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Abstract: The ESTree db represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics. With this aim, the db has been structured to be a repository of information and links related to the sequences and to provide a userfriendly interface to allow easy querying of all the db fields. Within the month of March 2005 the third release of ESTree will be online and will include 18630 sequences, encompassing 8 libraries at different peach fruit developmental stages. A second version of the db, including only the 6155 sequences produced by the FPTP-CERSA group will also be online. The major data resources that are included in the ESTree db are: annotation both with BLASTx versus the NCBI nr database and with BLASTx versus the GO viridiplantae subset of sp-trembl; contig assembly and display; SNP analysis with AutoSNP and links to the KEGG metabolic pathways and the enzyme entries of NiceZyme (Expasy). Gene Ontology statistics are also presented both for the whole set of sequences that are included in the db and for library-specific subsets.

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Abstract: Activated Protein C (APC) is a vitamin K-dependent anticoagulant plasma serin protease that exerts its action through the inactivation of factors Va and VIIIa in presence of Ca++ and phospholipids. Deficiency of protein C is associated with the risk of developing venous thrombosis. APC shares homologies with other vitamin K-dependent coagulation proteins as a results of a common evolutionary pathway. The chymotrypsin-like serine proteases maintain a strictly conserved active site geometry among their catalytic Ser, His and Asp residues. The fact that this core is highly conserved both in sequence and structure among members of the serine protease family suggests that its shape has been finely tuned during evolution. 33 mutations (18 novel) in the promoter and coding regions of the PC gene were identified by PCR and sequencing in 46 patients reporting venous thromboembolic events. Here we present a computational analysis of three selected mutants (G43E, D194N, G216D) that are localized in the catalytic domain and determine a charge modification in the vicinity of the catalytic triad.

Abstract: The organic polychlorinated compounds like dichlorodiphenyltrichloroethane (DDT) with its metabolites and polychlorinated biphenyls (PCBs) are present in atmospheric particulate as persistent contaminants. They have been recognized to have detrimental health effects both on wildlife and humans acting as endocrine disrupters (EDC) due to their ability of mimicking the action of the steroid hormone thus interfering with hormone response. There are several experimental evidences that they bind and activate human steroid receptors. Despite the growing concern about the toxicological activity of EDC, molecular data of the interaction of this compounds with biological targets are still lacking. In order to better understand the ability of EDC to bind in the receptor hormone binding pocket, we have simulated by docking approach the molecular models of the complexes of estrogen, progesterone and androgen receptors with DDT and PCB family compounds.

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Abstract: A collection of about 8000 Expressed Sequence Tags (EST) sequences has been prepared starting from clones belonging to four cDNA peach libraries. Libraries have been prepared from Prunus persica mesocarps at four different developmental stages with the aim to collect data for deep investigation of the maturation process at the molecular level. A fully automated pipeline (ESTree DB) has been prepared to process EST sequences using public software integrated by in-house developed Perl scripts and data have been collected in a MySQL database called ESTree available at this URL: http://www.itb.cnr.it/ESTree. These data are produced in the frame of the activities of the National Consortium for Peach Genomics (ESTree), involving also the Universities of Padova, Udine and other research Institutions.

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Abstract: Data integration is a fundamental process in Bioinformatics because the enormous quantity of information available is often difficult to interpret. However, using a high performance platform such as GRID, it will be possible to complete important studies to improve the understanding of the biological process. Through facing this challenge, the importance of creating a data management system that guarantees efficiency on a distributed platform has emerged. This study concerns the definition of an innovative tool for the databases management in GRID technology and the implementation of a concrete case of use in integrating biological data. The core software is a Web Service that allows the execution of SQL query on a series of distributed databases, available on different computer, through the SOAP protocol. In this way, through the client, that can be run from a GRID Computing Element, it is possible to interact with the database. The data extracted from each local database are then integrated by the Web Server and sent to the application that asks for them, optimizing the communication times. Through this software it is possible to perform elaborations that involve data access and integration on GRID easily. This Web Service has been tested during the development of an integration pipeline among two important biological databases as UNIPROT and ENSEMBL in order to coordinate different information about a certain protein sequences. Thanks to this distributed system of data access it has been possible to conduct a systematic GRID analysis of the kinase sequence references in these important databases.

