Publish in OALib Journal

ISSN: 2333-9721

APC: Only $99


Any time

2019 ( 2 )

2018 ( 9 )

2017 ( 5 )

2016 ( 14 )

Custom range...

Search Results: 1 - 10 of 889 matches for " Yasushi Ishihama "
All listed articles are free for downloading (OA Articles)
Page 1 /889
Display every page Item
OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics
Mohamed Helmy, Masaru Tomita, Yasushi Ishihama
BMC Plant Biology , 2011, DOI: 10.1186/1471-2229-11-63
Abstract: Here, we present OryzaPG-DB, a rice proteome database based on shotgun proteogenomics, which incorporates the genomic features of experimental shotgun proteomics data. This version of the database was created from the results of 27 nanoLC-MS/MS runs on a hybrid ion trap-orbitrap mass spectrometer, which offers high accuracy for analyzing tryptic digests from undifferentiated cultured rice cells. Peptides were identified by searching the product ion spectra against the protein, cDNA, transcript and genome databases from Michigan State University, and were mapped to the rice genome. Approximately 3200 genes were covered by these peptides and 40 of them contained novel genomic features. Users can search, download or navigate the database per chromosome, gene, protein, cDNA or transcript and download the updated annotations in standard GFF3 format, with visualization in PNG format. In addition, the database scheme of OryzaPG was designed to be generic and can be reused to host similar proteogenomic information for other species. OryzaPG is the first proteogenomics-based database of the rice proteome, providing peptide-based expression profiles, together with the corresponding genomic origin, including the annotation of novelty for each peptide.The OryzaPG database was constructed and is freely available at http://oryzapg.iab.keio.ac.jp/ webcite.Among high-throughput experimental methods, genome sequencing represents a turning point in the understanding of biological systems. Nevertheless, the biological significance of the sequenced genome cannot be understood unless the protein-coding genes and their products are accurately identified. Thus, genome annotation has become major issue [1-3]. Genome annotation is the process of gene structure and function determination, and it usually takes place after genome sequencing and before data deposition in a database or databank [2,4,5].In typical genome annotation work, experimental and computational methods are integrated to an
LGI1 and LGI4 bind to ADAM22, ADAM23 and ADAM11
Koji Sagane, Yasushi Ishihama, Hachiro Sugimoto
International Journal of Biological Sciences , 2008,
Abstract: The transmembrane protein ADAM22 is expressed at high levels in the brain. From its molecular structure, ADAM22 is thought to be an adhesion molecule or a receptor because it has functional disintegrin-like and cysteine-rich sequences in its ectodomain. The phenotypic analysis of ADAM22-deficient mice has indicated the important roles played by ADAM22 in proper neuronal function and peripheral nerve development, however, the precise molecular function of ADAM22 is still unknown. To understand the function of ADAM22 on a molecular basis, we identified ADAM22 binding proteins by using immunoprecipitation and mass spectrometric analysis. This analysis revealed that Leucine-rich glioma inactivated 1 (LGI1) is the most potent ADAM22 binding protein in mouse brain. By our quantitative cell-ELISA system, we demonstrated the specific binding of LGI1 with ADAM22. Furthermore, we showed that LGI4, a putative ADAM22 ligand, also bound to ADAM22. Characterization of the binding specificity of LGI1 and LGI4 suggested that ADAM22 is not a sole receptor, because ADAM11 and ADAM23 had a significant binding ability to LGI1 or LGI4. Therefore, LGI-ADAM system seems to be regulated not only by the affinity but also by the cell-type-specific expression of each protein. Our findings provide new clues to understand the functions of LGI1 and LGI4 as an ADAMs ligand.
Nestin Protein Is Phosphorylated in Adult Neural Stem/Progenitor Cells and Not Endothelial Progenitor Cells
Jun Namiki,Sayuri Suzuki,Takeshi Masuda,Yasushi Ishihama,Hideyuki Okano
Stem Cells International , 2012, DOI: 10.1155/2012/430138
Abstract: An intermediate filament protein, Nestin, is known as a neural stem/progenitor cell marker. It was shown to be required for the survival and self-renewal of neural stem cells according to the phenotypes of Nestin knockout mice. Nestin expression has also been reported in vascular endothelial cells, and we recently reported Nestin expression in proliferating endothelial progenitor cells, but not in mature endothelial cells. Using quantitative phosphoproteome analysis, we studied differences in phosphorylation levels between CNS Nestin in adult neural stem cells and vascular Nestin in adult bone-marrow-derived endothelial progenitor cells. We detected 495 phosphopeptides in the cell lysates of adult CNS stem/progenitor cells and identified 11 significant phosphorylated amino acid residues in the Nestin protein. In contrast, endothelial progenitor cells showed no significant phosphorylation of Nestin. We also measured neoplastic endothelial cells of the mouse brain and identified 13 phosphorylated amino acid residues in the Nestin protein. Among the 11 phosphorylated amino acids of adult CNS Nestin, five (S565, S570, S819, S883, and S886) were CNS Nestin-specific phosphorylation sites. Detection of the CNS-specific phosphorylation sites in Nestin, for example, by a phospho-specific Nestin antibody, may allow the expression of CNS Nestin to be distinguished from vascular Nestin. 1. Introduction Nestin is a class VI intermediate filament protein expressed in undifferentiated central nervous system (CNS) cells during development. The protein is known as a neural stem/progenitor cell marker and required for the survival and self-renewal of neural stem cells (NSCs) [1]. Nestin expression is downregulated when CNS stem/progenitor cells differentiate into neurons or glial cells [2, 3], and the expression is kept in adult CNS stem/progenitor cells that reside in the forebrain neurogenic regions [4, 5]. Nestin expression has also been reported in vascular endothelial cells (ECs) from a variety of adult human non-CNS tissues [6, 7]. We recently reported Nestin expression in proliferating endothelial progenitor cells (EPCs), but not in mature ECs [8]. We utilized E/nestin?:?EGFP transgenic mice using its second intronic enhancer element to study neural-specific nestin gene expression [9, 10] and demonstrated that vascular nestin expression is not activated by the CNS-specific enhancer of the nestin gene [8]. This finding indicated that the Nestin expressed in EPCs is cytochemically similar to the protein expressed in CNS stem/progenitor cells, but the regulatory
