Biomedical subjects

J Dopazo

Publications and source records attributed to J Dopazo.

At least 19 recordsLinked to original sources

PubMed2003

Gene expression data preprocessing.

We present an interactive web tool for preprocessing microarray gene expression data. It analyses the data, suggests the most appropriate transformations and proceeds with them after user agreement. The normal preprocessing steps include scale transformations, management of missing values, replicate handling, flat pattern filtering and pattern standardization and they are required before performing any pattern analysis. The processed data set can be sent to other pattern analysis tools.

Database Management Systems↗

PubMed2001

Phylogenetic analysis of viroid and viroid-like satellite RNAs from plants: a reassessment.

The proposed monophyletic origin of a group of subviral plant pathogens (viroids and viroid-like satellite RNAs), as well as the phylogenetic relationships and the resulting taxonomy of these entities, has been recently questioned. The criticism comes from the (apparent) lack of sequence similarity among these RNAs necessary to reliably infer a phylogeny. Here we show that, despite their low overall sequence similarity, a sequence alignment manually adjusted to take into account all the local similarities and the insertions/deletions and duplications/rearrangements described in the literature for viroids and viroid-like satellite RNA, along with the use of an appropriate estimator of genetic distances, constitutes a data set suitable for a phylogenetic reconstruction. When the likelihood-mapping method was applied to this data set, the tree-likeness obtained was higher than that corresponding to a sequence alignment that does not take into consideration the local similarities. In addition, bootstrap analysis also supports the major groups previously proposed and the reconstruction is consistent with the biological properties of this RNAs.

Evolution, Molecular↗

PubMed2001

Methods and approaches in the analysis of gene expression data.

The application of high-density DNA array technology to monitor gene transcription has been responsible for a real paradigm shift in biology. The majority of research groups now have the ability to measure the expression of a significant proportion of the human genome in a single experiment, resulting in an unprecedented volume of data being made available to the scientific community. As a consequence of this, the storage, analysis and interpretation of this information present a major challenge. In the field of immunology the analysis of gene expression profiles has opened new areas of investigation. The study of cellular responses has revealed that cells respond to an activation signal with waves of co-ordinated gene expression profiles and that the components of these responses are the key to understanding the specific mechanisms which lead to phenotypic differentiation. The discovery of 'cell type specific' gene expression signatures have also helped the interpretation of the mechanisms leading to disease progression. Here we review the principles behind the most commonly used data analysis methods and discuss the approaches that have been employed in immunological research.

Classification↗

PubMed2001

Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate.

The public availability of numerous microbial genomes is enabling the analysis of bacterial biology in great detail and with an unprecedented, organism-wide and taxon-wide, broad scope. Streptococcus pneumoniae is one of the most important bacterial pathogens throughout the world. We present here sequences and functional annotations for 2.1-Mbp of pneumococcal DNA, covering more than 90% of the total estimated size of the genome. The sequenced strain is a clinical isolate resistant to macrolides and tetracycline. It carries a type 19F capsular locus, but multilocus sequence typing for several conserved genetic loci suggests that the strain sequenced belongs to a pneumococcal lineage that most often expresses a serotype 15 capsular polysaccharide. A total of 2,046 putative open reading frames (ORFs) longer than 100 amino acids were identified (average of 1,009 bp per ORF), including all described two-component systems and aminoacyl tRNA synthetases. Comparisons to other complete, or nearly complete, bacterial genomes were made and are presented in a graphical form for all the predicted proteins.

DNA, Bacterial↗

PubMed2001

A hierarchical unsupervised growing neural network for clustering gene expression patterns.

MOTIVATION: We describe a new approach to the analysis of gene expression data coming from DNA array experiments, using an unsupervised neural network. DNA array technologies allow monitoring thousands of genes rapidly and efficiently. One of the interests of these studies is the search for correlated gene expression patterns, and this is usually achieved by clustering them. The Self-Organising Tree Algorithm, (SOTA) (Dopazo,J. and Carazo,J.M. (1997) J. Mol. Evol., 44, 226-233), is a neural network that grows adopting the topology of a binary tree. The result of the algorithm is a hierarchical cluster obtained with the accuracy and robustness of a neural network. RESULTS: SOTA clustering confers several advantages over classical hierarchical clustering methods. SOTA is a divisive method: the clustering process is performed from top to bottom, i.e. the highest hierarchical levels are resolved before going to the details of the lowest levels. The growing can be stopped at the desired hierarchical level. Moreover, a criterion to stop the growing of the tree, based on the approximate distribution of probability obtained by randomisation of the original data set, is provided. By means of this criterion, a statistical support for the definition of clusters is proposed. In addition, obtaining average gene expression patterns is a built-in feature of the algorithm. Different neurons defining the different hierarchical levels represent the averages of the gene expression patterns contained in the clusters. Since SOTA runtimes are approximately linear with the number of items to be classified, it is especially suitable for dealing with huge amounts of data. The method proposed is very general and applies to any data providing that they can be coded as a series of numbers and that a computable measure of similarity between data items can be used. AVAILABILITY: A server running the program can be found at: http://bioinfo.cnio.es/sotarray.