Abstract: Prediction of protein-coding genes in newly sequenced DNA becomes very important in large genome sequencing projects. In order to integrate the promoter with the gene structure information we have developed the GeneBuilder system able to predict the main functional signals (promoters, splice sites, TATA-box and Poly-A sites) and the coding regions (CDS). The program use several parameters and modules for gene structure analysis, homology search and automatic annotations. To improve the accuracy of the gene structure prediction the GeneBuilder program is also able to define new gene models by using different exon homology levels with a protein sequence selected from a list of homologous proteins. By using a Java based graphical interface the user can visualise the gene models and the sequence pattern of features predicted (http://www.itba.mi.cnr.it/webgene)

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Abstract: Prediction of protein-coding genes in newly sequenced DNA becomes very important in large genome sequencing projects. These problems are complicated due to exon-intron of the eukaryotic genes. Currently existing collections of expressed sequence tags (ESTs) are very large and thus very useful for gene mapping. Gene identification in the newly-discovered DNA sequences is an important problem in current molecular biology studies. A number of programs have been developed for predicting the protein coding genes. The most common approach is based on the combination of the potential functional signals with global statistical properties of protein coding regions. Another approach for gene structure prediction is based on the homology detection throughout the databases of nucleotide or amino acid sequences. By using the information available on homologous protein sequences, it is possible to significantly improve the accuracy of gene structure prediction. Currently existing collections of expressed sequence tags (ESTs) are very large and can be very useful for gene mapping. Homology searches against the EST Division of GenBank (dbEST) and Unigene database can be used for this purpose. ESTs (Expressed Sequence Tags) offer a rapid route to gene identification (Adams, et al, 1991, Adams , et al, 1992), analysis of expression and regulation data, and can highlight multigene family diversity and gene alternative splicing). EST matches may identify more than half of the known human genes (Hillier et al, 1996). The price of the high-volume and high-throughput nature of the data, however, is that ESTs contain high error rates (Aaronson, et al 1996), do not have a defined protein product, are not well annotated and present only a raw substrate for sequence matching. The ESTMAP system involves the following procedures: 1) Repeat masking. The repeated elements (for example, the human Alu elements) can be automatically masked in a query sequence before the homology search. Homology searches against the collection of repeated element (Jurka et al., 1992) are used for repeats detection. We implemented a program REPEAT for that purpose. A censored sequence (with 'N's instead of repeated elements) is automatically produced by REPEAT. 2) Homology searches. BLASTN (Altschul et al. 1990) is used for homology searches of the censored query sequence against the EST Division of GenBank (dbEST) and the Unigene database of sequences (www. ncbi.nlm.nih.gov) This step is most time-consuming since these EST datsets are very large. 3) EST mapping. The BLASTN output is used as input information by a EST_GENE program. Information about an EST sequence is used only when the similarity between the EST sequence and the query sequence is greater then 95%. The module EST_GENE is also able to predict the introns in DNA comparing ESTs and a query sequence based on the alignment method suggested by Huang (1994) (a linear-space divide-and-conquer strategy). The GT/AG splicing sites rule is used by EST_GENE, however non-canonical splicing signals (Milanesi and Rogozin, 1998) can also be predicted in cases of unambiguous alignment. 4) Output of results. The graphical visualization of the results is particularly important for the analysis of alternative splicing in a query sequence. By using a Java based graphical interface the user can visualize the EST maps and the sequence pattern of predicted features. Homology searches are very important for functional mapping, homology with a known functional region can suggest the function of a query sequence. In particular, when the homologous protein sequence is already known and EST matches are detected, then the gene structure can be reconstructed with high accuracy. Information about EST matches is automatically used by the GeneBuilder system (Milanesi et al., 1999). Acknowledgment This work was supported by Italian CNR Genetic Engineering Project

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Abstract: Eukaryotic protein kinase (ePKs) constitute one of the largest recognized protein families represented in the human genome and are important players in virtually every signaling pathway involved in normal development and disease. The key feature that distinguishes ePKs superfamily members from other proteins is the sequence of contiguous stretch of approximately 250 aminoacids that constitutes the catalytic domain [1-2] . Around half the human kinases contain other domains in addition to the catalytic domain, which often are involved in kinases regulation, interactions with other partners or subcellular localization [3]. Domains present one of the most useful levels at which to understand protein function and domain family-based analysis, so we developed an automated analysis system for studying domain statistic distribution of kinase superfamily.

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