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Takashi Komori

Publications and source records attributed to Takashi Komori.

At least 19 recordsLinked to original sources
PubMed2006

fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences.

There are abundance of transcripts that code for no particular protein and that remain functionally uncharacterized. Some of these transcripts may have novel functions while others might be junk transcripts. Unfortunately, the experimental validation of such transcripts to find functional non-coding RNA candidates is very costly. Therefore, our primary interest is to computationally mine candidate functional transcripts from a pool of uncharacterized transcripts. We introduce fRNAdb: a novel database service that hosts a large collection of non-coding transcripts including annotated/non-annotated sequences from the H-inv database, NONCODE and RNAdb. A set of computational analyses have been performed on the included sequences. These analyses include RNA secondary structure motif discovery, EST support evaluation, cis-regulatory element search, protein homology search, etc. fRNAdb provides an efficient interface to help users filter out particular transcripts under their own criteria to sort out functional RNA candidates. fRNAdb is available at http://www.ncrna.org/

Base Sequence↗
PubMed2006

Parvalbumin and calbindin D-28k immunoreactivity in transgenic mice with a G93A mutant SOD1 gene.

Immunohistochemical study was performed to examine if calcium-binding proteins are involved in the degeneration of motor neurons in the brain stems and the spinal cords of transgenic mice carrying a G93A mutant human SOD1 gene. Specimens from age-matched non-transgenic wild-type mice served as controls. In the spinal cord of the controls, the density of parvalbumin-immunoreactive neurons was highest in the large anterior horn neurons and lower in the posterior horn neurons in the spinal cord. On the other hand, calbindin D-28k immunoreactivity was much less apparent than that observed with parvalbumin antisera. Rexed's lamina II was densely immunostained for calbindin D-28k, whereas, in the anterior horn, calbindin-D-28k-positive small neurons were barely dispersed in a scattered pattern. In transgenic mice, parvalbumin-positive anterior horn neurons were severely reduced, even at the presymptomatic stage, whereas calbindin-positive neurons were largely preserved. At the symptomatic stage, both parvalbumin and calbindin D-28k immunoreactivity markedly diminished or disappeared in the anterior horn. Immunoblotting analysis revealed a significant reduction of immunoreactivity to parvalbumin antibody in transgenic mice compared with the controls. In the brain stem, parvalbumin-positive oculomotor and abducens neurons and the calbindin D-28k-positive sixth nucleus were well-preserved in transgenic mice as well as in the controls. Thus, the diffuse and severe loss of parvalbumin immunoreactivity of large motor neurons even at early stages in SOD1-transgenic mice and the absence of calbindin D-28k immunoreactivity of normal large motor neurons suggest that these calcium-binding proteins may contribute to selective vulnerability and an early loss of function of large motor neurons in this SOD1-transgenic mouse model.

Abducens Nerve↗
PubMed2006

Papillary glioneuronal tumor with minigemistocytic components and increased proliferative activity.

Papillary glioneuronal tumor (PGNT) is a rare and new type of glioneuronal neoplasm of the central nervous system. It is characterized by pseudopapillary structures composed of hyalinized vessels rimmed by cuboidal glial cells and the proliferation of neuronal cells. We report a peculiar PGNT arising in the parietal lobe of a 67-year-old man, which was characterized by proliferation of minigemistocytic cells as well as typical components. The minigemistocytic cells had eccentric nuclei and plump eosinophilic cytoplasm that was filled with glial filaments. The Ki-67 labeling index was as high as 10% in the minigemistocytic areas. Recently, the presence of oligodendroglial-like component was suggested in PGNT. Considering that oligodendroglioma sometimes accompanies minigemistocytic components, the minigemistocytic cells in PGNT were suggested to be a part of oligodendroglial differentiation. Although PGNT is defined as an indolent glioneuronal tumor, the presence of minigemistocytic components with the high Ki-67 labeling index may indicate more aggressive nature.

Aged↗
PubMed2006

Neuronal inclusions in sporadic motor neuron disease are negative for alpha-synuclein.

