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Search Results: 1 - 10 of 2504 matches for " Rintaro Saito "
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Measure of synonymous codon usage diversity among genes in bacteria
Haruo Suzuki, Rintaro Saito, Masaru Tomita
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-167
Abstract: The application of Dmean to 268 bacterial genomes shows that in bacteria with extremely biased genomic G+C compositions there is little diversity in synonymous codon usage among genes. Furthermore, our findings contradict previous reports. For example, a low level of diversity in codon usage among genes has been reported for Helicobacter pylori, but based on Dmean, the diversity level of this species is higher than those of more than half of bacteria tested here. The discrepancies between our findings and previous reports are probably due to differences in the methods used for measuring codon usage diversity.We recommend that Dmean be used to measure the diversity level of codon usage among genes. This measure can be applied to other compositional features such as amino acid usage and dinucleotide relative abundance as a genomic signature.Most amino acids can be encoded by more than one codon (i.e., a triplet of nucleotides); such codons are described as being synonymous, and usually differ by one nucleotide in the third position. In most bacteria, alternative synonymous codons are not used with equal frequencies. Grantham et al. [1] showed that genes from same species often show similar patterns of codon usage, and proposed the 'genome hypothesis' that there exists a species-specific pattern of codon usage. Then, it was shown that in many organisms there are also considerable differences in codon usage among genes within a genome [2]. Previous analyses of codon usage diversity in bacteria have mostly focused on individual genomes, with no quantitative attempt to compare the diversity levels among different genomes. For comparative genomic analysis, it is desirable to quantify the level of codon usage diversity among genes in such a way that the estimates could be compared among genomes.Different factors have been proposed to explain the preferential usage of a subset of synonymous codons, including biased mutation pressure (genome-wide mutational bias toward G/C or
Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria
Haruo Suzuki, Rintaro Saito, Masaru Tomita
EURASIP Journal on Bioinformatics and Systems Biology , 2007, DOI: 10.1155/2007/61374
Abstract: [1234567891011121314151617181920212223]
Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria
Suzuki Haruo,Saito Rintaro,Tomita Masaru
EURASIP Journal on Bioinformatics and Systems Biology , 2007,
Abstract: G + C composition at the third codon position (GC3) is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this correlation among different genomes. Here, we applied Shannon entropy from information theory to measure the degree of GC3 bias and that of synonymous codon usage bias of each gene. The strength of the correlation of GC3 with synonymous codon usage bias, quantified by a correlation coefficient, varied widely among bacterial genomes, ranging from 0.07 to 0.95. Previous analyses suggesting that the relationship between GC3 and synonymous codon usage bias is independent of species are thus inconsistent with the more detailed analyses obtained here for individual species.
Integrative Features of the Yeast Phosphoproteome and Protein–Protein Interaction Map
Nozomu Yachie,Rintaro Saito ,Naoyuki Sugiyama,Masaru Tomita,Yasushi Ishihama
PLOS Computational Biology , 2011, DOI: 10.1371/journal.pcbi.1001064
Abstract: Following recent advances in high-throughput mass spectrometry (MS)–based proteomics, the numbers of identified phosphoproteins and their phosphosites have greatly increased in a wide variety of organisms. Although a critical role of phosphorylation is control of protein signaling, our understanding of the phosphoproteome remains limited. Here, we report unexpected, large-scale connections revealed between the phosphoproteome and protein interactome by integrative data-mining of yeast multi-omics data. First, new phosphoproteome data on yeast cells were obtained by MS-based proteomics and unified with publicly available yeast phosphoproteome data. This revealed that nearly 60% of ~6,000 yeast genes encode phosphoproteins. We mapped these unified phosphoproteome data on a yeast protein–protein interaction (PPI) network with other yeast multi-omics datasets containing information about proteome abundance, proteome disorders, literature-derived signaling reactomes, and in vitro substratomes of kinases. In the phospho-PPI, phosphoproteins had more interacting partners than nonphosphoproteins, implying that a large fraction of intracellular protein interaction patterns (including those of protein complex formation) is affected by reversible and alternative phosphorylation reactions. Although highly abundant or unstructured proteins have a high chance of both interacting with other proteins and being phosphorylated within cells, the difference between the number counts of interacting partners of phosphoproteins and nonphosphoproteins was significant independently of protein abundance and disorder level. Moreover, analysis of the phospho-PPI and yeast signaling reactome data suggested that co-phosphorylation of interacting proteins by single kinases is common within cells. These multi-omics analyses illuminate how wide-ranging intracellular phosphorylation events and the diversity of physical protein interactions are largely affected by each other.
