzymatic activities, genes and regulation. Data on genes make it possible to establish a link with existing computer structures specialized for genomic sequences. The present structure of the database presented here consists of three environments. The first environment is graphic; it is modeled upon the Boehringer table, but is more convenient to use. The second environment provides the user with all kinds of manipulations of data (entries, corrections, deletions, consistency, limiting redundancy, etc.). These operations either are automatic or depend on a user-friendly interface (menus selected with the mouse) and so allow biologists at all levels to use the database and to develop it for their own particular needs. Finally, the third environment offers various procedures that make it possible to carry out multicriteria research on all the data in the database at once. This database can thus be substituted for the Boehringer table as a standard reference. It is also a tool that can be used to develop information systems not only in the domain of metabolism but also in the study of genomes (modeling, analysis of data, predictions, etc.).

Summary This paper describes software (written in Pascal and running on Macintosh computers) allowing localization of unknown DNA fragments from the Escherichia coli chromosome on the restriction map established by Kohara et al. (1987). The program identifies the segment's map position using a restriction pattern analysis obtained with all, or some, of the eight enzymes used by Kohara et al. (1987). Therefore, the sequenced genes available in the EMBL library may be localized on the E. coli chromosome restriction map. This allowed correction of the map (mainly by introducing missing sites in the published maps) at the corresponding positions. Analysis of the data indicates that there is only a very low level of polymorphism, at the nucleotide level, between the E. coli K12 strains used by the various laboratories involved in DNA sequencing. The program is versatile enough to be used with other genomes.

Background The tetranucleotide GATC is methylated in Escherichia. coli by the DNA methyltransferase (Dam) and is known to be implicated in numerous cellular processes. Mutants lacking Dam are characterized by a pleiotropic phenotype. The existence of a GATC regulated network, thought to be involved in cold and oxygen shift, had been proposed and its existence has recently been confirmed. The aim of this article is to describe the components of the GATC regulated network of E. coli in detail and propose a role of this network in the light of an evolutionary advantage for the organism. Results We have classified the genes of the GATC network according to the EcoCyc functional classes. Comparisons with all of E. coli's genes and the genes involved in the SOS and stress response show that the GATC network forms a group apart. The functional classes that characterize the network are the Energy metabolism (in particular respiration), Fatty acid/ Phospholipid metabolism and Nucleotide metabolism. Conclusions The network is thought to come into play when the cell undergoes coldshock and is likely to enter stationary phase. The respiration is almost completely under GATC control and according to our hypothesis it will be blocked at the moment of coldshock; this might give the cell a selective advantage as it increases its chances for survival when entering stationary phase under coldshock. We predict the accumulation of formate and possibly succinate, which might increase the cell's resistance, in this case to antimicrobial agents, when entering stationary phase.

In global gene expression profiling experiments, variation in the expression of genes of interest can often be hidden by general noise. To determine how biologically significant variation can be distinguished under such conditions we have analyzed the differences in gene expression when Bacillus subtilis is grown either on methionine or on methylthioribose as sulfur source. An unexpected link between arginine metabolism and sulfur metabolism was discovered, enabling us to identify a high-affinity arginine transport system encoded by the yqiXYZ genes. In addition, we tentatively identified a methionine/methionine sulfoxide transport system which is encoded by the operon ytmIJKLMhisP and is presumably used in the degradation of methionine sulfoxide to methane sulfonate for sulfur recycling. Experimental parameters resulting in systematic biases in gene expression were also uncovered. In particular, we found that the late competence operons comE, comF and comG were associated with subtle variations in growth conditions. Using variance analysis it is possible to distinguish between systematic biases and relevant gene-expression variation in transcriptome experiments. Co-variation of metabolic gene expression pathways was thus uncovered linking nitrogen and sulfur metabolism in B. subtilis.

The graphical representation of distance matrices in a Euclidean space allows the merging of two distance matrices since the two matrices have shared elements. The graphical representation of the merging of the two distance matrices is associated with a robust method of classification that allows one to distinguish species for which membership to a cluster cannot be established with certainty. These possibilities are exploited to test the consistency of phylogenetic trees, and to establish exact relations between species for which one possesses different independent distance measurements (distance matrices established from several types of sequences for instance). The whole set of programs is written in BASIC and runs on microcomputers.

