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As more and more insect genomes are fully sequenced and annotated, omics technologies, including transcriptomic, proteomic, peptidomics, and metobolomic profiling, as well as bioinformatics, can be used to exploit this huge amount of sequence information for the study of different biological aspects of insect model organisms. Omics experiments are an elegant way to deliver candidate genes, the function of which can be further explored by genetic tools for functional inactivation or overexpression of the genes of interest. Such tools include mainly RNA interference and are currently being developed in diverse insect species. In this manuscript, we have reviewed how omics technologies were integrated and applied in insect biology. [ABSTRACT FROM AUTHOR]

One restriction to the cultivation of common bean, Phaseolus vulgaris L., is its limited tolerance to low temperatures. In the present study, subtraction suppression hybridization was employed to enrich for stress responsive genes in both a chilling-susceptible common bean and a relatively more chilling-tolerant wild bean species, Phaseolus angustissimus. For each species, approximately 11 000 expressed sequence tags were generated. Comparative sequence analysis of the EST collection with the available annotated genome sequences of the model Fabaceae species Medicago truncatula and Glycine max identified protein homologues for approximately 65% and 80% of the Phaseolus sequences, respectively. This difference reflects the closer phylogenetic relationship between the genera Phaseolus and Glycine compared with Medicago. Annotation of the Phaseolus sequences was facilitated through this comparative analysis and indicated that several heat shock proteins, cytochrome P450s, and DNA binding factors were uniquely found among the sequences from the wild species P. angustissimus. The Phaseolus sequences have been made available on a GBrowse implementation using M. truncatula as the reference genome, providing rapid access to the sequence data and associated comparative genome data. [ABSTRACT FROM AUTHOR]

Abstract: Gene regulation is a major source of phenotypic diversity between and within species. This aspect of evolution has long been addressed from the sole point of view of the genome sequence. The incredible development of transcriptomics approaches now allows one to actually study the topology and the properties of regulatory networks on an evolutionary perspective. This new discipline is called comparative functional genomics or comparative transcriptomics. This article reviews some of the main advances made in this field, using yeast species, and especially the species sequenced in the frame of the Genolevures program, as a model. [Copyright &y& Elsevier]

Plant-transformation-ready, large-insert binary bacterial artificial chromosome (BIBAC) libraries are of significance for functional and network analysis of large genomic regions, gene clusters, large-spanning genes, and complex loci in the post-genome era. Here, we report the characterization of a plant-transformation-ready BIBAC library of the sequenced Arabidopsis genome for which such a library is not available to the public, the transformation of a large-insert BIBAC of the library into tobacco by biolistic bombardment, and the expression analysis of its containing genes in transgenic plants. The BIBAC library was constructed from nuclear DNA partially digested with BamHI in the BIBAC vector pCLD04541. It contains 6144 clones and has a mean insert size of 108 kb, representing 5.2× equivalents of the Arabidopsis genome or a probability of greater than 99% of obtaining at least one positive clone from the library using a single-copy sequence as a probe. The transformation of the large-insert BIBAC and analyses of the transgenic plants showed that not only did transgenic plants have intact BIBAC DNA, but also could the BIBAC be transmitted stably into progenies and its containing genes be expressed actively. These results suggest that the large-insert BIBAC library, combined with the biolistic bombardment transformation method, could provide a useful tool for large-scale functional analysis of the Arabidopsis genome sequence and applications in plant-molecular breeding. [ABSTRACT FROM AUTHOR]

We have produced the largest population of activation-tagged poplar trees to date, approximately 1800 independent lines, and report on phenotypes of interest that have been identified in tissue culture and greenhouse conditions. Activation tagging is an insertional mutagenesis technique that results in the dominant upregulation of an endogenous gene. A large-scale Agrobacterium-mediated transformation protocol was used to transform the pSKI074 activation-tagging vector into Populus tremula × Populus alba hybrid poplar. We have screened the first 1000 lines for developmental abnormalities and have a visible mutant frequency of 2.4%, with alterations in leaf and stem structure as well as overall stature. Most of the phenotypes represent new phenotypes that have not previously been identified in poplar and, in some cases, not in any other plant either. Molecular analysis of the T-DNA inserts of a subpopulation of mutant lines reveal both single and double T-DNA inserts with double inserts more common in lines with visible phenotypes. The broad range of developmental mutants identified in this pilot screen of the population reveals that it will be a valuable resource for gene discovery in poplar. The full value of this population will only be realized as we screen these lines for a wide range of phenotypes. [ABSTRACT FROM AUTHOR]

