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Search Results: 1 - 10 of 128 matches for " Nozomu Yachie "
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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
HybGFS: a hybrid method for genome-fingerprint scanning
Kosaku Shinoda, Nozomu Yachie, Takeshi Masuda, Naoyuki Sugiyama, Masahiro Sugimoto, Tomoyoshi Soga, Masaru Tomita
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-479
Abstract: Here, we present a hybrid method for genome-fingerprint scanning, known as HybGFS. This technique combines genome sequence-based peptide MS/MS ion searching with liquid-chromatography elution-time (LC-ET) prediction, to improve the reliability of identification. The hybrid method allows the simultaneous identification and mapping of proteins without a priori information about their coding sequences. The current study used standard LC-MS/MS data to query an in silico-generated six-reading-frame translation and the enzymatic digest of an entire genome. Used in conjunction with precursor/product ion-mass searching, the LC-ETs increased confidence in the peptide-identification process and reduced the number of false-positive matches. The power of this method was demonstrated using recombinant proteins from the Escherichia coli K12 strain.The novel hybrid method described in this study will be useful for the large-scale experimental confirmation of genome coding sequences, without the need for transcriptome-level expression analysis or costly MS database searching.Mass spectrometry (MS) is one of the major proteomics tools of the post-genomic era. Protein identification has traditionally been conducted by peptide mass fingerprinting (PMF) [1-3] or tandem MS (MS/MS) database searching and, while the former performs well with highly purified samples, the latter is the de facto standard for identifying proteins in complex samples. However, these approaches are only capable of detecting proteins already listed in databases. PMF implicitly assumes that all genes are annotated and that their complete protein sequences, including post-translational modifications, are known; however, in reality, most of these sequences are inadequately represented in existing databases. As alternative approaches, de novo peptide sequencing can be performed by the Edman degradation method [4], MS/MS [5,6], and controlled protein hydrolysis [7]. However, although amino-acid sequences can provide 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"
38-year-old woman with recurrent abdominal pain, but no fever
Iwata K, Toma T, Yachie A
International Journal of General Medicine , 2012, DOI: http://dx.doi.org/10.2147/IJGM.S30867
Abstract: r-old woman with recurrent abdominal pain, but no fever Case report (2714) Total Article Views Authors: Iwata K, Toma T, Yachie A Published Date March 2012 Volume 2012:5 Pages 265 - 268 DOI: http://dx.doi.org/10.2147/IJGM.S30867 Received: 14 February 2012 Accepted: 22 February 2012 Published: 22 March 2012 Kentaro Iwata1, Tomoko Toma2, Akihiro Yachie2 1Department of Infectious Diseases, Kobe University Hospital, Kobe, Japan; 2Department of Pediatrics, Graduate School of Medical Science and School of Medicine, Kanazawa University, Kanazawa, Japan Abstract: A 38-year-old woman presented with 2 days history of left-flank pain. She had similar episodes of abdominal pain as well as chest pain several times, but symptoms disappeared spontaneously. Each time she developed pain, there was no fever. After ruling out common causes of recurrent abdominal pain, familial Mediterranean fever (FMF) was considered as a potential diagnosis. Genetic tests revealed multiple heterozygote mutations, which may be associated with FMF. Patients with Mediterranean fever mutations may present with atypical presentations without fever, like in this case. Astute clinical suspicion is required to make an accurate diagnosis.
38-year-old woman with recurrent abdominal pain, but no fever
Iwata K,Toma T,Yachie A
International Journal of General Medicine , 2012,
Abstract: Kentaro Iwata1, Tomoko Toma2, Akihiro Yachie21Department of Infectious Diseases, Kobe University Hospital, Kobe, Japan; 2Department of Pediatrics, Graduate School of Medical Science and School of Medicine, Kanazawa University, Kanazawa, JapanAbstract: A 38-year-old woman presented with 2 days history of left-flank pain. She had similar episodes of abdominal pain as well as chest pain several times, but symptoms disappeared spontaneously. Each time she developed pain, there was no fever. After ruling out common causes of recurrent abdominal pain, familial Mediterranean fever (FMF) was considered as a potential diagnosis. Genetic tests revealed multiple heterozygote mutations, which may be associated with FMF. Patients with Mediterranean fever mutations may present with atypical presentations without fever, like in this case. Astute clinical suspicion is required to make an accurate diagnosis.Keywords: familial Mediterranean fever, MEFV mutation, afebrile
Nucleosynthesis of 56Ni in wind-driven Supernova Explosions and Constraints on the Central Engine of Gamma-Ray Bursts
Keiichi Maeda,Nozomu Tominaga
Physics , 2009, DOI: 10.1111/j.1365-2966.2009.14460.x
Abstract: Theoretically expected natures of a supernova driven by a wind/jet are discussed. Approximate analytical formulations are derived to clarify basic physical processes involved in the wind/jet-driven explosions, and it is shown that the explosion properties are characterized by the energy injection rate (Edot_iso) and the mass injection rate (Mdot_iso). To explain observations of SN 1998bw associated with Gamma-Ray Burst (GRB) 980425, the following conditions are required: Edot_iso Mdot_iso > ~ 10^{51} erg M_sun s^{-2} and Edot_iso > ~ 2 x 10^{52} erg s^{-1} (if the wind Lorentz factor Gamma_w ~ 1) or Edot_iso > ~ 7 x 10^{52} erg s^{-1} (if Gamma_w >> 1). In SN 1998bw, 56Ni (~ 0.4M_sun) is probably produced in the shocked stellar mantle, not in the wind. The expected natures of SNe, e.g., ejected 56Ni masses and ejecta masses, vary depending on Edot_iso and Mdot_iso. The sequence of the SN properties from high Edot_iso and Mdot_iso to low Edot_iso and Mdot_iso is the following: SN 1998bw-like -- intermediate case -- low mass ejecta (< ~ 1M_sun$) where 56Ni is from the wind -- whole collapse. This diversity may explain the diversity of supernovae associated with GRBs. Our result can be used to constrain natures of the wind/jet, which is linked to the central engine of GRBs, by studying properties of the associated supernovae.