Algorithms↗

PubMed2000

Expression profiles and biological function.

Expression arrays facilitate the monitoring of changes in expression patterns of large collections of genes. It is generally expected that genes with similar expression patterns would correspond to proteins of common biological function. We assess this common assumption by comparing levels of similarity of expression patterns and statistical significance of biological terms that describe the corresponding protein functions. Terms are automatically obtained by mining large collections of Medline abstracts. We propose that the combined use of the tools for expression profiles clustering and automatic function retrieval, can be useful tools for the detection of biologically relevant associations between genes in complex gene expression experiments. The results obtained using publicly available experimental data show how, in general, an increase in the similarity of the expression patterns is accompanied by an enhancement of the amount of specific functional information or, in other words, how the selected terms became more specific following an increase in the specificity of the expression patterns. Particularly interesting are the discrepancies from this general trend, i.e. groups of genes with similar expression patterns but very little in common at the functional level. In these cases the similarity of their expression profiles becomes the first link between previously unrelated genes.

Cluster Analysis↗

PubMed1998

Self-organizing tree-growing network for the classification of protein sequences.

The self-organizing tree algorithm (SOTA) was recently introduced to construct phylogenetic trees from biological sequences, based on the principles of Kohonen's self-organizing maps and on Fritzke's growing cell structures. SOTA is designed in such a way that the generation of new nodes can be stopped when the sequences assigned to a node are already above a certain similarity threshold. In this way a phylogenetic tree resolved at a high taxonomic level can be obtained. This capability is especially useful to classify sets of diversified sequences. SOTA was originally designed to analyze pre-aligned sequences. It is now adapted to be able to analyze patterns associated to the frequency of residues along a sequence, such as protein dipeptide composition and other n-gram compositions. In this work we show that the algorithm applied to these data is able to not only successfully construct phylogenetic trees of protein families, such as cytochrome c, triosephophate isomerase, and hemoglobin alpha chains, but also classify very diversified sequence data sets, such as a mixture of interleukins and their receptors.

Algorithms↗

PubMed1998

A RT-PCR assay for the differential diagnosis of vesicular viral diseases of swine.

A RT-PCR assay based on specific amplification of RNA sequences from each of the etiological agents of three important vesicular diseases that affect swine, foot-and-mouth disease virus (FMDV), swine vesicular disease virus (SVDV), and vesicular stomatitis virus (VSV), was developed. Genotype-specific primers that amplified DNA fragments of differential size from SVDV 3D gene or VSV L gene were selected with the aid of a computer program. Experimental testing of the primers predicted as SVDV-specific identified a primer pair, SA2/SS4, that rendered a specific product from SVDV RNAs, but did not amplify RNA from either FMDV or coxsackie B5 virus (CV-B5), a highly related picornavirus. Primers SA2/SS4 were used in combination with primers 3D2/3D1, which amplify a product of different size on FMDV 3D gene (Rodriguez et al., 1992). This combined RT-PCR reaction allowed a sensitive and specific differential detection of FMDV and SVDV RNAs in a single tube, by means of the analysis of the amplified products in agarose gels. The results obtained were similar when RNA extracted from viral stocks or plastic wells coated with either viral supernatants or extracts from lesions of infected animals, were used as starting material in the reactions. Using a similar approach, VSV serotype-specific primers IA/IS and NA/NS were selected for the specific amplification of VSV-Indiana and VSV-New Jersey RNAs, respectively. The combined use of SVDV, FMDV and VSV specific primers in a single reaction resulted in a genotype-specific amplification of each of the viral RNAs. Thus, differential diagnosis of FMDV from SVDV and/or VSV can be carried out in a single RT-PCR reaction, using a rapid and simplified methodology.

Animals↗

PubMed1998

A procedure for detecting selection in highly variable viral genomes: evidence of positive selection in antigenic regions of capsid protein VP1 of foot-and-mouth disease virus.