Sequencing of the rice genome has provided a platform for functional genomics research of rice and other cereal species. However, multiple approaches are needed to determine the functions of its genes and sequences and to use the genome sequencing results for genetic improvement of cereal crops. Here, we report a plant-transformation-competent, binary bacterial artificial chromosome (BIBAC) and bacterial artificial chromosome (BAC) based map of rice to facilitate these studies. The map was constructed from 20 835 BIBAC and BAC clones, and consisted of 579 overlapping BIBAC/BAC contigs. To facilitate functional analysis of chromosome 8 genomic sequence and cloning of the genes and QTLs mapped to the chromosome, we anchored the chromosomal contigs to the existing rice genetic maps. The chromosomal map consists of 11 contigs, 59 genetic markers, and 36 sequence tagged sites, spanning a total of ca. 38 Mb in physical length. Comparative analysis between the genetic and physical maps of chromosome 8 showed that there are 3 “hot” and 2 “cold” spots of genetic recombination along the chromosomal arms in addition to the “cold spot” in the centromeric region, suggesting that the sequence component contents of a chromosome may affect its local genetic recombination frequencies. Because of its plant transformability, the BIBAC/BAC map could provide a platform for functional analysis of the rice genome sequence and effective use of the sequencing results for gene and QTL cloning and molecular breeding. [ABSTRACT FROM AUTHOR]

Abstract: Human embryonic stem cells (hESCs) are derived from pre-implantation embryos given to research with the informed consent of the parents. These cells cannot give rise to a human being: they are not totipotent. They have an unlimited self-renewal capacity and they can generate the three embryonic germ layers, their respective derivatives and the extra-embryonic tissues: they are pluripotent. These cells represent an outstanding material for understanding functional genomics of not yet characterized human genes. They will be an important tool for pharmaceutical and clinical research. [Copyright &y& Elsevier]

Assigning functional significance to completed genome sequences is one of the next challenges in biological science. Conventional genetic tools such as deficiency chromosomes help assign essential complementation groups to their corresponding genes. We describe an F2 genetic screen to identify lethal mutations within cytogenetic region 61D-61F of the third chromosome of Drosophila melanogaster. One hundred sixteen mutations were identified by their failure to complement both Df(3L)bab-PG and Df(3L)3C7. These alleles were assigned to 14 complementation groups and 9 deficiency intervals. Complementation groups were ordered using existing deficiencies, as well as new deficiencies generated in this study. With the aid of the genomic sequence, genetic and physical maps in the region were correlated by use of PCR to localize the breakpoints of deficiencies within a 268-kb genomic contig (GenBank accession No. AC005847). Six essential complementation groups were assigned to specific genes, including genes encoding a porphobilinogen deaminase and a Sac1-like protein. [ABSTRACT FROM AUTHOR]

This is an account of the development and use of genetic maps, from humble beginnings at the hands of Thomas Hunt Morgan, to the sophistication of genome sequencing. The review charters the emergence of molecular marker maps exploiting DNA polymorphism, the renaissance of cytogenetics through the use of fluorescence in situ hybridisation, and the discovery and isolation of genes by map-based cloning. The historical significance of sequencing of DNA prefaces a section describing the sequencing of genomes, the ascendancy of particular model organisms, and the utility and limitations of comparative genomic and functional genomic approaches to further our understanding of the control of biological processes. Emphasis is given throughout the treatise as to how the structure and biological behaviour of the DNA molecule underpin the technological development and biological applications of maps. [ABSTRACT FROM AUTHOR]

The molecular anatomy of the vertebrate embryo was systematically analysed through gene expression during early development of the Xenopus frog using whole-mount in situ hybridization. Expression patterns are documented and assembled into the database Axeldb (http://www.dkfz-heidelberg.de/abt0135/axeldb.htm). Synexpression groups representing genes with shared, complex expression pattern that predict molecular pathways involved in patterning and differentiation have been identified. These sets of co-regulated genes show a striking similarity with operons, and may be a key determinant facilitating evolutionary change leading to animal diversity. To cite this article: N. Pollet et al., C. R. Biologies 326 (2003). [Copyright &y& Elsevier]

The sequence of the human genome has been determined. The next task is to determine the function of the genes. Classifying cellular forms of proteins encoded by human cDNA clones is a primary step toward understanding the biological role of proteins and their coding genes. We report here our ongoing work on an automatic system to facilitate this classification. Our system handles the transfection, incubation, acquisition of microscopic images of the cells, and the classification of forms there appearing in the images. Our system correctly classified proteins by their forms at a rate of 90% in feasibility studies. To cite this article: R. Minamikawa-Tachino et al., C. R. Biologies 326 (2003). [Copyright &y& Elsevier]

To functionally characterize numerous novel proteins encoded by cDNAs sequenced by the German Consortium, 800 were tagged with green fluorescent protein. The subcellular localizations of the fusion proteins were examined in living cells, enabling their classification in subcellular groups. Their activity in cell growth, cell death, and protein transport was screened in high throughput using robotic liquid handling and reading stations. The resulting information is integrated with functional genomics and proteomics data for further understanding of protein functions in the cellular context. To cite this article: S. Wiemann et al., C. R. Biologies 326 (2003). [Copyright &y& Elsevier]

