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Katsumi Sakata

Publications and source records attributed to Katsumi Sakata.

16 recordsLinked to original sources
PubMed2005

Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.

A contig-oriented database for annotation of the rice genome has been constructed to facilitate map-based rice genomics. The Rice Annotation Database has the following functional features: (i) extensive effort of manual annotations of P1-derived artificial chromosome/bacterial artificial chromosome clones can be merged at chromosome and contig-level; (ii) concise visualization of the annotation information such as the predicted genes, results of various prediction programs (RiceHMM, Genscan, Genscan+, Fgenesh, GeneMark, etc.), homology to expressed sequence tag, full-length cDNA and protein; (iii) user-friendly clone / gene query system; (iv) download functions for nucleotide, amino acid and coding sequences; (v) analysis of various features of the genome (GC-content, average value, etc.); and (vi) genome-wide homology search (BLAST) of contig- and chromosome-level genome sequence to allow comparative analysis with the genome sequence of other organisms. As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results including 30 000 manually curated genes. The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome. The database can be accessed at http://rad.dna.affrc.go.jp/.

Chromosomes, Plant↗
PubMed2005

Transethmoidal meningoencephalocele in an elderly woman. Case report.

A 69-year-old woman presented with a transethmoidal meningoencephalocele manifesting as gradually developing anosmia. Examinations revealed a mass in the nasal cavity associated with multiple angiomas in her lip and orbit. Neuroimaging showed meningoencephalocele extending via the ethmoid sinus to the nasal cavity. She had no history of craniofacial trauma and intranasal or intracranial operation, and no skull base tumor was detected. Frontal base reconstruction was performed with a two-layer vascularized flap to prevent cerebrospinal fluid leakage. The dural defect was repaired with the pericranial flap, and the bony defect of the cribriform plate was reconstructed using the reversed U-shaped split temporalis musculofascial flap. Transethmoidal meningoencephalocele is a rare congenital malformation and almost half of the cases are identified in the first year of life. We should be aware of this clinical pathology and avoid unexpected rhinorrhea in elderly patients. The most important aspect of the operation is watertight closure of the patent passage to the intracranial compartment. The reversed U-shaped split temporalis musculofascial flap is useful to reconstruct the midline frontal base defect.

Aged↗
PubMed2005

Intraoperative power Doppler ultrasonography with a contrast-enhancing agent for intracranial tumors.

OBJECT: The goal of this study was to evaluate intraoperative power Doppler ultrasonography when used with a contrast-enhancing agent for operations on intracranial tumors. METHODS: Forty intracranial tumors were examined using power Doppler ultrasonography with a galactose microparticle-based ultrasonographic contrast-enhancing agent during operations on the brain. The tumors included 37 intracranial neoplasms (14 gliomas, six meningiomas, three hemangioblastomas, two malignant lymphomas, three other primary neoplasms, nine metastatic tumors, and three nonneoplastic lesions). All patients also underwent computerized tomography and magnetic resonance imaging, and all but three of the patients underwent digital subtraction (DS) angiography. Before injection of the ultrasonographic contrast agent, intra- and peritumoral power Doppler flow signals were detected in 32 of the intracranial tumors. After the injection, the signals were enhanced in blood vessels around the tumors and in the tumor parenchyma in 36 tumors. The duration of contrast enhancement continued for 70 to 365 seconds (mean 251.8 +/- 69 seconds) after the injection. Among the tumors, hemangioblastomas displayed particularly strong contrast enhancement. In these intracranial tumors, the echo signals obtained using contrast-enhanced power Doppler ultrasonography correlated with DS angiographic staining. Power Doppler ultrasonograms with the appropriate contrast agent provided better data on the precise real-time position of the tumors and their relationship to adjacent vessels than ultrasonograms obtained before the injection of the contrast agent. CONCLUSIONS: Intraoperative power Doppler ultrasonography performed using a contrast-enhancing agent can facilitate intraoperative real-time navigation and assessment of the intratumoral vasculature and peritumoral vessels, particularly for tumors having abundant vessels such as hemangioblastomas.