A new procedure is described for the detection of positive selection among sequences of viral proteins from highly variable viruses. The approach is based on the estimation of the rates of nonsynonymous to synonymous (ns/s) mutations to the overall genetic distances amongst the sequences compared. Rates of ns/s substitutions were calculated, and the individual profiles were arranged as a function of the genetic distance observed between the complete sequences. The resulting surfaces allowed identification of protein regions whose rates of ns/s substitutions were consistent with the existence of positive selection. This procedure has been applied to the study of a highly variable antigenic protein, VP1, a protein present in foot-and-mouth disease virus (FMDV). The analysis of groups of VP1 sequences corresponding to FMDV serotypes A, O and C, resulted in the identification of two regions, which contribute to an important antigenic site, where positive selection appears to operate.

Antigenic Variation↗

PubMed1998

The prognostic relevance of the nonstructural 5A gene interferon sensitivity determining region is different in infections with genotype 1b and 3a isolates of hepatitis C virus.

Hepatitis C virus (HCV) RNA serum concentration, quasispecies complexity, and sequence and phylogenetic analysis of the nonstructural 5A gene (NS5A) interferon sensitivity determining region (ISDR) were determined in pretreatment serum samples from 47 patients with chronic hepatitis C (36 infected by HCV genotype 1b and 11 by 3a). Among HCV genotype 1b-infected patients, virus load was lower (P = .003) and the number of NS5A-ISDR amino acid changes was higher (P = .001) in long-term responders than in non-long-term responders, but there were no differences in quasispecies complexity. Multivariate analysis showed a close association between response to interferon and NS5A-ISDR phenotype. Phylogenetic analysis showed that isolates from non-long-term responders clustered apart from the majority of isolates from long-term responders. There was no association between virologic features and therapeutic response in HCV genotype 3a-infected patients. In conclusion, low virus load and mutant NS5A-ISDR phenotype are closely associated with long-term response to interferon in HCV genotype 1b- but probably not in 3a-infected patients.

Adult↗

PubMed1998

Self-organizing tree growing network for classifying amino acids.

UNLABELLED: A self-organizing tree growing neural network was applied to classify amino acids and amino acid exchange matrices. AVAILABILITY: SOTA, is freely available by anonymous FTP or at http://www.cnb.uam.es/bioinfo/Software/so ta. CONTACT: carazo@cnb.uam.es

Algorithms↗

PubMed1998

New phylogenetic venues opened by a novel implementation of the DNAml algorithm.

SUMMARY: This note describes the parallelization of a key biological application, such as the construction of phylogenetic trees, using the DNAml program. A careful run-time analysis allowed us to propose an efficient parallelization that scaled very well to large problem sizes. AVAILABILITY: By anonymous ftp at ftp.ac.uma. es (/pub/ots/pDNAml) or from our web site http://www.cnb.uam. es/www/software/software_index.html CONTACT: ots@ac.uma.es

Algorithms↗

PubMed1998

Potato virus Y group C isolates are a homogeneous pathotype but two different genetic strains.

Potato virus Y group C isolates (PVYC) have been characterized according to biological, molecular and genetic criteria. Two genetic strains, PVYC1 and PVYC2, were identified on the basis of genetic distances (among them and other PVY strains), host range (ability or inability to infect pepper), MAb response (ELISA recognition with MAb 10E3) and coat protein processing site. Some characteristics, such as aphid transmission and ELISA using other MAbs, did not correlate with classification into these two genetic strains. All isolates tested induced a hypersensitive response on potatoes bearing the Nc resistance gene, confirming the nature of PVYC isolates as a homogeneous pathotype.

Amino Acid Sequence↗

PubMed1998

RT-PCR in foot-and-mouth disease diagnosis.

A RT-PCR assay for the specific detection of RNA sequences from foot-and-mouth disease virus (FMDV) has been developed. The procedure permits also the detection of sequences that correlate with established FMDV serotypes. A computer program that allows selection of genotype-specific primers for RT-PCR amplification was used for the identification of FMDV specific sequences for PCR amplification on RNA replicase (3D) gene regions. Specific, rapid and highly sensitive detection was achieved for a wide collection of RNA samples from FMDV types C, A and O, either purified from tissue culture or extracted from lesions of infected animals. Similarly, serotype-specific primers were designed to amplify the carboxy-terminal end of the VP1 gene of FMDV types either C, A or O. The results of PCR amplification of different FMDV RNAs using type-specific primers are in agreement with the serological typing of the corresponding viruses. A combination of this approach with a simplified sample processing, carried out following direct adsorption of viral suspensions to microtiter plates, provides a rapid, reliable method of viral diagnosis.

Animals↗

PubMed1997

Contribution of mutation and RNA recombination to the evolution of a plant pathogenic RNA.