Alpha-synuclein has been implicated in neurodegenerative diseases characterized by Lewy bodies. However, we have only scanty information on the immunoreactivity of alpha-synuclein in other inclusion bodies such as the Lewy body-like inclusions and the skein-like inclusions observed in motor neuron disease (MND). In this report, we immunocytochemically investigated inclusion bodies observed in the anterior horn neurons of the spinal cord in 29 patients with sporadic MND. Sixteen age-matched patients without any neurological disease served as controls. In MND patients, we recognized Lewy body-like hyaline inclusions, skein-like inclusions, Bunina bodies, basophilic inclusions, and intracytoplasmic hyaline (colloid) inclusions, but none of them were immunostained for alpha-synuclein. Our findings in this study do not support the hypothesis that MND could be classified as one of the diseases grouped as alpha-synucleinopathies.

Adult↗
PubMed2005

Genome sequencing and analysis of Aspergillus oryzae.

The genome of Aspergillus oryzae, a fungus important for the production of traditional fermented foods and beverages in Japan, has been sequenced. The ability to secrete large amounts of proteins and the development of a transformation system have facilitated the use of A. oryzae in modern biotechnology. Although both A. oryzae and Aspergillus flavus belong to the section Flavi of the subgenus Circumdati of Aspergillus, A. oryzae, unlike A. flavus, does not produce aflatoxin, and its long history of use in the food industry has proved its safety. Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans and Aspergillus fumigatus. Comparison of the three aspergilli species revealed the presence of syntenic blocks and A. oryzae-specific blocks (lacking synteny with A. nidulans and A. fumigatus) in a mosaic manner throughout the genome of A. oryzae. The blocks of A. oryzae-specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation.

Aspartic Acid Endopeptidases↗
PubMed2005

A distinct pattern of Olig2-positive cellular distribution in papillary glioneuronal tumors: a manifestation of the oligodendroglial phenotype?

Mixed neuronal-glial tumors of the central nervous system display a wide spectrum of differentiation. Among them, the papillary glioneuronal tumor (PGNT) is characterized by pseudopapillary structures composed of astroglial cells covering hyalinized vessels, and by neurocytic, ganglioid and ganglion cells. In addition, a "nonspecific" cell type, not similar to either astrocytes or neurocytes, has been recognized since the initial reports. Recently, minigemistocytic cells and a population immunostained by anti-Olig2 antibody have also been recognized in PGNT. Olig2 is a transcription factor that is specific for the cellular phenotype of oligodendrocytes. The aim of this study was to further investigate the histological diversity of PGNT. We examined six cases of PGNT, each of which showed Olig2 immunopositivity. Minigemistocytes were encountered in three cases at close proximity to the Olig2-positive area. Olig2-positive cells were negative for glial fibrillary acidic protein (GFAP) and neuronal nuclear antigen by double immunostaining, and mainly occupied the interpapillary area laterally adjacent to the GFAP-positive cells. They had relatively small, round and vesicular nuclei, and were formerly regarded as neurocytic cells or nonspecific cellular elements. Fluorescence in situ hybridization targeting chromosome 1p failed to demonstrate any deletion. This study disclosed an additional cellular component of PGNT that is characterized by Olig2 positivity, suggestive of oligodendroglial phenotype, and the results also encourage us to investigate oligodendroglial participation in various glioneuronal tumors.

Adolescent↗
PubMed2005

Stromal cells in hemangioblastoma: neuroectodermal differentiation and morphological similarities to ependymoma.

The histogenesis of stromal cells in hemangioblastoma is inconclusive despite a long-term controversy. An immunohistochemical and ultrastructural study was conducted for 17 cases of cerebellar hemangioblastoma. A wide range of immunohistological markers, targeting epithelial, mesenchymal, endothelial and neuroectodermal tissues, was used. In all cases, the microscopic hallmark characterizing hemangioblastomas, that is, lipid-containing stromal cells and a fine capillary network, known as a reticular variant, was noted. Stromal cells showed a variable immunoreactivity for neuroectodermal markers, such as S-100 protein, CD56, CD57, CD99, and neuron-specific enolase. This result, in conjunction with the absence of immunoreactivity for epithelial, mesenchymal, and endothelial markers, likely suggests neuroectodermal differentiation of stromal cells. In three cases, another component, known as a cellular variant, where epithelioid tumor cells were arranged in nests encircled by capillaries and/or in pseudorosette-like structures, was noted. Glial fibrillary acidic protein-immunoreactivity, which was totally absent in cases only showing the reticular pattern, was noted in two of them, suggesting a distinctive sign of glial differentiation in a proportion of hemangioblastomas. Ultrastructurally, microvilli-like projections in intracytoplasmic vacuoles were demonstrated in stromal cells. This result, taken together with the neuroectodermal hypothesis of stromal cells, suggests that hemangioblastomas may occasionally exhibit morphological similarities to ependymomas.

