RESUMEN
This paper reports the first computational estimation of the comb polymers' third virial coefficients. The number of the chains in the comb polymers range from 5 to 11. An algorithm that counts the contributing terms of the third virial coefficients in an accelerated manner is presented along with its efficiency dependence on the polymers' size. In addition, the second virial coefficients are estimated for the comb polymers and compared to previously reported results.
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Algoritmos , Modelos Químicos , Modelos Moleculares , Polímeros/química , Simulación por Computador , Modelos Estadísticos , Conformación Molecular , Método de MontecarloRESUMEN
BACKGROUND: Computational discovery of transcription factor binding sites (TFBS) is a challenging but important problem of bioinformatics. In this study, improvement of a Gibbs sampling based technique for TFBS discovery is attempted through an approach that is widely known, but which has never been investigated before: reduction of the effect of local optima. RESULTS: To alleviate the vulnerability of Gibbs sampling to local optima trapping, we propose to combine a thermodynamic method, called simulated tempering, with Gibbs sampling. The resultant algorithm, GibbsST, is then validated using synthetic data and actual promoter sequences extracted from Saccharomyces cerevisiae. It is noteworthy that the marked improvement of the efficiency presented in this paper is attributable solely to the improvement of the search method. CONCLUSION: Simulated tempering is a powerful solution for local optima problems found in pattern discovery. Extended application of simulated tempering for various bioinformatic problems is promising as a robust solution against local optima problems.
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Algoritmos , Alineación de Secuencia/métodos , Análisis de Secuencia de ADN/métodos , Análisis de Secuencia de Proteína/métodos , Programas Informáticos , Factores de Transcripción/genética , Secuencias de Aminoácidos , Sitios de Unión , Unión ProteicaRESUMEN
The difficulties of computational discovery of transcription factor binding sites (TFBS) are well represented by (l, d) planted motif challenge problems. Large d problems are difficult, particularly for profile-based motif discovery algorithms. Their local search in the profile space is apparently incompatible with subtle motifs and large mutational distances between the motif occurrences. Herein, an improved profile-based method called GibbsDST is described and tested on (15,4), (12,3), and (18,6) challenging problems. For the first time for a profile-based method, its performance in motif challenge problems is comparable to that of Random Projection. It is noteworthy that GibbsDST outperforms a pattern-based algorithm, WINNOWER, in some cases. Effectiveness of GibbsDST using a biological dataset as an example and its possible extension to more realistic evolution models are also introduced.
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Algoritmos , Secuencias de Aminoácidos/genética , Biología Computacional/métodos , Factores de Transcripción/genética , Sitios de Unión , Simulación por Computador , Secuencia de Consenso , Escherichia coli/genética , Genoma Bacteriano , Modelos Genéticos , Modelos Estadísticos , Mutación , Reconocimiento de Normas Patrones Automatizadas , Unión Proteica , Regulón , Homología de Secuencia de AminoácidoRESUMEN
Ascidian is a useful experimental animal for studying body planning principles and host defense mechanisms employed by the phylum chordata. Toward this goal, genome and cDNA/EST projects of Ciona intestinalis have been undertaken. Using cDNAs and ESTs derived from Ciona hemocytes, we identified 79 possible hemocyte-preferential transcripts and determined the cDNA sequence of each clone. The amino acid sequence of each encoded polypeptide was predicted as well. Among these cDNAs, we identified three transcripts that may be involved in characteristic cell-cell communication in Ciona. These transcripts encoded leucine-rich repeat-containing RP105-like, IL-17 receptor/similar expression to FGF-like, and ectodysplasin-like polypeptide of the tunmr necrosis factor famlly, and they are expressed abundantly in hemocytes.
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Comunicación Celular , Ciona intestinalis/genética , Hemocitos/metabolismo , ARN Mensajero/genética , Animales , ADN Complementario , Etiquetas de Secuencia Expresada , Reacción en Cadena de la Polimerasa de Transcriptasa InversaRESUMEN
Genome-wide sequence analysis in the invertebrate chordate, Ciona intestinalis, has provided a comprehensive picture of immune-related genes in an organism that occupies a key phylogenetic position in vertebrate evolution. The pivotal genes for adaptive immunity, such as the major histocompatibility complex (MHC) class I and II genes, T-cell receptors, or dimeric immunoglobulin molecules, have not been identified in the Ciona genome. Many genes involved in innate immunity have been identified, including complement components, Toll-like receptors, and the genes involved in intracellular signal transduction of immune responses, and show both expansion and unexpected diversity in comparison with the vertebrates. In addition, a number of genes were identified which predicted integral membrane proteins with extracellular C-type lectin or immunoglobulin domains and intracellular immunoreceptor tyrosine-based inhibitory motifs (ITIMs) and immunoreceptor tyrosine-based activation motifs (ITAMs) (plus their associated signal transduction molecules), suggesting that activating and inhibitory receptors have an MHC-independent function and an early evolutionary origin. A crucial component of vertebrate adaptive immunity is somatic diversification, and the recombination activating genes (RAG) and activation-induced cytidine deaminase (AID) genes responsible for the Generation of diversity are not present in Ciona. However, there are key V regions, the essential feature of an immunoglobulin superfamily VC1-like core, and possible proto-MHC regions scattered throughout the genome waiting for Godot.
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Ciona intestinalis/genética , Ciona intestinalis/inmunología , Animales , Presentación de Antígeno/genética , Citocinas/fisiología , Genes MHC Clase I/fisiología , Genes MHC Clase II/fisiología , Genoma , Inmunidad Innata/genética , Glicoproteínas de Membrana/fisiología , Fagocitosis , Receptores de Superficie Celular/fisiología , Transducción de Señal , Receptores Toll-LikeRESUMEN
Ascidians, which are classified as urochordata, appear to employ a primitive system of host defense that is considered to be a prototype of vertebrate innate immunity. We performed a cDNA/EST study to identify the genes expressed in the hemocytes of Ciona intestinalis. We obtained 3357 one-path reads that were then grouped into 1889 independent clusters. Although two thirds of the clusters could not be assigned to any particular gene, the remaining 530 clusters had significant homology to genes with known function. Of these, 62 clusters appeared to be related to host defense mechanisms. These include transcripts whose products are probably involved in cytotoxicity, detoxification, inflammation, and apoptosis. As expected, elements of acquired immunity were not detected. Thus, Ciona hemocytes appear to express a number of host defense-related genes involved in innate immune mechanisms.
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Ciona intestinalis/inmunología , Hemocitos/inmunología , Inmunidad Innata , Animales , Apoptosis/genética , Moléculas de Adhesión Celular/química , Ciona intestinalis/citología , Ciona intestinalis/genética , Etiquetas de Secuencia Expresada , Proteínas de la Matriz Extracelular/química , Expresión Génica , Perfilación de la Expresión Génica , Hemocitos/metabolismo , Hemocitos/fisiología , Isomerasa de Peptidilprolil/genética , ARN/genética , ARN/metabolismo , Estrés Fisiológico/genéticaRESUMEN
To improve the efficiency of brain image analysis, we propose a full-automatic method for extracting brain tissue from three-dimensional magnetic resonance imaging of T1-weighted data on the human head (brain tissue extraction method using erosion-dilation treatment [BREED]). The extraction processing is realized by combining signal intensity thresholding by means of the discriminant analysis method and an erosion-dilation treatment of the image. The accuracy of BREED is evaluated using both simulated and subject data. BREED can extract brain tissues with high accuracy (approximately 97%) for either simulated or subject data.