Structure
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| Finally, a specific interest in image analysis and its application to the study of cell movement led to the production of a number of tools aimed to store and process multidimensional images, generated in video time-lapse microscopy experiments, in order to extract statistics about motion features of fibroblasts and other cell lines. The role of oncogenes such as Ras and Src in cell motility has been evaluated, by using single cell transformed fibroblast cell lines. | Finally, a specific interest in image analysis and its application to the study of cell movement led to the production of a number of tools aimed to store and process multidimensional images, generated in video time-lapse microscopy experiments, in order to extract statistics about motion features of fibroblasts and other cell lines. The role of oncogenes such as Ras and Src in cell motility has been evaluated, by using single cell transformed fibroblast cell lines. | ||
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| PAOLELLA G., MARTINI G (2003). Bioinformatica. In TRECCANI Enciclopedia del Novecento ROMA: Istituto Enciclopedia Italiana (ITALY). | PAOLELLA G., MARTINI G (2003). Bioinformatica. In TRECCANI Enciclopedia del Novecento ROMA: Istituto Enciclopedia Italiana (ITALY). | ||
| - | == Bioinfo Services == | + | == [[Bioinfo Services]] == |
| - | == IT Services == | + | == [[IT Services]] == |
Revision as of 17:26, 1 June 2007
The group is mainly involved in genome analysis, aiming to identify novel functional elements through a comparative approach. Work in this area led to the generation of two databases containing a large number of conserved sequence elements (CSTs) identified within the human genome and their counterparts identified in the genome of other vertebrates, ranging from mouse to fish. Occasionally such elements are also found in more distant organisms such as insects and other invertebrates. CSTs have been searched in the genomic regions including and surrounding genes involved in genetically transmitted diseases (DG-CST) and genes coding for the full complement of human protein kinases (KinWeb). The two databases are being maintained and are made available online to the scientific community (http://dgcst.ceinge.unina.it, http://kinweb.ceinge.unina.it). An important goal of genome analysis is the identification of elements corresponding to non coding RNAs. Within this scope, 50 bacterial genomes have been used as a model system, and analyzed in search of families of repeated sequence elements characterized by the presence of stable stem-loop secondary RNA structures. This approach led to the identification of all previously described families and of several novel ones, which have been collected within an annotated database, currently in the process of being made available to the public. Finally, a specific interest in image analysis and its application to the study of cell movement led to the production of a number of tools aimed to store and process multidimensional images, generated in video time-lapse microscopy experiments, in order to extract statistics about motion features of fibroblasts and other cell lines. The role of oncogenes such as Ras and Src in cell motility has been evaluated, by using single cell transformed fibroblast cell lines.
Contents |
Research lines
Identification of functional elements in euchariotic genomes through analysis of conserved sequence tags (CSTs)
Comparative genomics offers the opportunity to identify sequences characterized by strong conservation between different species. Apart from coding sequences, these tend to include a relatively large number of functional elements, such as structural and regulatory non coding RNAs and DNA sequence elements involved in control of gene expression. Along this line a large number of CSTs, characterized by a variable degree of conservation in other species, were identified in the human genome, and collected in two databases (DG-CST, originally produced in a collaborative effort with a small group of italian research institutes and currently maintained at CEINGE, and KinWeb, in collaboration with ITB, Milano). The identified CSTs are currently being analyzed in a number of projects aimed to their functional evaluation by further computational characterization and, in collaboration with other groups, to evaluate their relevance for transcriptional regulation and their role in genetically transmitted diseases.
Analysis of populations of repeated bacterial RNA sequences, characterized by stable stem-loop structures.
Bacterial genomes are generally compact and most of their sequence is involved in protein coding, but a growing number of sequences, mostly located within the intergenic regions, have been shown to play a role in the control of gene expression. Many of these sequences are active as RNA and often contain simple stem-loop structures, essential to their functionality. A large collection of families of repeated stem-loop containing sequences has been identified by clustering stemloop structures according to sequence similarity in 40 bacterial species, representative of the whole bacterial world. Secondary structure analysis reveals the presence of a large number of sequences where a conserved secondary structure may be demonstrated within the family.
Image processing applied to the study of cell movement.
Cell motility is a complex phenomenon, which may be explored in a variety of experimental situations, ranging from in vitro cultured cells to cell migration in whole embryos or in the adult animal. By applying video time lapse techniques to the study of live fibroblasts, the role of specific molecules such as oncogenes and components of the extracellular matrix has been evaluated. The need for applying image processing techniques to the study, stimulated the development of a number of computational tools, including a system for centralized storage of experimental images, and a web based image processing tool. Statistical analysis of cell movement and study of multidimensional images may be performed within these systems.
References
PETRILLO M., SILVESTRO G., DI NOCERA P., BOCCIA A. and PAOLELLA G. Stem-loop structures in prokaryotic genomes (2006) BMC GENOMICS 2006, 7:170
BARONE MV, GIMIGLIANO A, CASTORIA G, PAOLELLA G, MAURANO F, PAPARO F, MARIA M, NANAYAKKARA M, MINEO A, MIELE E, TRONCONE R, AURICCHIO S. (2006) Growth factor-like activity of gliadin, an alimentary protein: implications for celiac disease (CD). Gut. 2006 Aug 4;
MILANESI L., PETRILLO M., SEPE L., BOCCIA A., D'AGOSTINO N., PASSAMANO M., DINARDO S., CASADIO R. and PAOLELLA G. (2005). Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity. BMC BIOINFORMATICS. 6(Suppl 4):S20 ISSN: 1471-2105.
BOCCIA A., PETRILLO M, DI BERNARDO D., GUFFANTI A., MIGNONE F., CONFALONIERI S., LUZI L, PESOLE G., PAOLELLA G., BALLABIO A., BANFI S. (2005). DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes. NUCLEIC ACIDS RESEARCH. vol. 33 pp. D505-D510 ISSN: 0305-1048
PAOLELLA G., MARTINI G (2003). Bioinformatica. In TRECCANI Enciclopedia del Novecento ROMA: Istituto Enciclopedia Italiana (ITALY).