12E7 Antigen↗
PubMed2005

[A case of black dot ringworm caused by Trichophyton tonsurans in Chiba Prefecture].

A 74-year-old woman visited a clinic in Kisarazu, Chiba Prefecture in December 2002 complaining of itching, scale and alopecia. She had been diagnosed as having tinea capitis by a direct microscopic examination of scales, and been treated with an antifungal cream and steroid lotion since 1999. The bald area spread from frontal to occipital in which multiple black dots and red papules were scattered. Abundant endothrix spores were observed in the hair shaft. A mycelial colony was isolated from the black dots. A giant colony on Sabouraud's agar was white, powdery and flattened with cottony elevation at the center in the obverse, and a reddish-brown pigmentation in the reverse. The isolate produced abundant microconidia that were round to club-and balloon-shaped with extreme swelling, while macroconidia and spiral bodies were few. Hair perforation test was negative and urease activity test was positive. ITS1-5.8S-ITS2 rDNA sequencing revealed 100% homology with T. tonsurans isolated from two old women in Niigata Prefecture. On the other hand, 3 bases were different from those of the outbreak isolates from judo and wrestling players infected through international matches. T. tonsurans has polymorphism and the present isolate might be an autochthonous genotype in Japan. This is the first time T. tonsurans was isolated in Chiba Prefecture. But this prefecture had been known as an endemic area of Trichophyton coccineum, which was very similar in morphological and physiological characteristics to those of T. tonsurans before World War II. These facts raise the question of whether T. tonsurans has existed in this prefecture before.

Aged↗
PubMed2005

Phylogenetic analysis of Histoplasma capsulatum based on partial sequence of the D1/D2 region of the 28S rRNA gene.

In order to confirm the phylogenetic relationships of Histoplasma capsulatum, the partial sequences of large subunit (28S) ribosomal gene (D1/D2 region) of 49 isolates were studied. The similarity values of the 49 isolates were more than 99.0% across 617 base pairs, however, the 49 isolates were divided into 9 groups. These 9 groups were independent of 3 varieties, var. capsulatum, var. farciminosum and var. duboisii. These results showed that analysis of the nucleotide sequence of the 28S rRNA gene was very effective for identification of H. capsulatum and that three varieties of H. capsulatum should be reclassified according to the phylogenetic relationship established from analysis of the D1/D2 region sequences.

Animals↗
PubMed2004

Ultrastructural study of aggregates in the spinal cord of transgenic mice with a G93A mutant SOD1 gene.

The ultrastructural features of SOD1-positive aggregates were determined to clarify whether these aggregates are associated with the pathogenesis of SOD1 mutant mice. We examined the spinal cord of transgenic mice expressing a G93A mutant human SOD1 gene with fewer copies (gene copy 10). At the early presymptomatic stage (age 24 weeks), SOD1- and ubiquitin-positive granular, linear, or round deposits were found occasionally in the neuropil of the anterior horns. Ultrastructurally, small filamentous aggregates were observed occasionally in the neuronal processes including the axons in the anterior horns. At the late presymptomatic stage (28 weeks), SOD1- and ubiquitin-positive deposits and Lewy body-like inclusions (LIs) were frequently demonstrated in the neuronal processes including cord-like swollen axons and in some remaining anterior horn neurons. Ultrastructurally, larger filamentous aggregates were frequent, predominating in the neuronal processes of the anterior horns including the proximal axons, but were rare in the somata and dendrites. The aggregates usually consisted of interwoven intermediate filaments (about 10-15 nm in diameter) and frequently contained electron-dense cores in the center resembling LIs. Occasionally the aggregates consisted mainly of granular, amorphous, or vesicular substance, showing fewer filamentous structures. At the symptomatic stages (32 and 35 weeks), LIs were frequently demonstrated within the neuronal processes in the anterior horns, particularly in the cord-like swollen axons. Many more prominent SOD1- and ubiquitin-positive deposits were observed over the whole white matter columns and in the gray matter of the anterior and posterior horns than at the previous stage. Ultrastructurally, aggregates frequently contained electron-dense cores, and were frequently observed in cord-like swollen axons consisting of accumulated neurofilaments. A high level of human SOD1-and ubiquitin-immunogold labeling was present in small to large aggregates even at the presymptomatic stages, and the aggregates increased in size and frequency with time. Compactly packed filaments and electron-dense cores of aggregates showed SOD1-and ubiquitin-immunogold labeling more prominently than in loosely packed filaments. These findings suggest that the accumulation of SOD1-positive aggregates in the neuronal processes, predominantly in the axons, constitutes an important determinant of neurotoxicity and the pathogenesis of this animal model, probably causing impairment of axonal transport by the sequestration of mutant SOD1 protein within aggregates, or in part by physically blocking the axonal transport.

