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Search Results: 1 - 10 of 10223 matches for " Javier Tamames "
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Evolution of gene order conservation in prokaryotes
Javier Tamames
Genome Biology , 2001, DOI: 10.1186/gb-2001-2-6-research0020
Abstract: Gene order is extensively conserved between closely related species, but rapidly becomes less conserved among more distantly related organisms, probably in a cooperative fashion. This trend could be universal in prokaryotic genomes, as archaeal genomes are likely to behave similarly to bacterial genomes. Gene order conservation could therefore be used as a valid phylogenetic measure to study relationships between species. Even between very distant species, remnants of gene order conservation exist in the form of highly conserved clusters of genes. This suggests the existence of selective processes that maintain the organization of these regions. Because the clusters often span more than one operon, common regulation probably cannot be invoked as the cause of the maintenance of gene order.Gene order conservation is a genomic measure that can be useful for studying relationships between prokaryotes and the evolutionary forces shaping their genomes. Gene organization is extensively conserved in some genomic regions, and further studies are needed to elucidate the reason for this conservation.Completely sequenced genomes enable the study of relations between organisms in terms of the complete set of genes they possess. Genomic properties have been proposed as the most convenient tool for studying these relationships, as they are global properties that may circumvent many of the difficulties of classical molecular phytogenies [1]. Common gene content [2,3] or conservation of families of proteins [4] are examples of this kind of genomic information. From this genomic perspective, conservation of gene order is a very informative measure that may provide information both about the function and interactions of the proteins these genes encode [5,6], and about the evolution of the genomes and the organisms themselves.Gene order is generally well preserved at close phylogenetic distances [7]. When the species are not closely related, the degree of gene order conservation is usu
The success (or not) of HUGO nomenclature
Javier Tamames, Alfonso Valencia
Genome Biology , 2006, DOI: 10.1186/gb-2006-7-5-402
Abstract: Ambiguous gene names impose a serious hurdle for the analysis of a wide range of high-throughput data, such as microarray experiments or protein-interaction maps. This sort of ambiguity also limits the efficiency of genome analysis and annotation and slows the implementation of automatic text-mining systems for using bibliographic information [1,2]. While systems for automatic gene name recognition in other domains (such as in business or news reports) perform very well, the best systems in the biological field perform just slightly better than 80% [3].Genes are commonly named using functional terms, such as 'insulin' or 'tumor necrosis factor', or symbols consisting of abbreviations such as INS for insulin or TNF for tumor necrosis factor. Functional names are usually unique, in the sense that a given name refers only to one gene family, even if not always to a single gene of the family. Ambiguity exists because often more than one functional name is used to refer to the same gene (synonymy), and also many functional names are descriptive of some phenotype of the gene (such as 'deafness' or 'wingless'), a practice that creates many complications [4]. The use of symbols should alleviate some of the problems created by the use of functional names, but in practice seems to produce even more ambiguities. In addition to extended synonymy (with many symbols describing the same gene), a given symbol can also be used to describe different genes (homonymy). Moreover, many other meanings can match the abbreviation used for the gene name (acronyms). Text-mining systems are severely limited by these factors, as ambiguities decrease the precision in the retrieval of correct articles, and synonyms limit the number of total retrieved articles.These limitations potentially impair the effective application of text mining and natural language processing (NLP) techniques in genomics. For instance, the comparison of microarray data from different sources requires the exact mapping of
EnvMine: A text-mining system for the automatic extraction of contextual information
Javier Tamames, Victor de Lorenzo
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-294
