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Yuji Shimizu

Publications and source records attributed to Yuji Shimizu.

12 recordsLinked to original sources
PubMed2007

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is approximately 32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.

Arabidopsis↗
PubMed2006

Efflux of sphingomyelin, cholesterol, and phosphatidylcholine by ABCG1.

Cholesterol and phospholipids are essential to the body, but an excess of cholesterol or lipids is toxic and a risk factor for arteriosclerosis. ABCG1, one of the half-type ABC proteins, is thought to be involved in cholesterol homeostasis. To explore the role of ABCG1 in cholesterol homeostasis, we examined its subcellular localization and function. ABCG1 and ABCG1-K120M, a WalkerA lysine mutant, were localized to the plasma membrane in HEK293 cells stably expressing ABCG1 and formed a homodimer. A stable transformant expressing ABCG1 exhibited efflux of cholesterol and choline phospholipids in the presence of BSA, and the cholesterol efflux was enhanced by the presence of HDL, whereas cells expressing ABCG1-K120M did not, suggesting that ATP binding and/or hydrolysis is required for the efflux. Mass and TLC analyses revealed that ABCG1 and ABCA1 secrete several species of sphingomyelin (SM) and phosphatidylcholine (PC), and SMs were preferentially secreted by ABCG1, whereas PCs were preferentially secreted by ABCA1. These results suggest that ABCA1 and ABCG1 mediate the lipid efflux in different mechanisms, in which different species of phospholipids are secreted, and function coordinately in the removal of cholesterol and phospholipids from peripheral cells.

ATP Binding Cassette Transporter, Subfamily G, Mem↗
PubMed2005

Measurement of residual adenoma after transurethral resection of the prostate by transurethral enucleation technique.

OBJECTIVE: Transurethral resection of the prostate (TURP) leaves a lot of residual adenoma and has a high recurrence rate, but the residual adenoma weight has not been measured surgically. Using surgery we tried to measure the residual adenoma after TURP. MATERIAL AND METHODS: Total adenoma resection was performed via standard TURP in 64 cases with benign prostatic hyperplasia and the weight of the residual adenoma was measured by transurethral enucleation (TUE) of the prostate. RESULTS: Prostate volume averaged 37.4 ml and adenoma volume averaged 20.6 ml by TRUS. The average weight of the prostate removed by TURP was 9.8 g. After TURP residual adenoma was confirmed in all cases by TUE, and the average weight of the residual adenoma was 10.2 g. The total average prostate volume removed by TURP and TUE was 20.1 g. The average residual rate of the adenoma removed by TURP was 54.5%. CONCLUSION: TURP leaves about half of the adenoma. Therefore, TURP might be very difficult for complete resection of an adenoma.

Aged↗
PubMed2003

New plant growth promoters, repraesentins A, B and C, from Lactarius repraesentaneus.

Three new plant growth regulatory sesquiterpenoids were isolated from the Lactarius repraesentaneus fungus. Their structures were elucidated to be a protoilludene sesquiterpene, namely repraesentin A (1), and two related sesquiterpenes, namely repraesentins B (2) and C (3). Compounds 1-3 showed promotion activities toward the radicle elongation of lettuce seedlings by 136%, 118% and 184% at 67 ppm, respectively.

Fungi↗
PubMed2002

4-Hydroxy-2-nonenal enhances fibronectin production by IMR-90 human lung fibroblasts partly via activation of epidermal growth factor receptor-linked extracellular signal-regulated kinase p44/42 pathway.

To elucidate the underlying mechanisms in oxidative stress-related airway remodeling observed in chronic inflammatory pulmonary diseases such as asthma, we studied the effects of a thiol antioxidant, N-acetylcysteine (NAC), a selective epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor, AG-1478, and tyrphostin-1 as a negative control for AG-1478 on an aldehydic product of lipid peroxidation 4-hydroxy-2-nonenal (HNE)-induced secretion of fibronectin by IMR-90 human lung fibroblasts. We also studied signal transduction pathways involved in the secretion of fibronectin evident after exposure of IMR-90 cells to HNE. Twenty-five-micromole HNE treatments of IMR-90 cells activated extracellular signal-regulated kinase p44/42 (Erk1/2) with little activation of p38 mitogen-activated protein kinase (p38MAPK) and no activation of c-Jun NH(2)-terminal kinase. HNE-induced secretion of fibronectin was inhibited by U-0126, an inhibitor of the Erk1/2 pathway, while no significant inhibition by SB-203580, an inhibitor of p38MAPK pathway, was observed. NAC and AG-1478, but not tyrphostin-1, inhibited HNE-induced fibronectin secretion accompanied by a pallarel inhibition of Erk1/2 activation. These data suggest that pulmonary oxidative stress-related lipid peroxidation may play an important role in developing airway remodeling through activating lung fibroblasts to further produce extracellular matrices, such as fibronectin, partly via activation of an EGFR-linked Erk1/2 signal transduction pathway, and that the antioxidant NAC and the EGFR tyrosine kinase inhibitor AG-1478 can be potentially useful in pulmonary diseases involving airway remodeling.

Acetylcysteine↗
PubMed2002

Recurrent bronchiolitis obliterans organizing pneumonia in a patient with limited cutaneous systemic sclerosis.