Adolescent↗
PubMed2003

Genomics approach to abscisic acid- and gibberellin-responsive genes in rice.

We used an 8987-EST collection to construct a cDNA microarray system with various genomics information (full-length cDNA, expression profile, high accuracy genome sequence, phenotype, genetic map, and physical map) in rice. This array was used as a probe to hybridize target RNAs prepared from normally grown callus of rice and from callus treated for 6 hr or 3 days with the hormones abscisic acid (ABA) or gibberellin (GA). We identified 509 clones, including many clones that had never been annotated as ABA-or GA-responsive. These genes included not only ABA- or GA-responsive genes but also genes responsive to other physiological conditions such as pathogen infection, heat shock, and metal ion stress. Comparison of ABA- and GA-responsive genes revealed antagonistic regulation for these genes by both hormones except for one defense-related gene, thionin. The gene for thionin was up-regulated by both hormone treatments for 3 days. The upstream regions of all the genes that were regulated by both hormones had cis-elements for ABA and GA response. We performed a clustering analysis of genes regulated by both hormones and various expression profiles that showed three notable clusters (seed tissues, low temperature and sugar starvation, and thionin-gene related). A comparison of the cis-elements for hormone response genes between rice and Arabidopsis thaliana, we identified cis-elements for dehydration-stress response or for expression of amylase gene as Arabidopsis gene-specific or rice gene-specific, respectively.

Abscisic Acid↗
PubMed2003

Fos-B expression is required for polyamine-induced increase in nuclear activator protein-1 DNA binding in discrete structures of murine brain.

Spermidine (SPD) and spermine (SPN) have been shown to be endogenous agonists for N-methyl-D-aspartate (NMDA) receptors that could lead to expression of the nuclear transcription factor activator protein-1 (AP1) complex in the mammalian central nervous system both in vitro and in vivo. In nuclear extracts of murine whole brain, AP1 DNA binding increased significantly in a concentration-dependent manner with the addition of either SPD or SPN at a concentration range of 50-500 microM. Similarly, the nuclear proteins histone and dephosphorylated casein, but not phosphorylated casein, significantly increased AP1 DNA binding alone but in the presence of either SPD or SPN did not increase further binding. By contrast, another endogenous polyamine, putrescine, significantly prevented AP1 DNA binding increases by histone and dephosphorylated casein, but did not by itself significantly alter binding. Invariably, SPD and SPN effected significantly increased AP1 DNA binding in neocortex, hippocampus, striatum, midbrain, hypothalamus and cerebellum, but not in medulla-pons and spinal cord. Supershift and Western blotting analyses revealed relatively high constitutive expression of Fos-B protein in neocortex and hippocampus, but not in medulla-pons and spinal cord. Immunoprecipitation of Fos-B led to complete abolition of the ability of SPN and SPD to increase AP1 DNA binding in neocortical and hippocampal nuclear extracts. These results suggest that expression of Fos-B protein may be required for modulation of nuclear gene transcription by both SPD and SPN through stimulation DNA-binding activity of AP1 complex in murine central structures.

Animals↗
PubMed2003

Possible correlation between abilities of a variety of polyamines to increase activator protein-1 DNA binding and to inhibit [3H]spermidine transport in nuclear fractions of murine brain.

The addition of a number of natural and synthetic polyamines significantly increased activator protein (AP1) DNA binding in nuclear extracts of murine whole brain, which occurred in a manner positively correlated with their potencies to inhibit temperature-dependent transport of [3H]spermidine in brain nuclear fractions. These results suggest that polyamines may affect gene transcription by AP1 complex after incorporation into the nucleus in rodent brain.

Animals↗
PubMed2003

A possible novel mechanism underlying temperature-dependent uptake of [3H]spermidine in nuclear fractions of murine brain.