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
Protein abundance profiling of the Escherichia coli cytosol
Yasushi Ishihama, Thorsten Schmidt, Juri Rappsilber, Matthias Mann, F Ulrich Hartl, Michael J Kerner, Dmitrij Frishman
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-102
Abstract: Here, we describe an experimental scheme to maximize the coverage of proteins identified by mass spectrometry of a complex biological sample. Using a combination of LC-MS/MS approaches with protein and peptide fractionation steps we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100. A measure of abundance is presented for each of the identified proteins, based on the recently developed emPAI approach which takes into account the number of sequenced peptides per protein. The values of abundance are within a broad range and accurately reflect independently measured copy numbers per cell.As expected, the most abundant proteins were those involved in protein synthesis, most notably ribosomal proteins. Proteins involved in energy metabolism as well as those with binding function were also found in high copy number while proteins annotated with the terms metabolism, transcription, transport, and cellular organization were rare. The barrel-sandwich fold was found to be the structural fold with the highest abundance. Highly abundant proteins are predicted to be less prone to aggregation based on their length, pI values, and occurrence patterns of hydrophobic stretches. We also find that abundant proteins tend to be predominantly essential. Additionally we observe a significant correlation between protein and mRNA abundance in E. coli cells.Abundance measurements for more than 1000 E. coli proteins presented in this work represent the most complete study of protein abundance in a bacterial cell so far. We show significant associations between the abundance of a protein and its properties and functions in the cell. In this way, we provide both data and novel insights into the role of protein concentration in this model organism.Proteins fulfill a wide variety of functions and are central to almost all processes in living cells. In order to improve our understanding of the complex network of protein interactions in the cell, it is of ce
Dps Is a Stationary Phase-Specific Protein of Escherichia coli Nucleoid  [PDF]
Ali Azam Talukder, Akira Ishihama
Advances in Microbiology (AiM) , 2014, DOI: 10.4236/aim.2014.415120
Abstract: Bacterial genomic DNA is highly organized into one or few compacted bodies known as nucleoid, which is composed of DNA, RNA and several DNA-binding proteins. These DNA-binding proteins require essential alterations in their expression during stationary phase of growth in order to re-spond to stressful environmental conditions. Dps (DNA-binding protein from starved cells) is one of such DNA-binding proteins, which accumulates most when E. coli cells reach to the stationary phase. Here, we have characterized Dps protein under various growth phases. Immunofluorescent microscopic observation reveals that Dps plays a key role in final round of genome compaction during the stationary phase. Similar results are also obtained by Western immunoblot analysis, after quantification of Dps protein from the exponential phase and early stationary phase nucleoid bound fractions, separated by sucrose density gradient centrifugation. Our results support the conclusion that Dps occupies more than half of the stationary phase nucleoid in E. coli.
Phosphorylation of Mitochondrial Polyubiquitin by PINK1 Promotes Parkin Mitochondrial Tethering
Kahori Shiba-Fukushima,Taku Arano,Gen Matsumoto,Tsuyoshi Inoshita,Shigeharu Yoshida,Yasushi Ishihama,Kwon-Yul Ryu,Nobuyuki Nukina,Nobutaka Hattori ,Yuzuru Imai
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004861
Abstract: The kinase PINK1 and the E3 ubiquitin (Ub) ligase Parkin participate in mitochondrial quality control. The phosphorylation of Ser65 in Parkin's ubiquitin-like (UBl) domain by PINK1 stimulates Parkin activation and translocation to damaged mitochondria, which induces mitophagy generating polyUb chain. However, Parkin Ser65 phosphorylation is insufficient for Parkin mitochondrial translocation. Here we report that Ser65 in polyUb chain is also phosphorylated by PINK1, and that phosphorylated polyUb chain on mitochondria tethers Parkin at mitochondria. The expression of Tom70MTS-4xUb SE, which mimics phospho-Ser65 polyUb chains on the mitochondria, activated Parkin E3 activity and its mitochondrial translocation. An E3-dead form of Parkin translocated to mitochondria with reduced membrane potential in the presence of Tom70MTS-4xUb SE, whereas non-phospho-polyUb mutant Tom70MTS-4xUb SA abrogated Parkin translocation. Parkin binds to the phospho-polyUb chain through its RING1-In-Between-RING (IBR) domains, but its RING0-linker is also required for mitochondrial translocation. Moreover, the expression of Tom70MTS-4xUb SE improved mitochondrial degeneration in PINK1-deficient, but not Parkin-deficient, Drosophila. Our study suggests that the phosphorylation of mitochondrial polyUb by PINK1 is implicated in both Parkin activation and mitochondrial translocation, predicting a chain reaction mechanism of mitochondrial phospho-polyUb production by which rapid translocation of Parkin is achieved.
Effects of Pitavastatin on the Intima-Media Thickness of the Carotid Artery in Patients with Ischemic Stroke: The Pitavastatin Efficacy Study on Surrogate Markers and Imaging for Stroke (PESSMIST)  [PDF]
Yasushi Shibata
World Journal of Neuroscience (WJNS) , 2014, DOI: 10.4236/wjns.2014.44034

