Proteins from bovine tissues and biological fluids: defining a reference electrophoresis map for liver,kidney, muscle,plasma and red blood cells

A number of high resolution two-dimensional electrophoresis (2-DE) reference maps for bovine tissues and biological fluids have been determined for animals in basal state. Among the 1863 distinct protein features detected in samples of liver, kidney, muscle, plasma and red blood cells, 509 species were identified and associated to 209 different genes. Difficulties in the identification were related to the poorly characterized Bos taurus genome and were solved by a combined matrix-assisted laser desorption/ionisation-mass spectrometry and liquid chromatography-electrospray ionization tandem mass spectrometry approach. The experimental output allowed us to establish a 2-DE database accessible through the World Wide Web network at the URL address (http://www.iabbam.na.cnr.it/Biochem). These reference maps may serve as a tool in future veterinary medical studies aimed at the evaluation of changes in protein repertoire for altered animal physiological conditions and infectious diseases, to the definition of molecular markers for novel diagnostic kits and vaccines, as well as the characterization of protein modifications in bovine materials following technological processes used in the food industry.     

Mining the bovine genome with the "Bovine SNP Retriever"

Online resources for the bovine genome analysis are provided at the most important Web sites. Nonetheless, retrieval of single-nucleotide polymorphism (SNP)-related information is not always easy when searches must focus on complementary features. In this work, we present the Bovine SNP Retriever: a user-friendly tool for bovine SNP retrieval that also facilities the retrieval of SNP-related information within user-selected quantitative traits loci regions and reverse electronic polymerase chain reaction analysis on the bovine genome. The Bovine SNP Retriever is available at http://www.itb.cnr.it/ptp/bovine_snp_retriever/.     

DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions

SUMMARY: DNAfan (DNA Feature ANalyzer) is a tool combining sequence-filtering and pattern searching. DNAfan automatically extracts user-defined sets of sequence fragments from large sequence sets. Fragments are defined by annotated gene feature keys and co- or non-occurring patterns within the feature or close to it. A gene feature parser and a pattern-based filter tool localizes and extracts the specific subset of sequences. The selected sequence data can subsequently be retrieved for analyses or further processed with DNAfan to find the occurrence of specific patterns or structural motifs. DNAfan is a powerful tool for pattern analysis. Its filter features restricts the pattern search to a well-defined set of sequences, allowing drastic reduction in false positive hits. AVAILABILITY: http://bighost.ba.itb.cnr.it:8080/Framework.     

PLANT-PIs: a database for plant protease inhibitors and their genes

PLANT-PIs is a database developed to facilitate retrieval of information on plant protease inhibitors (PIs) and related genes. For each PI, links to sequence databases are reported together with a summary of the functional properties of the molecule (and its mutants) as deduced from literature. PLANT-PIs contains information for 351 plant PIs, plus several isoinhibitors. The database is accessible at http://bighost.area.ba.cnr.it/PLANT-PIs.     

UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs

The 5' and 3' untranslated regions of eukaryotic mRNAs may play a crucial role in the regulation of gene expression controlling mRNA localization, stability and translational efficiency. For this reason we developed UTRdb, 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 implemented for retrieval and functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs are accessible at http://bigarea.area.ba.cnr.it:8000/EmbIT/UTRH ome/     

Update of KEYnet: a gene and protein names database for biosequences functional organisation

KEYnet is a database where gene and protein names are hierarchically structured. Particular care has been devoted to the search and organisation of synonyms. The structuring is based on biological criteria in order to assist the user in data search and to minimise the risk of information loss. Links to the EMBL data library by the entry name and the accession number are implemented. KEYnet is available through the WWW at the following site: http://www.ba.cnr.it/keynet.html     

Analysis of oligonucleotide AUG start codon context in eukariotic mRNAs

The AUG start codon context features have been investigated by analyzing eukaryotic mRNAs belonging to various taxonomic groups. The functional relevance of each specific position surrounding the AUG start codon has been established as a function of the measured shift between base composition observed at that particular position, and base composition averaged over all the 5'untranslated regions. A more detailed analysis carried out on human genes belonging to different isochores showed significant isochore-specific fea-tures that cannot be explained only by a mutational bias effect. The most represented heptamers spanning from position -3 to +4 with respect to the initiator AUG have been determined for mRNAs belonging to different taxonomic groups and a web page utility has been set up (http://bigarea.area.ba.cnr.it:8000/BioWWW/ATG.html) to determine the relative abundance of a user submitted oligonucleotide context in a given species or taxon.     

