Junko Shibato

Korea Basic Science Institute KBSI, Sŏul, Seoul, South Korea

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Publications (58)138.96 Total impact

  • [show abstract] [hide abstract]
    ABSTRACT: High ozone (O 3) concentrations not only damage plant life but also cause considerable losses in plant productivity. To screen for molecular factors usable as potential biomarkers to identify for O 3-sensitive and -tolerant lines and design O 3 tolerant crops, our project examines the effects of O 3 on rice, using high-throughput omics approaches. In this study, we examined growth and yield parameters of 4 rice cultivars fumigated for a life-time with ambient air (mean O 3: 31.4-32.7 ppb) or filtered air (mean O 3: 6.6-8.3 ppb) in small open-top chambers (sOTCs) to select O 3-sensitive (indica cv Takanari) and O 3-tolerant (japonica cv Koshihikari) cultivars for analysis of seed transcriptomes using Agilent 4 × 44K rice oligo DNA chip. Total RNA from dry mature dehusked seeds of Takanari and Koshihikari cultivars was extracted using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment, followed by DNA microarray analysis using the established dye-swap method. Direct comparison of Koshihikari and Takanari O 3 transcriptomes in seeds of rice plants fumigated with ambient O 3 in sOTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in sensitive cv Takanari and tolerant cv Koshihikari. MapMan analysis further mapped the molecular factors activated by O 3, confirming Takanari is rightly classified as an O 3 sensitive genotype.
    Plant signaling & behavior 09/2013; 8(11).
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    ABSTRACT: Human mesenchymal stem/stromal cells (hMSCs) have been reported to improve neural damage via anti-inflammation and multi-differentiation abilities. Here, we investigated immunosuppression effects of hMSCs by mixed-culturing with interferon-γ (IFNγ) stimulated BV-2 mouse microglial cells. We show that hMSCs decreased nitrite oxide (NO) production from BV-2 cells in cell density dependent manner. Aged hMSCs and peroxisome proliferator-activated receptor-γ (PPARγ) knockdown hMSCs decreased differentiation abilities but maintained NO suppressive function. We finally confirmed NO suppression activities of hMSCs in IFNγ-stimulated primary microglia/macrophages. It suggested that hMSCs significantly modified NO production in activated phagocytes and it might be preserved in late passage cultures.
    Journal of neuroimmunology 08/2013; · 2.84 Impact Factor
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    ABSTRACT: The Figure 2, X-axis description of each sample was inverted in the original publication [1]. Figure 2 The mRNA expression profiles of differentially expressed genes. Both the upregulated (A) and downregulated (B) genes were selected randomly. Gel images on top show the polymerase chain reaction (PCR) product bands stained with ethidium bromide; the band intensities are also presented graphically below for clarity. Lane numbers 1 to 8 indicate sham control (lanes 1, 2, 5, and 6) and permanent middle cerebral artery occlusion (PMCAO) treatment (lanes 3, 4, 7, and 8), respectively. P indicates pituitary adenylate cyclase-activating polypeptide (PACAP) treatment; C is the control (minus PACAP). GAPDH and beta-actin genes were used a positive control (C). Semi-quantitative RT-PCR was performed as described in Methods, and the specific 3'-UTR primers are detailed in Additional file 2: Table S2 With reference to corrected Figure 2, we have the following revised text. On Page 9, left column: lines 19-24 should read as - "Similarly, Il6, S100a5, Il22, Il1b, Igf1, and Ccl2 were highly expressed at 6 h in the PACAP-treated ischemic brain, whereas their expression level decreased at 24 h compared to the PMCAO effect alone (Figure 2). Fgf21, Pitpnc1, and Epha3 genes showed an increase in expression at 24 h over PMCAO alone (Figure 2)." On Page 11, right column: lines 16-19 should read as - "In the ischemic hemisphere at 24 h, the PACAP plus PMCAO expression level of Il6 was also reduced compared to the PMCAO plus saline control." We regret any inconvenience that this inaccuracy in Figure 2 and therein the figure legend, which could not be properly corrected at the proof stage, in the originally published manuscript might have caused.