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data
Haruna Imamura, Nozomu Yachie, Rintaro Saito, Yasushi Ishihama, Masaru Tomita
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-232
Abstract: We analyzed time-course phosphoproteome data obtained previously by liquid chromatography mass spectrometry with the stable isotope labeling using amino acids in cell culture (SILAC) method. This provides the relative phosphorylation activities of digested peptides at each of five time points after stimulating HeLa cells with epidermal growth factor (EGF). We initially calculated the correlations between the phosphorylation dynamics patterns of every pair of peptides and connected the strongly correlated pairs to construct a network. We found that peptides extracted from the same intracellular fraction (nucleus vs. cytoplasm) tended to be close together within this phosphorylation dynamics-based network. The network was then analyzed using graph theory and compared with five known signal-transduction pathways. The dynamics-based network was correlated with known signaling pathways in the NetPath and Phospho.ELM databases, and especially with the EGF receptor (EGFR) signaling pathway. Although the phosphorylation patterns of many proteins were drastically changed by the EGF stimulation, our results suggest that only EGFR signaling transduction was both strongly activated and precisely controlled.The construction of a phosphorylation dynamics-based network provides a useful overview of condition-specific intracellular signal transduction using quantitative time-course phosphoproteome data under specific experimental conditions. Detailed prediction of signal transduction based on phosphoproteome dynamics remains challenging. However, since the phosphorylation profiles of kinase-substrate pairs on the specific pathway were localized in the dynamics-based network, our method will be a complementary strategy to explore new components of protein signaling pathways in combination with previous methods (including software) of predicting direct kinase-substrate relationships.Post-translational modification (PTM) of proteins regulates many biological phenomena [1]. Among the s
Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification
Tadasu Nozaki, Nozomu Yachie, Ryu Ogawa, Anton Kratz, Rintaro Saito, Masaru Tomita
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-416
Abstract: Here, we performed a systematic analysis of transcription promoters and gene expression, as well as of epigenetic histone behaviors, including genomic position, stability within the chromatin, and several modifications. We found that, in humans, broad promoters, but not peak promoters, generally had significant associations with nucleosome positioning and modification. Specifically, around broad promoters histones were highly distributed and aligned in an orderly fashion. This feature was more evident with histones that were methylated or acetylated; moreover, the nucleosome positions around the broad promoters were more stable than those around the peak ones. More strikingly, the overall expression levels of genes associated with broad promoters (but not peak promoters) with modified histones were significantly higher than the levels of genes associated with broad promoters with unmodified histones.These results shed light on how epigenetic regulatory networks of histone modifications are associated with promoter architecture.Recent progress in high-throughput technologies has made it possible to collect a variety of "omics" data on transcripts and on the epigenetic behaviors of the histones that are often associated with these transcripts [1-5].Cap analysis of gene expression (CAGE) is a high-throughput method that enables large-scale identification of transcription start sites (TSSs) of eukaryotic species. This method measures gene expression levels simultaneously with TSS identification by counting the sequenced 5' ends of full-length cDNAs, termed CAGE tags [2,6]. With the development of deep sequencing methods, more high-throughput, and high resolution "tag depth" measurements have become available (DeepCAGE, nanoCAGE and CAGEscan) [1,7]. Such recent whole-cell-level pictures of quantitative transcriptomes have revealed the complex transcriptional network of mammalian species [1,2,6]. According to recent CAGE-based analyses of human TSSs, the human "promotome"
Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions
Yosuke Ozawa, Rintaro Saito, Shigeo Fujimori, Hisashi Kashima, Masamichi Ishizaka, Hiroshi Yanagawa, Etsuko Miyamoto-Sato, Masaru Tomita
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-350
