Research lines
From Wiki CEINGE
Research activity is organized along the following lines:
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.
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.
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.