    Journal of Neuroinflammation 01/2013; 10(1):18. · 4.35 Impact Factor
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    ABSTRACT: Jasmonic acid (JA) and salicylic acid (SA) are critical signaling components involved in various aspects of plant growth, development, and defense. Their constitutive levels vary from plant to plant and also from tissue to tissue within the same plant. Moreover, their quantitative levels change when plant is exposed to biotic and abiotic stresses. To better understand the JA- and SA-mediated signaling and metabolic pathways, it is important to precisely quantify their levels in plants/tissues/organs. However, their extraction and quantification are not trivial and still technically challenging. An effort has been made in various laboratories to develop a simple and standard procedure that can be utilized for quantification of JA and SA. Here, we present the experimental procedure and our decade of experience on extracting and quantifying them in an absolute manner in leaves of rice seedlings. We must mention that this method has been applied to both monocotyledonous and dicotyledonous plants for absolute quantification of JA and SA. As collaboration is the key towards rapid progress in science and technology, we are always open to sharing our experience in this field with any active research group with an aim to improve the procedure further and eventually to connect the importance of their (JA and SA) quantitative levels with networks of signaling and metabolic pathways in plants.
    Methods in molecular biology (Clifton, N.J.) 01/2013; 956:185-200.
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    ABSTRACT: Rice is one of the most important food and cereal crop plants in the world. Rice proteomics began in the 1990s. Since then, considerable progress has been made in establishing protocols from isolation of rice proteins from different tissues, organs, and organelles, to separation of complex proteins and to their identification by mass spectrometry. Since the year 2000, global proteomics studies have been performed during growth and development under numerous biotic and abiotic environmental conditions. Two-dimensional (2-D) gel-based proteomics platform coupled with mass spectrometry has been retained as the workhorse for proteomics of a variety of rice samples. In this chapter, we describe in detail the different protocols used for isolation of rice proteins, their separation, detection, and identification using gel-based proteomics and mass spectrometry approaches.
    Methods in molecular biology (Clifton, N.J.) 01/2013; 956:151-84.
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    ABSTRACT: The 'ozone (O(3))-responsive transcriptome' behavior in the panicles and grains of rice plant was studied individually through high-throughput oligo-DNA microarray technique. O(3) differentially and separately regulated 620 and 130 genes in the panicles and grains. Among the O(3)-responsive genes, 176 and 444 genes were up- and down-regulated in panicle compared to 24 and 106 genes in grain, respectively. Further mapping revealed that the majority of differentially expressed genes were mainly involved in signaling, hormonal, cell wall, transcription, proteolysis, and defense events. Many previously unknown O(3)-responsive novel genes were identified. Inventory of 745 O(3)-responsive genes and their mapping will expand our knowledge on novel regulatory processes in both panicles and grains of rice; and, serve as a resource towards the designing of rice crops for future high-O(3)world. PURPOSE OF WORK: Tropospheric ozone (O(3)) severely affects agricultural production worldwide. Present study aims to reveal a detailed O(3) responsive gene network in panicle and grains of rice plants through transcriptomics approach. Our results provide an insight into the basis of O(3)-response in rice plants, and will help to develop suitable rice genotype for future high O(3)- world.
    Biotechnology Letters 12/2012; · 1.85 Impact Factor
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    ABSTRACT: INTRODUCTION: The neuropeptide pituitary adenylate cyclase-activating polypeptide (PACAP) is considered to be a potential therapeutic agent for prevention of cerebral ischemia. Ischemia is a most common cause of death after heart attack and cancer causing major negative social and economic consequences. This study was designed to investigate the effect of PACAP38 injection intracerebroventrically in a mouse model of permanent middle cerebral artery occlusion (PMCAO) along with corresponding SHAM control that used 0.9% saline injection. METHODS: Ischemic and non-ischemic brain tissues were sampled at 6 and 24 hours post-treatment. Following behavioral analyses to confirm whether the ischemia has occurred, we investigated the genome-wide changes in gene and protein expression using DNA microarray chip (4x44K, Agilent) and two-dimensional gel electrophoresis (2-DGE) coupled with matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS), respectively. Western blotting and immunofluorescent staining were also used to further examine the identified protein factor. RESULTS: Our results revealed numerous changes in the transcriptome of ischemic hemisphere (ipsilateral) treated with PACAP38 compared to the saline-injected SHAM control hemisphere (contralateral). Previously known (such as the interleukin family) and novel (Gabra6, Crtam) genes were identified under PACAP influence. In parallel, 2-DGE analysis revealed a highly expressed protein spot in the ischemic hemisphere that was identified as dihydropyrimidinase-related protein 2 (DPYL2). The DPYL2, also known as Crmp2, is a marker for the axonal growth and nerve development. Interestingly, PACAP treatment slightly increased its abundance (by 2-DGE and immunostaining) at 6 h but not at 24 h in the ischemic hemisphere, suggesting PACAP activates neuronal defense mechanism early on. CONCLUSIONS: This study provides a detailed inventory of PACAP influenced gene expressions and protein targets in mice ischemic brain, and suggests new targets for thereaupetic interventions.