PLMItRNA,a database on the heterogeneous genetic origin of mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes

The updated version of PLMItRNA reports information and multialignments on 609 genes and 34 tRNA molecules active in the mitochondria of Viridiplantae (27 Embryophyta and 10 Chlorophyta), and photosynthetic algae (one Cryptophyta, four Rhodophyta and two Stramenopiles). Colour-code based tables reporting the different genetic origin of identified genes allow hyper-textual link to single entries. Promoter sequences identified for tRNA genes in the mitochondrial genomes of Angiospermae are also reported. The PLMItRNA database is accessible at http://bighost.area.ba.cnr.it/PLMItRNA/.     

WWW and the aerobiologist: operating instructions

For several years now, the World Wide Web (WWW) has left the realm of information technology and represents a fundamental everyday working tool for a wide variety of disciplines. Aerobiology, though a newcomer in this virtual space, is proceeding at a fast pace towards the creation of an easily accessible and effective information network. The web gives access to text, imagery, movie and sound with relatively low-cost and user-friendly interfaces conceived as graphical magazines. A practical way to start navigating and looking for information is to operate a ‘search engine’ which is a large database containing addresses on a wide spectrum of subjects. As an alternative, a few selected sites exist that can initialize your search by providing a thematic list of addresses. After leaving the entry ‘port’ you are directed from site to site and eventually end up with a lot more information than you initially thought. Excerpts: information on public and private institutions, access to databases and image catalogs, bibliographical information, overview of monitoring networks, directions on national and international research programs, news (calendar of meetings, courses, etc.). Information is provided for the non-expert user who asks himself the key questions: ‘Where do I start to browse the net?’ or ‘Can I become a provider of information on the net and, if so, is it terribly difficult?’ The idea is that everybody can in principle become a ‘surfer’ or a ‘provider’ dedicating a reasonable amount of time and effort to the task. What one ends up with is an easy-to-use and powerful tool that is already helping the whole aerobiological community to pursue its goals and reach out for necessary interdisciplinary approaches to unsolved scientific issues. The server AEROBIOLOGY INTERNATIONAL (http://www.fisbat.bo.cnr.it/AERO/) is presented as an example on how to proceed with the creation of a new server and its management.     

FASMA: a service to format and analyze sequences in multiple alignments

Multiple sequence alignments are successfully applied in many studies for under- standing the structural and functional relations among single nucleic acids and protein sequences as well as whole families. Because of the rapid growth of sequence databases, multiple sequence alignments can often be very large and difficult to visualize and analyze. We offer a new service aimed to visualize and analyze the multiple alignments obtained with different external algorithms, with new features useful for the comparison of the aligned sequences as well as for the creation of a final image of the alignment. The service is named FASMA and is available at http://bioinformatica.isa.cnr.it/FASMA/.     

UTRdb: a specialized database of 5' and 3' untranslated regions of eukaryotic mRNAs.

The 5' and 3' untranslated regions of eukaryotic mRNAs may play a crucial role in the regulation of gene expression controlling mRNA localization, stability and translational efficiency. For this reason we developed UTRdb (http://bigarea.area.ba.cnr.it:8000/BioWWW/#U TRdb), 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.     

Synaptic fusion pore structure and AMPA receptor activation according to Brownian simulation of glutamate diffusion

 The rising phase of fast, AMPA-mediated Excitatory Post Synaptic Currents (EPSCs) has a primary role in the computational ability of neurons. The structure and radial expansion velocity of the fusion pore between the vesicle and the presynaptic membrane could be important factors in determining the time course of the EPSC. We have used a Brownian simulation model for glutamate neurotransmitter diffusion to test two hypotheses on the fusion pore structure, namely, the proteinaceous pore and the purely lipidic pore. Three more hypotheses on the radial expansion velocity were also tested. The rising phases of the EPSC, computed under various conditions, were compared with experimental data from the literature. Our present results show that a proteinaceous fusion pore should produce a more marked foot at the beginning of the rising phase of the EPSC. They also confirm the hypothesis that the structure of the fusion pore and its radial expansion velocity play significant roles in shaping the fast EPSC time course. Received: 18 March 2002 / Accepted in revised form: 4 November 2002 / Published online: 19 February 2003 Correspondence to: F. Ventriglia (e-mail: franco@biocib.cib.na.cnr.it)     

Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences

The AMmtDB database (http://bighost.area.ba.cnr.it/mitochondriome) has been updated by collecting the multi-aligned sequences of Chordata and Invertebrata mitochondrial genes coding for proteins and tRNAs. Links to the multi-aligned mtDNA intraspecies variants, collected in VarMmtDB at the Mitochondriome web site, have been introduced. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. AMmtDB data selected through SRS can be viewed and 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 CLUSTALW and PILEUP programs and then carefully optimized manually.     

GeneBuilder: interactive in silico prediction of gene structure.

MOTIVATION: Prediction of gene structure in newly sequenced DNA becomes very important in large genome sequencing projects. This problem is complicated due to the exon-intron structure of eukaryotic genes and because gene expression is regulated by many different short nucleotide domains. In order to be able to analyse the full gene structure in different organisms, it is necessary to combine information about potential functional signals (promoter region, splice sites, start and stop codons, 3' untranslated region) together with the statistical properties of coding sequences (coding potential), information about homologous proteins, ESTs and repeated elements. RESULTS: We have developed the GeneBuilder system which is based on prediction of functional signals and coding regions by different approaches in combination with similarity searches in proteins and EST databases. The potential gene structure models are obtained by using a dynamic programming method. The program permits the use of several parameters for gene structure prediction and refinement. During gene model construction, selecting different exon homology levels with a protein sequence selected from a list of homologous proteins can improve the accuracy of the gene structure prediction. In the case of low homology, GeneBuilder is still able to predict the gene structure. The GeneBuilder system has been tested by using the standard set (Burset and Guigo, Genomics, 34, 353-367, 1996) and the performances are: 0.89 sensitivity and 0.91 specificity at the nucleotide level. The total correlation coefficient is 0.88. AVAILABILITY: The GeneBuilder system is implemented as a part of the WebGene a the URL: http://www.itba.mi. cnr.it/webgene and TRADAT (TRAncription Database and Analysis Tools) launcher URL: http://www.itba.mi.cnr.it/tradat.     

GALT Protein Database, a Bioinformatics Resource for the Management and Analysis of Structural Features of a Galactosemia-related Protein and Its Mutants

We describe the GALT-Prot database and its related web-based application that have been developed to collect information about the structural and functional effects of mutations on the human enzyme galactose-1-phosphate uridyltransferase (GALT) involved in the genetic disease named galactosemia type Ⅰ. Besides a list of missense mutations at gene and protein sequence levels, GALT-Prot reports the analysis results of mutant GALT structures. In addition to the structural information about the wild-type enzyme, the database also includes structures of over 100 single point mutants simulated by means of a computational procedure, and the analysis to each mutant was made with several bioinformatics programs in order to investigate the effect of the mutations. The web-based interface allows querying of the database, and several links are also provided in order to guarantee a high integration with other resources already present on the web. Moreover, the architecture of the database and the web application is flexible and can be easily adapted to store data related to other proteins with point mutations. GALT-Prot is freely available at http://bioinformatica.isa.cnr.it/GALT/.     

MitoNuc and MitoAln: two related databases of nuclear genes coding for mitochondrial proteins

Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many degenerative diseases. All functions of mitochondria depend on the interaction of nuclear and organellar genomes. Mitochondrial genomes have been extensively sequenced and analysed and the data collected in several specialised databases. In order to collect information on nuclear coded mitochondrial proteins we developed MitoNuc and MitoAln, two related databases containing, respectively, detailed information on sequenced nuclear genes coding for mitochondrial proteins in Metazoa and yeast, and the multiple alignments of the relevant homologous protein coding regions. MitoNuc and MitoAln retrieval through SRS at http://bio-www.ba.cnr.it:8000/srs6/ can easily allow the extraction of sequence data, subsequences defined by specific features and nucleotide or amino acid multiple alignments.