BackgroundCurrent histo-pathological prognostic factors are not very helpful in predicting the clinical outcome of breast cancer due to the disease's heterogeneity. Molecular profiling using a large panel of genes could help to classify breast tumours and to define signatures which are predictive of their clinical behaviour.MethodsTo this aim, quantitative RT-PCR amplification was used to study the RNA expression levels of 47 genes in 199 primary breast tumours and 6 normal breast tissues. Genes were selected on the basis of their potential implication in hormonal sensitivity of breast tumours. Normalized RT-PCR data were analysed in an unsupervised manner by pairwise hierarchical clustering, and the statistical relevance of the defined subclasses was assessed by Chi2 analysis. The robustness of the selected subgroups was evaluated by classifying an external and independent set of tumours using these Chi2-defined molecular signatures.ResultsHierarchical clustering of gene expression data allowed us to define a series of tumour subgroups that were either reminiscent of previously reported classifications, or represented putative new subtypes. The Chi2 analysis of these subgroups allowed us to define specific molecular signatures for some of them whose reliability was further demonstrated by using the validation data set. A new breast cancer subclass, called subgroup 7, that we defined in that way, was particularly interesting as it gathered tumours with specific bioclinical features including a low rate of recurrence during a 5 year follow-up.ConclusionThe analysis of the expression of 47 genes in 199 primary breast tumours allowed classifying them into a series of molecular subgroups. The subgroup 7, which has been highlighted by our study, was remarkable as it gathered tumours with specific bioclinical features including a low rate of recurrence. Although this finding should be confirmed by using a larger tumour cohort, it suggests that gene expression profiling using a minimal set of genes may allow the discovery of new subclasses of breast cancer that are characterized by specific molecular signatures and exhibit specific bioclinical features.

We present in the first part an algebraic residual characterizationof usual trace-forms on local analytic hypersurfaces. We thus obtain a stronger version of the Abel-inverse theorem by Passare and Henkin in projective space and we relate it to the theorem by Wood on the algebraicity of local analytic hypersurfaces. We show how those inversion theorems can be anderstood as a rigidity propriety of a particular differential system linked to the wave chocequation and we obtain a new method to compute the dimension of the vector space of abelian forms of maximal degree on a projective hypersurface.The second part begins with a combinatorial characterization of satisfactory families of line bundles on a smooth complete toric variety to obtain an intrinsec notion of toric concavity allowing a toric generalisation of the trace. The use of toric residues and residue currents permits to show a toric version of Wood's and inverse Abel's theorem, providing a more precise description of the definingpolynomial in the hypersurface case.; On étudie la notion de trace et les problèmes d'Abel-inverse àl'aide du calcul résiduel dans les cadres projectifs et toriques.Dans la première partie, on obtient une caractérisation algébrique des formes traces sur une hypersurface analytique à l'aide du calcul résiduel élémentaire d'une variable. En conséquence, une version plus forte du théorème d'Abel-inverse de Henkin et Passare est prouvée. On montre que ce théorème est conséquence de la rigidité d'un système différentiel particulier lié à une équation de type ”onde de choc” et on établit le lien avec le théorème de Wood sur l'algébricité d'une famille de germes d'hypersurfaces analytiques. Enfin, on obtient une nouvelle méthode pour calculer la dimension de l'espace des formes abéliennes de degré maximal sur une hypersurface projective.Dans la seconde partie, on caractérise de manière combinatoire les familles de fibrés en droites permettant de définir une notion intrinsèque de concavité dans une variété torique complète lisse et on étudie les ensembles analytiques dégénérés correspondants. On étend ainsi la notion de trace au cas torique. Courants résidus, résidus toriques et résultants donnent une borne optimale sur le degrés des traces en les différents paramètres. Si la variété torique est projective, on obtient finalement une version torique des théorèmes de Wood et d'Abel-inverse, permettant une description plus précise du support du polynôme construit dans le cas hypersurface.