    Journal of Neuroinflammation 11/2012; 9(1):256. · 4.35 Impact Factor
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    04/2012; , ISBN: 978-953-51-0527-5
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    ABSTRACT: Brain ischemia, also termed cerebral ischemia, is a condition in which there is insufficient blood flow to the brain to meet metabolic demand, leading to tissue death (cerebral infarction) due to poor oxygen supply (cerebral hypoxia). Our group is interested in the protective effects of neuropeptides for alleviating brain ischemia, as well as the underlying mechanisms of their action. The present study was initiated to investigate molecular responses at the level of gene expression in ischemic brain tissue. To achieve this, we used a mouse permanent middle cerebral artery occlusion (PMCAO) model in combination with high-throughput DNA microarray analysis on an Agilent microarray platform. Briefly, the right (ipsilateral) and left (contralateral) hemispheres of PMCAO model mice were dissected at two time points, 6 and 24 hours post-ischemia. Total RNA from the ischemic (ipsilateral) hemisphere was subjected to DNA microarray analysis on a mouse whole genome 4x44K DNA chip using a dye-swap approach. Functional categorization using the gene ontology (GO, MGD/AMIGO) of numerous changed genes revealed expression pattern changes in the major categories of cellular process, biological regulation, regulation of biological process, metabolic process and response to stimulus. Reverse-transcriptase PCR (RT-PCR) analysis on randomly selected highly up- or downregulated genes validated, in general, the microarray data. Using two time points for this analysis, major and minor trends in gene expression and/or functions were observed in relation to early- and late-response genes and differentially regulated genes that were further classified into specific pathways or disease states. We also examined the expression of these genes in the contralateral hemisphere, which suggested the presence of bilateral effects and/or differential regulation. This study provides the first ischemia-related transcriptome analysis of the mouse brain, laying a strong foundation for studies designed to elucidate the mechanisms regulating ischemia and to explore the neuroprotective effects of agents such as target neuropeptides.
    Disease Models and Mechanisms 03/2012; 5(2):270-83. · 4.96 Impact Factor
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    ABSTRACT: MALAT-1 noncoding RNA is localized to nuclear speckles despite its mRNA-like characteristics. Here, we report the identification of several key factors that promote the localization of MALAT-1 to nuclear speckles and also provide evidence that MALAT-1 is involved in the regulation of gene expression. Heterokaryon assays revealed that MALAT-1 does not shuttle between the nucleus and cytoplasm. RNAi-mediated repression of the nuclear speckle proteins, RNPS1, SRm160, or IBP160, which are well-known mRNA processing factors, resulted in the diffusion of MALAT-1 to the nucleoplasm. We demonstrated that MALAT-1 contains two distinct elements directing transcripts to nuclear speckles, which were also capable of binding to RNPS1 in vitro. Depletion of MALAT-1 represses the expression of several genes. Taken together, our results suggest that RNPS1, SRm160, and IBP160 contribute to the localization of MALAT-1 to nuclear speckles, where MALAT-1 could be involved in regulating gene expression.
    RNA 02/2012; 18(4):738-51. · 5.09 Impact Factor
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    ABSTRACT: Mechanisms underlying behavioral abnormalities of patients with attention-deficit hyperactivity disorder (ADHD) disorder are still unknown. It is worth clarifying alterations in the brain of animal models for ADHD. The animals with neonatal treatment with 6-hydroxydopamine (6-OHDA) and congenic wiggling (Wig) rats show motor hyperactivities during a period of darkness at 4 weeks of age. In rats with 6-OHDA lesions, subcutaneous injection of methamphetamine attenuates hyperactivity, the reverse of its effect in Wig rats. To understand mechanisms underlying such behavioral abnormalities, transcriptomics and proteomics analyses may provide novel information in brain research. The expression of genes and proteins in brain regions can be measured by DNA microarray and two-dimensional gel electrophoresis, respectively. We have shown different expressions of genes and proteins in brains of rats with neonatal 6-OHDA lesions and Wig rats.
    Methods in molecular biology (Clifton, N.J.) 01/2012; 829:505-30.
