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The 5′- and 3′-untranslated regions (5′- and 3′-UTRs) of eukaryotic mRNAs are known to play a crucial role in post-transcriptional regulation of gene expression modulating nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and stability. UTRdb is a specialized database of 5′ and 3′ untranslated sequences of eukaryotic mRNAs cleaned from redundancy. UTRdb entries are enriched with specialized information not present in the primary databases including the presence of nucleotide sequence patterns already demonstrated by experimental analysis to have some functional role. All these patterns have been collected in the UTRsite database so that it is possible to search any input sequence for the presence of annotated functional motifs. Furthermore, UTRdb entries have been annotated for the presence of repetitive elements. All Internet resources we implemented for retrieval and functional analysis of 5′- and 3′-UTRs of eukaryotic mRNAs are accessible at http://bighost.area.ba.cnr.it/BIG/UTRHome/.

The LIBI project (International Laboratory of BioInformatics), which started in 2005 and will end in 2009, was initiated with the aim of setting up an advanced bioinformatics and computational biology laboratory, focusing on basic and applied research in modern biology and biotechnologies. One of the goals of this project has been the development of a Grid Problem Solving Environment, built on top of EGEE, DEISA and SPACI infrastructures, to allow the submission and monitoring of jobs mapped to complex experiments in bioinformatics. In this work we describe the architecture of this environment and describe several case studies and related results which have been obtained using it.

The present paper describes AMmtDB, a database collecting the multi-aligned sequences of vertebrate mitochondrial genes coding for proteins and tRNAs, as well as the multiple alignment of the mammalian mtDNA main regulatory region (D-loop) sequences. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. As far as the genes coding for tRNAs are concerned, the multi-alignments based on the primary and the secondary structures are both provided; for the mammalian D-loop multi-alignments we report the conserved regions of the entire D-loop (CSB1, CSB2, CSB3, the central region, ETAS1 and ETAS2) as defined by Sbisà et al. [ Gene (1997), 205, 125-140). A flatfile format for AMmtDB has been designed allowing its implementation in SRS (http://bio-www.ba.cnr.it:8000/BioWWW/#AMMTDB ). Data selected through SRS can be managed using GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system. The multiple alignments have been produced with CLUSTALV and PILEUP programs and then carefully optimized manually.

The International Laboratory of BioInformatics (LIBI - www.libi.it) aims at setting up of an advanced Bioinformatics and Computational Biology Laboratory, focusing on the central activities of basic and applied research in modern Biology and Biotechnologies. The main activities include the construction and the maintenance of general genomic, proteomic and transcriptomic databases (e.g. ENSEMBL) as well as specialized databases developed by LIBI partners (e.g. MitoRes, UTRdb, UTRSite, ASPicDB, CSTdb, etc.); the design and implementation of new algorithms and software for the analysis of genomes and their expression products and for the prediction of the structure of proteins; the development of a Grid Problem Solving Environment in order to exploit the distributed computational infrastructure.

The study of the mechanisms underlying the coevolution processes of these gene families and how they correlate with the increased complexity of the vertebrate nervous system. In order to improve our current knowledge of the molecular evolution of neurotrophins and receptors, we have collected all information available in the literature and analyzed the genome database for each of them. Statistical analysis of aminoacid and nucleotide sequences of the neurotrophin and Trk family genes was applied to both complete genes and mature sequences, and different phylogenetic methods were used to compare aminoacid and nucleotide sequences variability among the different species. All collected data favor a model in which several rounds of genome duplications might have facilitated the generation of the many different neurotrophins and the acquisition of specific different functions correlated with the increased complexity of the vertebrate nervous system during evolution. We report findings that refine the structure of the evolutionary trees for neurotrophins and Trk receptors families, indicate different rates of evolution for each member of the two families.

Nowday oncologic surgery is defining new criterias in the treatment of rectal cancer, preservation of sfincterial function, ultra-low resections with distal margin at only 2 cm distally to the tumor, role of mesorectum as preferential site of limphatic diffusion, preservation of lombo-aortic and pelvic nerves. Laparoscopy is showing good results m bowel surgery so as previously got on biliary tract: less visceral manipulation, less stimutation of immunologic system, less pain, early resumption of peristalsis and food intake, better ricovery, less hospital stay. We experimented on pig ultra-low laparoscopic resection of the rectum, with preservation of sfincterial function, and mechanical anastomosis at the upper edge of the sfincterial ring. The evaluation of surgical technique, post-operative supervision, and follow-up instrumental control (anal manometry, endo-rectal ultrasonography, sfincterial elettromano-metry, Rx barium enema) show technical feseability and confirm a better recovery with regular defecatory function.

In part of the patients with a disturbance in the mitochondrial energy metabolism, the defect can not be ascribed to a default in the respiratory chain, citric acid cycle or pyruvate dehydrogenase complex. Incubations of muscle mitochondria with various substrates under different conditions render it likely that defects in transport systems in the mitochondrial membranes, besides the known enzyme deficiencies, can be the cause of the biochemical abnormalities in human mitochondriopathies. This approach has resulted in the detection of two rare deficiencies: one in the ATP/ADP-translocator and another in the voltage-dependent anion channel (VDAC) protein.