Abstract: Here, we introduce a combinatorial approach for prediction of protein complexes focusing not only on determining member proteins in complexes but also on the DDI/PPI organization of the complexes. Our method analyzes complex candidates predicted by the existing methods. It searches for optimal combinations of domain-domain interactions in the candidates based on an assumption that the proteins in a candidate can form a true protein complex if each of the domains is used by a single protein interaction. This optimization problem was mathematically formulated and solved using binary integer linear programming. By using publicly available sets of yeast protein-protein interactions and domain-domain interactions, we succeeded in extracting protein complex candidates with an accuracy that is twice the average accuracy of the existing methods, MCL, MCODE, or clustering coefficient. Although the configuring parameters for each algorithm resulted in slightly improved precisions, our method always showed better precision for most values of the parameters.Our combinatorial approach can provide better accuracy for prediction of protein complexes and also enables to identify both direct PPIs and DDIs that mediate them in complexes.Recently developed high-throughput methods such as yeast two-hybrid or mass spectrometry to obtain protein-protein interactions (PPIs) have provided a global view of the interaction network [1-5]. As a PPI network grows, it becomes increasingly important to detect functional modules for understanding cellular organization and its dynamics [6]. Protein complexes are clusters of multiple proteins, and they often play a crucial part in basal cellular mechanism. Therefore, computational methods to predict protein complexes are becoming important.There are four steps in characterizing a protein complex [7]. The first step is to identify its member proteins. The second step is to determine its topology by identifying pairs of proteins which have direct inte
Self-initiated Self-repair Attempts by Japanese High School Learners While Speaking English
Rintaro Sato
Brain. Broad Research in Artificial Intelligence and Neuroscience , 2012,
Abstract: In Japanese high school English classes, students are often left to have interactions or perform communicative activities not with a teacher but with other students due to a large class size. In the situation, students are ideally notice their own insufficient utterances in order to carry out self-initiated self-repair. This study investigated self-initiated self-repair attempts and their effects on Japanese high school learners. Thirty-two Japanese high school students with low-intermediate English ability and a native speaker of English participated in the study, with the native speaker interviewing the students. The students’ utterances were quantitatively and qualitatively analyzed, and it was found that: self-initiated self-repair occurred frequently and, in general, successfully; error repair was most frequently recorded; the success rate of lexical repair was the lowest. Findings observed during the students’ self-initiated self-repair attempts are discussed, followed by discussion of their possible effects. Finally, suggestions are given based on the pedagogical implications from the study.
Elliptic curves related to cyclic cubic extensions
Rintaro Kozuma
Mathematics , 2007,
Abstract: The aim of this paper is to study certain family of elliptic curves $\{\mathscr{X}_H\}_H$ defined over a number field $F$ arising from hyperplane sections of some cubic surface $\mathscr{X}/F$ associated to a cyclic cubic extension $K/F$. We show that each $\mathscr{X}_H$ admits a 3-isogeny $\phi$ over $F$ and the dual Selmer group $S^{(\hat{\phi})}(\hat{\mathscr{X}_H}/F)$ is bounded by a kind of unit/class groups attached to $K/F$. This is proven via certain rational function on the elliptic curve $\mathscr{X}_H$ with nice property. We also prove that the Shafarevich-Tate group $\text{\cyr X} (\hat{\mathscr{X}_H}/\rat)[\hat{\phi}]$ coincides with a class group of $K$ as a special case.
On some questions of Fisk and Br?ndén
Rintaro Yoshida
Mathematics , 2010,
Abstract: P. Br\"and\'en recently proved a conjecture due to S. Fisk, R. P. Stanley, P. R. W. McNamara and B. E. Sagan. In addition, P. Br\"and\'en gave a partial answer to a question posed by S. Fisk regarding the distribution of zeros of polynomials under the action of certain non-linear operators. In this paper, we give an extension to a result of P. Br\"and\'en, and we also answer a question posed by S. Fisk.
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