Systems biology is the iterative and integrative study of biological systems as systems in response to perturbations. It is founded on hypotheses formalized in models built from the results of global functional genomics analyses of the complexity of the genome, transcriptome, proteome, metabolome, etc. Its implementation by cross-disciplinary teams in a standardized mode under quality assurance should allow accessing the small variations of the large number of elements determining functioning of biological systems. Galactose utilization in yeast, and sea urchin development are two examples of emerging systems biology. To cite this article: C. Auffray et al., C. R. Biologies 326 (2003). [Copyright &y& Elsevier]

This thematic issue issue of the Comptes rendus Biologies contains review articles, original papers and conference reports presented at the first two Transcriptome conferences From Functional Genomics to Systems Biology and IMAGE Consortium Invitational workshops (Paris, November 2000 and Seattle, March 2002), and discussed during the inaugural meetings of the Systemoscope International Consortium (Paris, June 2003). We describe the founding principles, missions, working plan and policy for partnership and industrial development of Systemoscope to promote the study of the complexity of biological systems by integrating scientific, medical, ethical and economic issues in implementation of interdisciplinary projects for human health. To cite this article: C. Auffray et al., C. R. Biologies 326 (2003). [Copyright &y& Elsevier]

Large-scale analysis of gene expression with cDNA arrays is spreading over many biological fields, including rheumatology. In this report, we wish to explain the principle and main advantages of this tool in the context of our discipline. Until 1995, analysis of gene expression was conducted for a few genes at a time but DNA chips now allow one to monitor the expression of thousands of genes in a single experiment and analyze the transcriptome, i.e. the whole of the transcripts in a given cell or tissue. Whatever the platform used (macro- or microarrays, oligo-chips), this technology rests upon the hybridization of i) a set of cDNA clones tethered to a solid support (nylon or glass) as probes, and ii) labelled cDNAs that are reverse-transcribed from bulk mRNAs extracted from a cell or tissue sample as a target. The end result is information on the relative abundance of every mRNA between two or more samples. The transcriptome analysis has two main objectives in rheumatology: i) identifying a gene expression profile that is a hallmark of a pathology and using it for a diagnostic or prognostic purpose, and ii) gathering genes with similar changes of expression, which allows one to specify the identity of novel proteins involved in a well-known intracellular cascade of regulation or even to identify new cascades. [Copyright &y& Elsevier]

Résumé: En rhumatologie, nous sommes déjà dans l’ère de la prédiction. Les progrès en cours devraient nous permettre d’aboutir à terme à une médecine personnalisée basée sur l’administration de traitements ayant une action de plus en plus ciblée à des patients sélectionnés au moyen de biomarqueurs. L’identification et la validation de ces biomarqueurs permettra ainsi le développement de tests dîts « compagnons » à l’image de ce qui a déjà été réalisé en cancérologie. Cette médecine personnalisée est possible grâce à l’avènement des stratégies « omics/omiques » (protéome, transcriptome…). Dans ce cadre, les approches sans à priori ou à priori (basées sur des données physiopathologiques permettant une approche ciblée) sont complémentaires. Elles ont permis ainsi d’identifier des signatures moléculaires propres à certaines pathologies ou à des sous-groupes de malades et un grand nombre de marqueurs d’intérêt diagnostique, pronostique ou théranostique, non seulement dans la PR mais aussi dans le syndrome de Gougerot-Sjögren, l’arthrose et les spondylarthropathies. Malgré des avancées sur le plan technologique et l’utilisation d’outils bio-informatiques et bio-statistiques de plus en plus performants, le principal écueil de ces approches de génomique fonctionnelle reste l’absence de validation des données dans de larges populations indépendantes. C’est donc une étape essentielle dans les années à venir, qui devrait s’inspirer des approches pangénétiques de type GWAS qui ont permis de valider un grand nombre de variants génétiques dans différentes pathologies. Toutefois, ces allèles à risque ont permis avant tout une meilleure compréhension des maladies et ne sont pas utilisés actuellement en tant que biomarqueurs. Dans le domaine de la génétique, une des perspectives est sans doute la mise en évidence d’une frome particulière de polymorphisme représentée par les CNV (Copy Number Variation). Les perspectives ne se limitent pas au diagnostic, au pronostic et à la prédiction de réponse. Elles résideront également dans notre capacité à évaluer l’activité de la maladie lorsque les paramètres usuels font défaut et à optimiser le monitorage des immunosuppresseurs et des biomédicaments. A cet égard, des tests multiplex basés sur des combinaisons de biomarqueurs semblent prometteurs. La médecine devrait considérablement évoluer dans les prochaines années. Nous sommes déjà dans l’ère de la prédiction. Elle sera certainement de plus en plus participative (auto-mesure, auto-évaluation…). Les progrès en cours devraient aboutir à une médecine personnalisée. Celle-ci répond à un objectif d’optimisation des soins et représente un enjeu de santé publique. En effet, 20 à 75% des patients sont traités de façon peu optimale d’où l’idée de majorer le bénéfice thérapeutique en proposant des traitements ayant une action de plus en plus ciblée à des groupes de patients sélectionnés au moyen de biomarqueurs. [ABSTRACT FROM AUTHOR]