Abstract: EnvMine is capable of retrieving the physicochemical variables cited in the text, by means of the accurate identification of their associated units of measurement. In this task, the system achieves a recall (percentage of items retrieved) of 92% with less than 1% error. Also a Bayesian classifier was tested for distinguishing parts of the text describing environmental characteristics from others dealing with, for instance, experimental settings.Regarding the identification of geographical locations, the system takes advantage of existing databases such as GeoNames to achieve 86% recall with 92% precision. The identification of a location includes also the determination of its exact coordinates (latitude and longitude), thus allowing the calculation of distance between the individual locations.EnvMine is a very efficient method for extracting contextual information from different text sources, like published articles or web pages. This tool can help in determining the precise location and physicochemical variables of sampling sites, thus facilitating the performance of ecological analyses. EnvMine can also help in the development of standards for the annotation of environmental features.One of the main objectives of microbial ecology is to address how the variations in environmental conditions can shape the composition and structure of prokaryotic communities. For this purpose, it is critical to count on accurate estimates of the composition of the prokaryotic communities, and on a precise description of the environment in study. Nowadays, the current knowledge about how the different environmental factors shape the distribution and diversity of prokaryotes is still scarce. Although the influence of some of these factors, salinity for instance, has been widely studied and discussed [1,2], the influence of many others, and especially the combination of different factors, is yet rather unknown.A very complete ontology, EnvO, has been developed for the annotation of the
Estimating the extent of horizontal gene transfer in metagenomic sequences
Javier Tamames, Andrés Moya
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-136
Abstract: We have created two different methods that are suitable for the study of HGT in metagenomic samples. The methods are based on phylogenetic and DNA compositional approaches, and have allowed us to assess the extent of possible HGT events in metagenomes for the first time. The methods are shown to be compatible and quite precise, although they probably underestimate the number of possible events. Our results show that the phylogenetic method detects HGT in between 0.8% and 1.5% of the sequences, while DNA compositional methods identify putative HGT in between 2% and 8% of the sequences. These ranges are very similar to these found in complete genomes by related approaches. Both methods act with a different sensitivity since they probably target HGT events of different ages: the compositional method mostly identifies recent transfers, while the phylogenetic is more suitable for the detections of older events. Nevertheless, the study of the number of HGT events in metagenomic sequences from different communities shows a consistent trend for both methods: the lower amount is found for the sequences of the Sargasso Sea metagenome, while the higher quantity is found in the whale fall metagenome from the bottom of the ocean. The significance of these observations is discussed.The computational approaches that are used to find possible HGT events in complete genomes can be adapted to work with metagenomic samples, where a level of high performance is shown in different metagenomic samples. The percentage of possible HGT events that were observed is close to that found for complete genomes, and different microbiomes show diverse ratios of putative HGT events. This is probably related with both environmental factors and the composition in the species of each particular community.Horizontal gene transfer (HGT) is believed to be a very important phenomenon in prokaryotic evolution, as it enables the acquisition of new genes or sets of genes that can accelerate evolution and adap
Modular organization in the reductive evolution of protein-protein interaction networks
Javier Tamames, Andrés Moya, Alfonso Valencia
Genome Biology , 2007, DOI: 10.1186/gb-2007-8-5-r94
Abstract: We have studied the reduction in genome size of Buchnera compared to its close relative Escherichia coli. In this well defined evolutionary scenario, we found that among all the properties of the protein interaction networks, it is the organization of networks into modules that seems to be directly related to the evolutionary process of genome reduction.In Buchnera, the apparently non-random reduction of the modular structure of the networks and the retention of essential characteristics of the interaction network indicate that the roles of proteins within the interaction network are important in the reductive process.Bacterial endosymbionts of insects, such as Buchnera aphidicola [1,2], Blochmannia floridanus [3] and Wigglesworthia glossinidia [4], are paradigms of reductive evolution. These bacteria live in a stable and isolated environment, the bacteriocyte of insects, where the host provides most of their nutritional requirements. As a consequence, the genomes of these bacteria have undergone a process of reduction, losing around 90% of their ancestral genes. These endosymbionts also fail to acquire new genes due to their incapacity to incorporate DNA via lateral gene transfer and their isolated environment. Nevertheless, although their genomes represent a subset of the genome of their ancestors, these gamma-proteobacteria remain closely related to Escherichia coli (98% of the genes in Buchnera have clear orthologues in E. coli). Accordingly, the process of genome shrinkage that these species have undergone has been well documented in terms of the evolution of the corresponding protein families [1,2].Recent research indicates that the capacity of an organism for adaptation depends not only on the properties of its individual molecular components, but also on the structure and organization of its underlying network of molecular interactions. Indeed, it was recently proposed that the modular organization of the network of interactions is necessary to adapt to chan