The nucleotide sequence of 17 variants of the satellite RNA of cucumber mosaic virus (CMV-satRNA) isolated from field-infected tomato plants in the springs of 1989, 1990, and 1991 was determined. The sequence of each of the 17 satRNAs was unique and was between 334 and 340 nucleotides in length; 57 positions were polymorphic. There was much genetic divergence, ranging from 0.006 to 0.141 nucleotide substitutions per site for pairwise comparisons, and averaging 0.074 for any pair. When the polymorphic positions were analyzed relative to a secondary structure model proposed for CMV-satRNAs, it was found that there were significantly different numbers of changes in base-paired and non-base-paired positions, and that mutations that did not disrupt base pairing were preferred at the putatively paired sites. This supports the concept that the need to maintain a functional structure may limit genetic divergence of CMV-satRNA. Phylogenetic analyses showed that the 17 CMV-satRNA variants clustered into two subgroups, I and II, and evolutionary lines proceeding by the sequential accumulation of mutations were apparent. Three satRNA variants were outliers for these two phylogenetic groups. They were shown to be recombinants of subgroup I and II satRNAs by calculating phylogenies for different molecular regions and by using Sawyer's test for gene conversion. At least two recombination events were required to produce these three recombinant satRNAs. Thus, recombinants were found to be frequent ( approximately 17%) in natural populations of CMV-satRNA, and recombination may make an important contribution to the generation of new variants. To our knowledge this is the first report of data allowing the frequency of recombinant isolates in natural populations of an RNA replicon to be estimated.

Base Sequence↗

PubMed1997

Phylogenetic reconstruction using an unsupervised growing neural network that adopts the topology of a phylogenetic tree.

We propose a new type of unsupervised, growing, self-organizing neural network that expands itself by following the taxonomic relationships that exist among the sequences being classified. The binary tree topology of this neutral network, contrary to other more classical neural network topologies, permits an efficient classification of sequences. The growing nature of this procedure allows to stop it at the desired taxonomic level without the necessity of waiting until a complete phylogenetic tree is produced. This novel approach presents a number of other interesting properties, such as a time for convergence which is, approximately, a lineal function of the number of sequences. Computer simulation and a real example show that the algorithm accurately finds the phylogenetic tree that relates the data. All this makes the neural network presented here an excellent tool for phylogenetic analysis of a large number of sequences.

Algorithms↗

PubMed1997

Genetic characterization of populations of a de novo arisen sugar beet pest, Aubeonymus mariaefranciscae (Coleoptera, Curculionidae), by RAPD analysis.

The weevil Aubeonymus mariaefranciscae is an important pest of sugar beet crops in southern Spain that was first described as a new species in 1979. We have studied the genetic variability of this insect by RAPD analysis of 122 individuals using eight primers. The high resolution provided by random amplified polymorphic DNA (RAPDs), in combination with efficient genetic distance estimators, allowed a very detailed description of the ecology and evolution of the populations of this insect in the south of Spain. The results are compatible with a unique event of colonization, followed by the spreading of the weevil across the surrounding areas. A comparison of the results obtained with different genetic distance estimators is presented. RAPD is shown to be a powerful technique for reconstructing the phylogenetic history of insect populations, even if they have diverged recently, which seems to be the case for A. mariaefranciscae.

Animals↗

PubMed1997

Antigenic structure of the human respiratory syncytial virus G glycoprotein and relevance of hypermutation events for the generation of antigenic variants.

A set of monoclonal antibodies (MAbs) specific for the attachment (G) glycoprotein of a recently isolated strain of human respiratory syncytial virus (HRSV) is described. Antibody reactivity with a series of HRSV isolates belonging to antigenic groups A and B identified three epitope categories: (i) strain-specific or variable epitopes that were present in a limited set of viruses from the same antigenic group, (ii) group-specific epitopes shared by viruses from the same antigenic group and (iii) conserved epitopes present in all HRSV isolates. Sequence analysis of escape mutants was used to map relevant antigenic sites of the G glycoprotein. Strain-specific epitopes were located preferentially in the variable C-terminal third of the G polypeptide, in agreement with previous studies of the Long strain. However, a new strain-specific epitope was mapped into another variable region, N-terminal to the cluster of cysteines in the G protein ectodomain. In contrast, the group-specific and conserved epitopes were located in the central conserved region of the G protein primary structure. These results, together with previous analysis of the Long strain, provide a detailed antigenic map of the HRSV attachment protein. Some mutants selected with group-specific antibodies contain multiple A-G substitutions (hypermutations) and lack one or two of the four cysteines which are conserved in all HRSV isolates. The genetic mechanism implicated in the generation of the hypermutated viruses and its relevance for the natural history of HRSV are discussed.

Amino Acid Substitution↗