New Method for Exploring Super-Eddington AGNs by Near-infrared Observations
Nozomu Kawakatu,Ken Ohsuga
Physics , 2011, DOI: 10.1111/j.1365-2966.2011.19422.x
Abstract: We propose a new method to explore the candidate super-Eddington active galactic nuclei (AGNs). We examine the properties of infrared (IR) emission from the inner edge of the dusty torus in AGNs, which are powered by super- or sub-Eddington accretion flows around black holes, by considering the dependence of the polar angle on the radiation flux of accretion flows (Watarai et al. 2005). We find that for super-Eddington AGNs, of which the mass accretion rate is more than 10^2 times larger than the Eddington rate, the ratio of the AGN IR luminosity and the disc bolometric luminosity is less than 10^-2, unless the half opening angle of the torus (theta_torus) is small (theta_torus <65 degree). This is due to the self-occultation effect, whereby the self-absorption at the outer region of the super-Eddington flow dilutes the illumination of the torus. Such a small luminosity ratio is not observed in sub-Eddington AGNs, whose mass accretion rate is comparable to or no more than 10 times larger than the Eddington mass accretion rate, except for extremely thin tori (theta_torus >85 degree). We also consider the properties of the near-IR (NIR) emission radiated from hot dust >1000 K. We find that super-Eddington AGNs have a ratio of the NIR luminosity to the bolometric luminosity, L_NIR,AGN/L_bol,disc, at least one order of magnitude smaller than for sub-Eddington AGNs for a wide range of half opening angle (theta_torus > 65 degree), for various types of dusty torus model. Thus, a relatively low L_NIR,AGN/L_bol,disc is a property that allows identification of candidate super-Eddington AGNs. Lastly, we discuss the possibility that NIR-faint quasars at redshift z=6 discovered by a recent deep SDSS survey may be young quasars whose black holes grow via super-Eddington accretion.
Nuclear Composition of Magnetized GRB Jets
Sanshiro Shibata,Nozomu Tominaga
Physics , 2015, DOI: 10.1093/pasj/psv020
Abstract: We investigate the fraction of metal nuclei in the relativistic jets of gamma-ray bursts associated with core-collapse supernovae. We simulate the fallback in jet-induced explosions with two-dimensional relativistic hydrodynamics calculations and the jet acceleration with steady, radial, relativistic magnetohydrodynamics calculations, and derive detail nuclear composition of the jet by postprocessing calculation. We found that if the temperature at the jet launch site is above $4.7\times 10^9$K, quasi-statistical equilibrium (QSE) is established and heavy nuclei are dissociated to light particles such as $^4$He during the acceleration of the jets. The criterion for the survival of metal nuclei is written in terms of the isotropic jet luminosity as $L_{\rm j}^{\rm iso} \lesssim 3.9\times 10^{50}(R_{\rm i}/10^7{\rm cm})^2 (1+\sigma_{\rm i})~{\rm erg~s^{-1}}$, where $R_{\rm i}$ and $\sigma_{\rm i}$ are the initial radius of the jets and the initial magnetization parameter, respectively. If the jet is initially dominated by radiation field (i.e., $\sigma_{\rm i} \ll 1$) and the isotropic luminosity is relatively high ($L_{\rm j}^{\rm iso}\gtrsim 4\times 10^{52}~{\rm erg s^{-1}}$), the metal nuclei cannot survive in the jet. On the other hand, if the jet is mainly accelerated by magnetic field (i.e., $\sigma_{\rm i} \gg1$), metal nuclei initially contained in the jet can survive without serious dissociation even for the case of high luminosity jet. If the jet contains metal nuclei, the dominant nuclei are $^{28}$Si, $^{16}$O, and $^{32}$S and the mean mass number can be $\langle$A$\rangle\sim25$.
Formation of High-redshift (z>6) Quasars Driven by Nuclear Starbursts
Nozomu Kawakatu,Keiichi Wada
Physics , 2009, DOI: 10.1088/0004-637X/706/1/676
Abstract: Based on the physical model of a supermassive black hole (SMBH) growth via gas accretion in a circumnuclear disk (CND) proposed by Kawakatu & Wada (2008), we describe the formation of high-$z$ ($z > 6$) quasars (QSOs) whose BH masses are M_{BH}> 10^{9} M_{\odot}. We derive the necessary conditions to form QSOs at z > 6 by only gas accretion: (i) A large mass supply with M_{sup} > 10^{10}M_{\odot} from host galaxies to CNDs, because the final BH mass is only 1-10% of the total supplied mass from QSO hosts. (ii) High star formation efficiency for a rapid BH growth. We also find that if the BH growth is limited by the Eddington accretion, the final BH mass is greatly suppressed. Thus, the super-Eddington growth is required for the QSO formation. The evolution of the QSO luminosity depends on the redshift z_{i} at which accretion onto a seed BH is initiated. In other words, the brighter QSOs at z >6 favor the late growth of SMBHs (i.e., z_{i}=10) rather than early growth (i.e., z_{i}=30). Moreover, we predict the observable properties and the evolution of QSOs at z >6. In a QSO phase, there should exist a stellar rich massive CND, whose gas mass is about 10% of the dynamical mass inside 0.1-1 kpc}. On the other hand, in a phase where the BH grows (i.e., a proto-QSO phase), the proto-QSO has a gas rich massive CNDs whose gas mass is comparable to the dynamical mass (abridged).
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