The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii
Javier Tamames, Rosario Gil, Amparo Latorre, Juli Peretó, Francisco J Silva, Andrés Moya
BMC Evolutionary Biology , 2007, DOI: 10.1186/1471-2148-7-181
Abstract: The detailed analysis of the gene content of C. ruddii shows that the extensive degradation of the genome is not compatible with its consideration as a mutualistic endosymbiont and, even more, as a living organism. The ability to perform most essential functions for a cell to be considered alive is heavily impaired by the lack of genes involved in DNA replication, transcription and translation. Furthermore, the shortening of genes causes, in some cases, the loss of essential domains and functional residues needed to fulfill such vital functions. In addition, at least half of the pathways towards the biosynthesis of essential amino acids, its proposed symbiotic function, are completely or partially lost.We propose that this strain of C. ruddii can be viewed as a further step towards the degeneration of the former primary endosymbiont and its transformation in a subcellular new entity between living cells and organelles. Although the transition of genes from C. ruddii to the host nucleus has been proposed, the amount of genes that should have been transferred to the germinal line of the insect would be so big that it would be more plausible to consider the implication of the mitochondrial machinery encoded in the insect nucleus. Furthermore, since most genes for the biosynthesis of essential amino acids have also been lost, it is likely that the host depends on another yet unidentified symbiont to complement its deficient diet.Obligate mutualistic symbioses between insects and proteobacteria have been extensively studied in recent years [1]. The bacteria live in specialized host cells and synthesize those nutrients that are defective in the insects' restricted diets, as confirmed by genomic analyses of several endosymbionts from different insect species. Thus, Buchnera aphidicola and Blochmannia spp. provide mainly amino acids to their hosts, aphids and ants respectively [2-7], whereas Wigglesworthia glossinidia supplies vitamins and cofactors to the tsetse fly [8]. I
The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene
Rafael Silva-Rocha, Hidde de Jong, Javier Tamames, Víctor de Lorenzo
BMC Systems Biology , 2011, DOI: 10.1186/1752-0509-5-191
Abstract: The most salient feature of the whole TOL regulatory network is the control exerted by two distinct but still intertwined regulators (XylR and XylS) on expression of two separated catabolic operons (upper and lower) for catabolism of m-xylene. Following model reduction, a minimal modular circuit composed by five basic variables appeared to suffice for fully describing the operation of the entire system. In silico simulation of the effect of various perturbations were compared with experimental data in which specific portions of the network were activated with selected inducers: m-xylene, o-xylene, 3-methylbenzylalcohol and 3-methylbenzoate. The results accredited the ability of the model to faithfully describe network dynamics. This analysis revealed that the entire regulatory structure of the TOL system enables the action an unprecedented metabolic amplifier motif (MAM). This motif synchronizes expression of the upper and lower portions of a very long metabolic system when cells face the head pathway substrate, m-xylene.Logic modeling of the TOL circuit accounted for the intricate regulatory topology of this otherwise simple metabolic device. The found MAM appears to ensure a simultaneous expression of the upper and lower segments of the m-xylene catabolic route that would be difficult to bring about with a standard substrate-responsive single promoter. Furthermore, it is plausible that the MAM helps to avoid biochemical conflicts between competing plasmid-encoded and chromosomally-encoded pathways in this bacterium.Prokaryotic regulatory networks are organized in a hierarchical way, on top of which a few transcriptional factors (TF) may coordinate the expression of hundreds of genes of different functional categories (including other downstream TFs), thus linking extracellular conditions to distinct physiological states [1]. It is generally accepted that cell-wide regulatory and metabolic circuits acquire an optimum of performance by connecting a large number of d
Environmental distribution of prokaryotic taxa
Javier Tamames, Juan Abellán, Miguel Pignatelli, Antonio Camacho, Andrés Moya
BMC Microbiology , 2010, DOI: 10.1186/1471-2180-10-85