Age Factors↗
PubMed2004

Detection of gp43 of Paracoccidioides brasiliensis by the loop-mediated isothermal amplification (LAMP) method.

Paracoccidioidomycosis is a deep mycosis caused by the thermo-dependent dimorphic fungus Paracoccidioides brasiliensis and is prevalent in Latin American countries. We detected the species specific gp43 gene of P. brasiliensis by loop-mediated isothermal amplification (LAMP) in 22 clinical and seven armadillo-derived isolates. The amplified DNA appeared as a ladder with a specific banding pattern. The advantage of the LAMP method is speed; only 3 h were necessary for identification of the organism and diagnosis of the disease. We were also able to obtain positive results from DNA extracted from a paraffin-embedded tissue sample of paracoccidioidomycosis, suggesting that this method may achieve clinical application in the near future.

Animals↗
PubMed2004

Microglial activation parallels system degeneration in multiple system atrophy.

Multiple system atrophy (MSA) is a neurodegenerative disorder that predominantly affects motor-related neuroanatomic structures. The role of microglia in MSA is unknown. To address this issue, we conducted quantitative image studies on the brains from 13 cases of MSA, comprising 8 cerebellar and 5 parkinsonian variants. Microglial and glial cytoplasmic inclusion (GCI) burdens were determined with image analysis on brain sections immunostained with antibodies to HLA-DR and alpha-synuclein. Many activated microglia, as well as GCIs, were noted in motor-related structures, including the cerebellar input, extrapyramidal motor, and pyramidal motor structures, but not in the cerebellar output structures. This result indicates that microglial activation, as well as the distribution of GCIs, is system-specific in MSA. The correlation analysis between the microglial and GCI burdens yielded variable yet significant correlations in the cerebellar input, extrapyramidal motor, and pyramidal motor systems, but not in the cerebellar output system. This result suggests that microglial activation is at least partly determined by GCIs or oligodendroglial alpha-synuclein in specific neuroanatomic systems affected in MSA. Taken together, considering the known toxic effects of microglia in neurodegenerative diseases, microglia may play a part in the development of system-specific tissue injuries, contributing to the system-bound clinical and pathological phenotypes.

Aged↗
PubMed2003

Expression of apolipoprotein E in ballooned neurons-comparative immunohistochemical study on neurodegenerative disorders and infarction.

Apolipoprotein E (ApoE) in neurons is suggested to play crucial roles in neuronal degeneration and regeneration. We used antibodies against ApoE and phosphorylated neurofilament (pNF) to investigate the immunohistochemical features of ballooned neurons (BNs) in infarction and in various chronic degenerative disorders, including Pick body disease, corticobasal degeneration/progressive supranuclear palsy, Alzheimer's disease, and frontotemporal dementia. BNs in these chronic degenerative processes were intensely labeled with the anti-pNF as reported, whereas BNs in infarction showed less intense pNF-like immunoreactivity (IR). In addition, BNs in infarction were characterized by an intense ApoE-like IR. This ApoE-like IR was inconsistent or less intense in BNs in the chronic degenerative processes. The rarity of ApoE-positive glial cells in the vicinity of ApoE-positive BNs suggests that accumulated ApoE in BNs is generated in the neurons. Accumulation of ApoE in BNs in infarction may be linked to a regenerative process after acute transection of axons, which seems compromised in chronic degenerative processes.

Aged↗
PubMed2003

Immunoexpression of 14-3-3 proteins in glial cytoplasmic inclusions of multiple system atrophy.