[3H]Spermidine (SPD) was accumulated in subcellular fractions enriched of the nucleus in a temperature-dependent manner with a saturable profile in murine brain. The accumulation reached a plateau within 30 min at 2 degrees C and 30 degrees C, while excess unlabeled SPD significantly inhibited the accumulation at 2 degrees C without markedly affecting that at 30 degrees C when added after equilibrium. The temperature-dependent accumulation of [3H]SPD was significantly inhibited by the triamine SPD and the tetraamine spermine, but not by the diamine putrescine. Phospholipases were invariably effective in significantly inhibiting the accumulation at 30 degrees C in a concentration-dependent manner. Amongst different discrete murine central structures examined, the temperature-dependent [3H]SPD accumulation was highest in neocortex with progressively lower activities in striatum, hypothalamus, spinal cord, medulla-pons, hippocampus, midbrain and cerebellum. These results suggest the possible presence of a hitherto unidentified nuclear transport system for particular polyamines in murine brain.

Adenosine Triphosphate↗
PubMed2003

Modulation of DNA binding of nuclear transcription factors with leucine-zipper motifs by particular endogenous polyamines in murine central and peripheral excitable tissues.

Transcriptional regulation is one of the most important functions of polyamines in the nucleus of eukaryotic cells. The addition of the endogenous polyamines spermine and spermidine markedly increased DNA binding activity of the transcription factor activator protein-1 (AP1) in a concentration-dependent manner at a concentration range of 50 to 500 microM in nuclear extracts of murine whole brain when determined in the absence of added MgCl(2) on gel retardation electrophoresis. Similar but less potent potentiation was seen with DNA binding of cAMP responsive element binding protein (CREB), while both polyamines were ineffective in affecting that of c-Myc irrespective of the addition of MgCl(2). Unlabeled AP1 probe was invariably more potent in competing for AP1 binding than unlabeled CREB probe in either the presence or absence of spermine and spermidine. In addition to whole brain, both polyamines significantly increased AP1 binding in retina, adrenal and pituitary, without significantly affecting that in spleen. Moreover, ultraviolet and circular dichroism spectra analyses revealed that these two polyamines induced DNA topological transition of AP1 probe under the conditions favorable for the increase in AP1 binding. These results suggest that both spermine and spermidine may modulate gene transcription through cis- and trans-actions on AP1 binding in the nucleus in murine central and peripheral structures with high excitability.

Animals↗
PubMed2003

Rice gene expression in response to N-acetylchitooligosaccharide elicitor: comprehensive analysis by DNA microarray with randomly selected ESTs.

N-acetylchitooligosaccharides are potent elicitors to suspension-cultured rice cells, inducing a set of defense reactions. Expression of defense-related genes is considered to play an important role in defense reactions, and we employed microarray analysis of 8987 randomly selected expressed sequence tags to analyze the changes in gene expression caused by N-acetylchitooctaose. In this experiment, 166 genes were significantly induced and 93 genes were repressed. RNA gel blot analysis of 16 of these genes confirmed the microarray results. Of the 259 ESTs identified as responsive to N-acetylchytooctaose, 18 genes are related to signal transduction, including five calcium-dependent protein kinases (CDPKs). Among these, three novel CDPKs responsive to N-acetylchitooctaose were isolated.

Amino Acid Sequence↗
PubMed2003

Novel gene encoding a Ca2+-binding protein and under hexokinase-dependent sugar regulation.

A cDNA encoding a predicted 15-kDa protein was earlier isolated from sugar-induced genes in rice embryos (Oryza sativa L.) by cDNA microarray analysis. Here we report that this cDNA encodes a novel Ca2+-binding protein, named OsSUR1 (for Oryza sativa sugar-up-regulated-1). The recombinant OsSUR1 protein expressed in Escherichia coli had 45Ca2+-binding activity. Northern analysis showed that the OsSUR1 gene was expressed mainly in the internodes of mature plants and in embryos at an early stage of germination. Expression of the OsSUR1 gene was induced by sugars that could serve as substrates of hexokinase, but expression was not repressed by Ca2+ signaling inhibitors, calmodulin antagonists and inhibitors of protein kinase or protein phosphatase. These results suggested that Os-SUR1 gene expression was stimulated by a hexokinase-dependent pathway not mediated by Ca2+.

Amino Acid Motifs↗
PubMed2002

The genome sequence and structure of rice chromosome 1.