Abstract: We used 16S rDNA sequences from 3,502 sampling experiments in natural and artificial sources. These sequences were taxonomically assigned, and the corresponding samples were also classified into a hierarchical classification of environments. We used several statistical methods to analyze the environmental distribution of taxa. Our results indicate that environmental specificity is not very common at the higher taxonomic levels (phylum to family), but emerges at lower taxonomic levels (genus and species). The most selective environmental characteristics are those of animal tissues and thermal locations. Salinity is another very important factor for constraining prokaryotic diversity. On the other hand, soil and freshwater habitats are the less restrictive environments, harboring the largest number of prokaryotic taxa. All information on taxa, samples and environments is provided at the envDB online database, http://metagenomics.uv.es/envDB webcite.This is, as far as we know, the most comprehensive assessment of the distribution and diversity of prokaryotic taxa and their associations with different environments. Our data indicate that we are still far from characterizing prokaryotic diversity in any environment, except, perhaps, for human tissues such as the oral cavity and the vagina.The patterns of species distribution and diversity, which are fairly well-known for macroorganisms, are not altogether understood for microorganisms. Some ecological trends that have already been observed for macroorganisms, such as taxa-area or distance-decay relationships [1], and especially the existence of biogeographical patterns, have been proposed to possibly exist also for microorganisms, thus pointing to the existence of common, global rules that govern the ecology of all living forms. Some analyses support the ubiquity of several prokaryotic species [2,3], but also the apparent existence of biogeographic patterns for some others [3-7].The study of ecological trends in microorg
Factores determinantes de la estancia inadecuada en un hospital de tercer nivel
Luquero Alcalde,Francisco Javier; Santos Sanz,Sara; Pérez Rubio,Alberto; Tamames Gómez,Sonia; Cantón álvarez,M. Belén; Castrodeza Sanz,Javier;
Gaceta Sanitaria , 2008,
Abstract: background: to identify the factors associated with a higher risk of inappropriate days of stay. material and method: crude and adjusted inappropriateness rates were calculated using negative binomial regression to obtain information about the relative risk of each variable. the appropriateness evaluation protocol (aep) was applied to collect information about patients' hospital stays. results: a total of 34.17% (95%ci, 33.28-35.08) of the stays were inappropriate. women, age older than 65 years, elective admission, and stays in medical services showed the highest inappropriateness risk. lack of correct patient follow-up in the medical record increased the risk of inappropriateness to 36%. conclusions: lack of continual registration of the patient's clinical course increased the risk of inappropriate days of stay in the hospital. the use of the negative binomial is a valid and simple option for analysis of this type of phenomenon.
Factors associated with the appropriate use of preoperatory hospital stays: historical cohort study
Sonia Tamames, Alberto Perez Rubio, Javier Castrodeza Sanz, Maria Belen Canton Alvarez, Francisco J Luquero, Sara Santos Sanz, Placido Lopez Encinar, Maria Paz de la Torre Pardo, Juan Manuel Gil Gonzalez
BMC Health Services Research , 2007, DOI: 10.1186/1472-6963-7-187
Abstract: Historical cohort study. The histories of 440 hospitalised patients who underwent at least one surgical procedure were analysed. Data collection was carried out by doctors not involved in the services studied, following the Appropriateness Evaluation Protocol. A bivariate and multivariate analysis of the factors associated with the appropriateness of preoperatory stays was carried out.The mean number of days of preoperatory stay was 5.5 (SD 5.11), of which a mean number of 2.5 days were considered to be inappropriate (SD 4.11). The overall rate of inappropriateness was 45.2% (CI 95% 43.3–47.1). The multivariate analysis showed a positive association of the inappropriateness of the preoperatory stay with weekend days, programmed admission, hospital stays longer than 7 days, medical records incorrectly or incompletely documented and the age groups of 45–65 and the >65 with respect to the <45 age group. Sex and an incorrect or incomplete nursing register did not show such an association.The inappropriate use of hospital stay during preoperatory care affects almost half the period and there are some risk determinants that could act as indicators at admission. In addition, the efficiency of care provision was found to vary greatly from the point of view of its appropriateness.Increased healthcare expenditure in developed countries is influenced by several complex factors, among which can be numbered the population's own expectations concerning their health and their demographic structure [1]. The ability to guarantee the sustainability of Europe's healthcare systems, without detriment to accessibility or efficiency, is an ever growing preoccupation. Some of the proposed strategies for keeping down expenditure on healthcare include the provision of services at an 'as simple as possible assistance level', thus optimising the use of available resources [2]. In this sense, a review of the appropriate use of hospital care is especially relevant, as it allows inappropriate sta
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