Glial cytoplasmic inclusions (GCIs) are the histological hallmark of multiple system atrophy (MSA). In six postmortem brains of patients with MSA, 14-3-3-protein immunoreactivity was identified in GCIs predominately in the white matter tissue of the basal forebrain and cerebellum. Using double immunohistochemistry, co-localization of 14-3-3-protein and alpha-synuclein immunoreactivities in the GCIs was confirmed. The immunolabeling rate of GCIs with 14-3-3 proteins varied regionally from approximately 40% to 90%. Semiquantitative analysis yielded a significant negative correlation between degree of tissue degeneration and density of 14-3-3-protein-immunoreactive GCIs. The 14-3-3 proteins are active cofactors involved in cellular regulation through binding to phosphorylated motifs in target proteins and alpha-synuclein is a known target of 14-3-3. Our study suggests that 14-3-3 proteins are closely associated with alpha-synuclein in GCIs and 14-3-3 proteins may be candidate cofactors of alpha-synuclein in GCI formation.

14-3-3 Proteins↗
PubMed2003

Peculiar form of cerebral microdysgenesis characterized by white matter neurons with perineuronal and perivascular glial satellitosis: A study using a variety of human autopsied brains.

Microdysgenesis (MD) is a neuropathological term that implies a variety of minor developmental abnormalities of the brain. Recently, MD has been used for pathological diagnosis of cerebral tissues surgically resected from epileptic patients. However, criteria or consensus on pathological diagnosis of MD is still vague and controversial because of the lack of control studies. Therefore, this study paid special attention to the presence of white matter neurons with perineuronal glial satellitosis (WMN-GS) and perivascular glial satellitosis (PVGS) in the white matter, which are occasionally observed in epileptic foci, in order to clarify whether they could be handled as definite findings of MD. The materials included 80 autopsied whole brains ranging from normal subjects to patients with cerebrovascular disorder, neurodegenerative diseases and malformations. In each case, the presence of WMN-GS and/or PVGS was searched in 10 gyri in all five lobes (rostral frontal lobe, caudal frontal lobe, parietal lobe, temporal lobe and oc-cipital lobe) and evaluated. Statistically significant, WMN-GS and/or PVGS preferentially appeared in a diseased group consisting of neuronal migration disorder and related conditions, such as polymicrogyria, nodular heterotopia or tuberous sclerosis, leading to a suggestive conclusion that the presence of WMN-GS and/or PVGS could be a peculiar form of MD possibly derived from neuronal migrational arrest or related events, even if they appear alone without any other gross abnormalities.

Adolescent↗
PubMed2002

Hyperphosphorylated tau deposition parallels prion protein burden in a case of Gerstmann-Sträussler-Scheinker syndrome P102L mutation complicated with dementia.

Hyperphosphorylated tau (p-tau) deposition has been documented in a limited population of patients with Gerstmann-Sträussler-Scheinker syndrome (GSS) with particular point mutations of the prion protein (PrP) gene. Although its pathogenesis is only poorly understood, p-tau in GSS is known to be identical to that in Alzheimer's disease (AD). We conducted immunohistochemical and quantitative image studies on the brain from a 44-year-old man with a 7-year history of dementia, diagnosed as having GSS with a point mutation of the PrP gene at codon 102 (GSS102), the commonest mutation in GSS. Severe spongiform degeneration and numerous PrP plaques were disclosed in the cerebral cortices and hippocampus, consistent with the diagnosis. However, rarely described in GSS102, prominent p-tau deposits as pretangles, neurofibrillary tangles and degenerating neurites were demonstrated adjacent to or around PrP plaques. beta-Amyloid protein (Abeta) plaques were generally sparse and appeared invariably to be of a diffuse type. Double-labeling immunohistochemistry yielded co-localization of p-tau with PrP but not with Abeta. Most PrP plaques did not contain Abeta. These results excluded a diagnosis of concomitant AD. Quantitative analysis on a fractional area density of immunoreactive pixels demonstrated that burdens of PrP and p-tau but not Abeta were significantly correlated. These results suggest that p-tau deposition in this GSS102 is secondarily induced by PrP but not by Abeta (secondary tauopathy). Our study also suggests that p-tau deposition might be a more common phenomenon in long-standing GSS.

Adult↗