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    ABSTRACT: Proteolysis-related genes have diverse functions across taxa and have long been considered as key players for intracellular protein turnover. Growing evidence indicates the biological significance of peptidases in degradation, maturation and modulation of bioactive peptides/proteins. By screening T-DNA tagged lines and functional analysis approaches we unraveled the Arabidopsis leucine aminopeptidase (AtLAP2) function in amino acid turnover. Transcriptomics and metabolomics profiling data suggested involvement of AtLAP2 in specific metabolic pathways. Loss-of-function of AtLAP2 resulted in early-leaf senescent and stress-sensitive phenotypes. Our work indicates an important in planta role for AtLAP2 contributing to a further understanding of the proteases having several implications in higher plants.
    Plant signaling & behavior 10/2011; 6(10):1581-3.
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    ABSTRACT: Human epidemiological evidence has led scientists to theorize that undernutrition during gestation is an important early origin of adult diseases. Animal models have successfully demonstrated that maternal diet could contribute to some adult diseases. Undernutrition is perceived harmful in pregnant women, whereas calorie restriction is a strategy proven to extend healthy and maximum lifespan in adult. This diagrammatically opposite effect of nutritional condition might provide us with hints to search for genes underlying health conditions. Here, we have initiated a study examining the effect of undernutrition on maternal and fetal livers, utilizing high-throughput DNA microarray analysis for screening genome-wide changes in their transcriptomes. Briefly, pregnant mice were exposed to food deprivation (FD) on gestation day (GD) 17, and cesarean section was performed on GD18. Control mice were supplied with chow ad libitum until sacrifice. Total RNA extracted from mother and fetal livers for each control and treatment (FD) was analyzed with an Agilent mouse whole genome DNA chip. A total of 3058 and 3126 up- (>1.5-fold) and down- (<0.75-fold) regulated genes, and 1475 and 1225 up- (>1.5-fold) and down- (<0.75-fold) regulated genes showed differential expression at the mRNA level, in the maternal and fetal livers, respectively. Interestingly, 103 genes up-regulated in the mother were down-regulated in the fetus, whereas 108 down-regulated maternal genes were up-regulated in the fetus; these 211 genes are potential candidates related to longevity or health. The role of some of these genes, in context of the proposed mechanisms for developmental origins of health and disease is discussed.
    Congenital Anomalies 09/2011; 51(3):110-25.
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    ABSTRACT: Peptidases are known to play key roles in multiple biological processes in all living organisms. In higher plants, the vast majority of putative aminopeptidases remain uncharacterized. In this study, we performed functional and expression analyses of the Arabidopsis LAP2 through cDNA cloning, isolation of T-DNA insertional mutants, characterization of the enzymatic activity, characterization of gene expression and transcriptomics and metabolomics analyses of the mutants. Loss of function of LAP2, one of the 28 aminopeptidases in Arabidopsis, reduced vegetative growth, accelerated leaf senescence and rendered plants more sensitive to various stresses. LAP2 is highly expressed in the leaf vascular tissue and the quiescent center region. Integration of global gene expression and metabolite analyses suggest that LAP2 controlled intracellular amino acid turnover. The mutant maintained free leucine by up-regulating key genes for leucine biosynthesis. However, this influenced the flux of glutamate strikingly. As a result, γ-aminobutyric acid, a metabolite that is derived from glutamate, was diminished in the mutant. Decrements in these nitrogen-rich compounds are associated with morphological alterations and stress sensitivity of the mutant. The results indicate that LAP2 is indeed an enzymatically active aminopeptidase and plays key roles in senescence, stress response and amino acid turnover.
    New Phytologist 05/2011; 191(4):958-69. · 6.74 Impact Factor
  • Fuel and Energy Abstracts 01/2011; 205.