Pitavastatin is a strong statin that was developed in Japan. The clinical impact of pitavastatin treatment in patients with ischemic stroke has not been reported. We conducted a prospective, open label, clinical case-control study to determine the secondary preventive effects of pitavastatin for patients with cerebral infarction and hyperlipidemia. The pitavastatin group included 20 Japanese patients diagnosed with cerebral infarction and hyperlipidemia without previous statin intake. The control group included 22 patients diagnosed with cerebral infarction without hyperlipidemia. The pitavastatin group of patients received 2 mg of pitavastatin once a day after dinner. The mean age of the patients was 69.3 and 75.5 years for the pitavastatin and control groups, respectively, and the age of the pitavastatin group was significantly younger than that of the control group (P < 0.05). The serum TCho and LDL-C levels significantly decreased two months after the initiation of pitavastatin treatment. The mean and maximum intima-media thickness (IMT) also decreased after the initiation of pitavastatin. The mean and maximum IMT did not show any significant changes in the control group. The change of IMT %/year was less than zero for the pitavastatin group, and was almost zero or higher for the control group. Pitavastatin showed beneficial effects by improving the surrogate makers of stroke. These surrogate makers were effective to evaluate the efficacy of pitavastatin to prevent secondary stroke. Although a prospective randomized study is required to elucidate the long-term effects of pitavastatin, the current study suggests that pitavastatin may be effective to prevent secondary stroke in patients with stroke and hyperlipidemia.

Optimum-Welfare and Maximum-Revenue Tariffs in Vertically Related Markets  [PDF]
Yasushi Kawabata
Modern Economy (ME) , 2014, DOI: 10.4236/me.2014.55055

This paper compares the optimum-welfare tariffs with the maximum-revenue tariffs in a model of vertically related markets characterized by Cournot competition. It shows that the optimum-welfare tariff on the intermediate good exceeds the maximum-revenue tariff if the home intermediate-good firm is much more cost-competitive than the foreign intermediate-good firm. Further, the optimum-welfare tariff on the final good exceeds the maximum-revenue tariff if the home intermediate-good firm is significantly inefficient compared to the foreign intermediate-good firm. It is less likely that the optimum-welfare tariffs on the intermediate and the final good, respectively, exceed the maximum-revenue tariffs on the intermediate and the final good in the presence of vertical trade structures than in their absence.

Page 1 /889
Display every page Item

Copyright © 2008-2017 Open Access Library. All rights reserved.