Systemic sclerosis (SSc) is a generalized disorder characterized by fibrosis and vascular obliteration in the skin, lung, gastrointestinal tract, and kidney. One of its two subsets is a stable, limited cutaneous group (lSSc). Pulmonary involvement in scleroderma is common, and several types of pulmonary disorders are associated with SSc. Bronchiolitis obliterans organizing pneumonia (BOOP) is a rare finding in lung disorders associated with SSc. We describe a case of lSSc with BOOP that was responsive to steroid therapy. Of interest is that the lung disorders appeared in different periods and areas. It might be important to diagnose abnormal shadows in lung fields before treatment of patients with SSc.

Aged↗
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

Colocalization of CA19-9 and KL-6 to epithelial cells in dilated bronchioles in a patient with idiopathic pulmonary fibrosis complicated by diffuse alveolar damage.

A 73-year-old woman with idiopathic pulmonary fibrosis (IPF) had an elevated serum CA19-9 level, but not KL-6. Her condition worsened and she subsequently died and this was associated with a rise in the serum KL-6 level. At autopsy, the lung showed a honeycomb appearance macroscopically and, microscopically, hyaline membrane formation was seen. Immunohistochemical staining revealed partial colocalization of KL-6 and CA19-9 to dilated bronchiolar cells. These features suggest that the mechanisms that cause the synthesis and release of CA19-9 and KL-6 from damaged lung tissue in IPF are likely to differ from those in diffuse alveolar damage. In addition, serum KL-6 levels may reflect the severity of disease more sensitively than CA19-9 levels.

Aged↗
PubMed2002

KL-6-producing invasive thymoma.

We report a patient with KL-6-producing invasive thymoma. A 58-year-old man was admitted complaining of dyspnea and fatigability. Computed tomography of the chest revealed interstitial pneumonia and an anterior mediastinal tumor. The tumor was surgically extirpated and diagnosed as invasive thymoma. Serum KL-6 levels later increased further and another tumor was found in the liver. That liver tumor was resected and histologically diagnosed as a metastasis of thymoma. Following resection, the serum KL-6 level decreased. Tumor cells of both primary and metastatic lesions exhibited positive reactivity to immunohistochemical staining for KL-6. A review of this case is presented.

Humans↗
PubMed2002

Low-protein diet induces oral tolerance to ovalbumin in mice.

The suitable development of oral tolerance against ingested dietary foods is of critical importance to escaping food allergy. Using mice as an animal model for oral tolerance against ovalbumin (OVA) as a dietary antigen, we investigated the effects of dietary protein on their immunological tolerance. Female BALB/c mice fed either a 20% or 5% protein diet were orally administered 5 mg of OVA for four consecutive days, then immunized intraperitoneally with 100 microg of OVA. The immunized group of mice were fed and treated in the same manner, except that they received orally distilled water for four consecutive days before receiving intraperitoneal immunization with the antigen. Immunization alone with OVA elevated the total IgE and induced the production of OVA-specific antibodies IgE, IgG, IgG1, and IgG2a in the sera of both the 20% and 5% protein diet groups. The oral administration of OVA to mice before intraperitoneal immunization significantly reduced the total IgE and OVA-specific antibodies in mice fed 5% protein diet, but it had hardly any effect on those in mice fed a 20% protein diet. When spleen cells from these groups of mice were cultured with OVA as a mitogen, they responded substantially to OVA in the immunized groups fed 20% and 5% protein diets and in the presensitized group fed 20% protein, but those from the presensitized group fed a 5% protein diet did not respond. Furthermore, when IL-4 was assayed in the spleen cell cultures of the 20% and 5% groups, mice in the presensitized group fed a 5% protein diet produced a significantly less amount of IL-4 than those fed a 20% protein diet. Moreover, irrelevant to the protein amount in the diet, the production of IFN-gamma from spleen cell cultures dramatically decreased in the group without presensitization and profoundly increased in the presensitized group of mice fed a 5% protein diet. These findings suggest that a low-protein diet leads to an induction of oral tolerance against dietary antigens; this appears to involve a clear down-regulation of Th2 cytokine, IL-4.

Administration, Oral↗
PubMedDate not supplied

Interobserver variation in diagnosis of dementia by brain perfusion SPECT.

Brain perfusion SPECT (BP-SPECT) has characteristic patterns of abnormality, enabling the differential diagnosis of dementia. The purpose of this study was to measure interobserver variations in the diagnosis of dementia using BP-SPECT. BP-SPECT images of 57 cases, 19 of Alzheimer's disease (AD), eight of multi-infarct dementia (MID), three of Pick's disease, five of other dementias, and 22 normal controls, were interpreted by ten nuclear medicine physicians with varying levels of experience. Brain MR images of the cases were then interpreted apart from SPECT. The physicians independently rated all of the diagnoses listed beforehand according to a five-point scale, with clinical information provided. Receiver-operating characteristic (ROC) curves and the area under the ROC curve (Az) were calculated. Az varied from 0.48 to 0.87. Mean Az's were significantly larger (p<0.05) in the diagnosis by SPECT than in that by MRI (0.715 and 0.629 for dementia vs. normal, 0.670 and 0.560 for AD or MID vs. normal, 0.610 and 0.416 for AD vs. normal, and 0.672 and 0.412 for AD vs. MID, respectively). Considerable interobserver variation was present in BP-SPECT interpretation. BP-SPECT may be more effective for the evaluation of dementia than MRI when the same nuclear medicine physicians interpret both images.

Aged↗