The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins of Arabidopsis thaliana, another model plant. About 30% (2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and is characterized by several gene families that are dispersed or arranged in tandem repeats. Comparison with a draft sequence indicates the importance of a high-quality finished sequence.

Arabidopsis↗
PubMed2002

RiceGAAS: an automated annotation system and database for rice genome sequence.

An extensive effort of the International Rice Genome Sequencing Project (IRGSP) has resulted in rapid accumulation of genome sequence, and >137 Mb has already been made available to the public domain as of August 2001. This requires a high-throughput annotation scheme to extract biologically useful and timely information from the sequence data on a regular basis. A new automated annotation system and database called Rice Genome Automated Annotation System (RiceGAAS) has been developed to execute a reliable and up-to-date analysis of the genome sequence as well as to store and retrieve the results of annotation. The system has the following functional features: (i) collection of rice genome sequences from GenBank; (ii) execution of gene prediction and homology search programs; (iii) integration of results from various analyses and automatic interpretation of coding regions; (iv) re-execution of analysis, integration and automatic interpretation with the latest entries in reference databases; (v) integrated visualization of the stored data using web-based graphical view. RiceGAAS also has a data submission mechanism that allows public users to perform fully automated annotation of their own sequences. The system can be accessed at http://RiceGAAS.dna.affrc.go.jp/.

Automation↗
PubMed2002

cDNA microarray analysis of gene expression during Fe-deficiency stress in barley suggests that polar transport of vesicles is implicated in phytosiderophore secretion in Fe-deficient barley roots.

To acquire Fe from soil, graminaceous plants secrete mugineic acid family phytosiderophores (MAs) from their roots. The secretion of MAs increases in response to Fe deficiency, and shows a distinct diurnal rhythm. We used a microarray that included 8987 cDNAs of rice EST clones to examine gene expression profiles in barley roots during Fe-deficiency stress. Approximately 200 clones were identified as Fe-deficiency-inducible genes, of which seven had been identified previously. In order to meet the increased demand for methionine to produce MAs, Fe-deficiency enhances the expression of genes that participate in methionine synthesis, as well as recycling methionine through the Yang cycle. Of these 200 genes, approximately 50 exhibited different transcription levels in Fe-deficient roots at noon and at night. Northern blot analysis of time course experiments confirmed that five of these genes exhibited a diurnal change in their level of expression. The diurnal changes in the expression of these genes suggest that polar vesicle transport is involved in the diurnal secretion of MAs.

Azetidinecarboxylic Acid↗
PubMed2002

Intramedullary spinal cord germinoma: case report and review of the literature.

A 33-year-old man with an intramedullary spinal cord germinoma was treated successfully with partial resection, combined chemotherapy with carboplatin and etoposide, and reduced-dose local-field radiation therapy. The authors believe this is the first case without syncytiotrophoblastic giant cells so treated. The literature is reviewed, and the appearance, radiologic and histopathologic features, and treatment of germinomas are discussed.

Adult↗
PubMedDate not supplied

Clinical evaluation of choline measurement by proton MR spectroscopy in patients with malignant tumors.

PURPOSE: To examine whether choline measurement by proton magnetic resonance (MR) spectroscopy in patients with malignant tumors is clinically meaningful in addition to routine MR imaging. MATERIALS AND METHODS: MR spectroscopy and MR imaging were performed in 27 consecutive patients with suspected malignant disease. Malignancy was assessed based on total choline compound levels using proton MR spectroscopy, and the results were compared with MR imaging findings. RESULTS: The sensitivity of MR imaging (84%, 21/25) was not significantly different from that of MR spectroscopy (88%, 22/25) among the 25 actual malignant diseases. Both MR imaging and MR spectroscopy produced two false-negative results. In one case, MR spectroscopy produced a false-negative result, whereas MR imaging produced a true-positive result. In two cases of benign breast disease, MR imaging produced false-positive results. MR spectroscopy produced one true-negative result and one false-positive result. CONCLUSION: Although choline measurement by MR spectroscopy is a useful tool in the evaluation of malignant disease, it should be reserved for patients with suspected malignant disease that cannot be detected by MR imaging, such as those with non-palpable prostate tumor with elevated sPSA levels.

Adult↗