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    Sample Preparation In Biological Mass Spectrometry. 01/2011;
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    ABSTRACT: Ozone is now considered to be the second most important gaseous pollutant in our environment. The phytotoxic potential of O₃ was first observed on grape foliage by B.L. Richards and coworkers in 1958 (Richards et al. 1958). To date, unsustainable resource utilization has turned this secondary pollutant into a major component of global climate change and a prime threat to agricultural production. The projected levels to which O₃ will increase are critically alarming and have become a major issue of concern for agriculturalists, biologists, environmentalists and others plants are soft targets for O₃. Ozone enters plants through stomata, where it disolves in the apoplastic fluid. O₃ has several potential effects on plants: direct reaction with cell membranes; conversion into ROS and H₂O₂ (which alters cellular function by causing cell death); induction of premature senescence; and induction of and up- or down-regulation of responsive components such as genes , proteins and metabolites. In this review we attempt to present an overview picture of plant O₃ interactions. We summarize the vast number of available reports on plant responses to O₃ at the morphological, physiological, cellular, biochemical levels, and address effects on crop yield, and on genes, proteins and metabolites. it is now clear that the machinery of photosynthesis, thereby decreasing the economic yield of most plants and inducing a common morphological symptom, called the "foliar injury". The "foliar injury" symptoms can be authentically utilized for biomonitoring of O₃ under natural conditions. Elevated O₃ stress has been convincingly demonstrated to trigger an antioxidative defense system in plants. The past several years have seen the development and application of high-throughput omics technologies (transcriptomics, proteomics, and metabolomics) that are capable of identifying and prolifiling the O₃-responsive components in model and nonmodel plants. Such studies have been carried out ans have generated an inventory of O₃-Responsive components--a great resource to the scientific community. Recently, it has been shown that certain organic chemicals ans elevated CO₂ levels are effective in ameliorating O₃-generated stress. Both targeted and highthroughput approaches have advanced our knowledge concerning what O₃-triggerred signaling and metabolic pathways exist in plants. Moreover, recently generated information, and several biomarkers for O₃, may, in the future, be exploited to better screen and develop O₃-tolerant plants.
    Reviews of environmental contamination and toxicology 01/2011; 212:61-111. · 4.13 Impact Factor
  • 01/2011: pages 453–477; , ISBN: 978-1-4398-2504-4
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    ABSTRACT: Hydrostatic pressure is a physical factor that can induce stress in organisms. This stress leads to growth inhibition, cellular arrest, and cellular death, and these effects depend on the degree of pressure, temperature, and sensitivity of the organisms to hydrostatic pressure. Genomics studies of yeast cells under conditions recovering from high pressure-induced cellular damage showed evidence that multiprotein complexes or membrane proteins, and not soluble proteins, are the critical targets. We performed a metabolomic analysis. The metabolomics results suggested that membrane-spanning proteins broke down after high pressure treatment and recovery conditions. We also found 13 genes that were common to essential and pressure-induced gene groups. Among these 13 genes, more than 10 were associated with proteasome structure and functions. This suggests that proteasome structure or functions can be the critical target or a highly important factor. This hypothesis is supported by the fact that yeast cells are sensitive to the proteasome inhibitor MG132 after high pressure treatment.
    High Pressure Research 12/2010; 30(4):519-523. · 0.90 Impact Factor
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    ABSTRACT: SII-K1 is a member of the transcription elongation factor S-II family. In the mouse, SII-K1 is expressed exclusively in the liver, kidney, heart, and skeletal muscle. Here, we report that deletion of the SII-K1 gene in mice resulted in the downregulation of the synaptotagmin-like 1 (Sytl 1) gene in liver and of the coiled-coil domain-containing 21 (Ccdc21) gene in liver and kidney. Moreover, the induction of the metallothionein I (Mt I) gene in SII-K1-deficient mice liver was impaired in diethyl maleate-induced oxidative stress conditions. Our results suggest that SII-K1 regulates these genes in vivo.
    Drug discoveries & therapeutics. 10/2010; 4(5):368-72.

Publication Stats

539 Citations
138.96 Total Impact Points


  • 2013
    • Korea Basic Science Institute KBSI
      Sŏul, Seoul, South Korea
  • 2011–2013
    • Showa University
      • • Department of Medicine
      • • Department of Anatomy
      Shinagawa, Tōkyō, Japan
  • 2007–2013
    • Chonnam National University
      • • College of Agriculture and Life Sciences
      • • Division of Applied Bioscience and Biotechnology
      Yeoju, Gyeonggi, South Korea
    • University of Tsukuba
      Tsukuba, Ibaraki, Japan
  • 2012
    • Kyoto University
      • Department of Forensic Medicine and Molecular Pathology
      Kyoto, Kyoto-fu, Japan
  • 2010–2012
    • Toho University
      • • Department of Biology
      • • Faculty of Science
      Edo, Tōkyō, Japan
  • 2008–2012
    • National Institute for Environmental Studies
      Tsukuba, Ibaraki, Japan
    • Seoul National University
      • Department of Food and Nutrition
      Seoul, Seoul, South Korea
    • Ibaraki University
      Mito-shi, Ibaraki, Japan
  • 2003–2012
    • National Institute of Advanced Industrial Science and Technology
      • Health Research Institute
      Tsukuba, Ibaraki, Japan
  • 2006–2008
    • Sejong University
      • College of Natural Sciences
      Seoul, Seoul, South Korea
    • Hokkaido University Hospital
      Sapporo, Hokkaidō, Japan