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Manabu Yamada

Publications and source records attributed to Manabu Yamada.

33 records · Page 2Linked to original sources
PubMed2003

Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803.

The genome of the unicellular cyanobacterium Synechocystis sp. PCC 6803 consists of a single chromosome and several plasmids of different sizes, and the nucleotide sequences of the chromosome and three small plasmids (5.2 kb, 2.4 kb, and 2.3 kb) have already been sequenced. We newly determined the nucleotide sequences of four large plasmids, which have been identified in our laboratory (pSYSM:120 kb, pSYSX:106 kb, pSYSA:103 kb, and pSYSG:44 kb). Computer-aided analysis was performed to explore the genetic information carried by these plasmids. A total of 397 potential protein-encoding genes were predicted, but little information was obtained about the functional relationship of plasmids to host cell, as a large portion of the predicted genes (77%) were of unknown function. The occurrence of the potential genes on plasmids was divergent, and parA was the only gene common to all four large plasmids. The distribution data of a Cyanobacterium-specific sequence (HIP1: 5'-GCGATCGC-3') suggested that respective plasmids could have originated from different cyanobacterial strains.

Base Sequence↗
PubMed2003

Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids.

The nucleotide sequence of the entire genome of a cyanobacterium Gloeobacter violaceus PCC 7421 was determined. The genome of G. violaceus was a single circular chromosome 4,659,019 bp long with an average GC content of 62%. No plasmid was detected. The chromosome comprises 4430 potential protein-encoding genes, one set of rRNA genes, 45 tRNA genes representing 44 tRNA species and genes for tmRNA, B subunit of RNase P, SRP RNA and 6Sa RNA. Forty-one percent of the potential protein-encoding genes showed sequence similarity to genes of known function, 37% to hypothetical genes, and the remaining 22% had no apparent similarity to reported genes. Comparison of the assigned gene components with those of other cyanobacteria has unveiled distinctive features of the G. violaceus genome. Genes for PsaI, PsaJ, PsaK, and PsaX for Photosystem I and PsbY, PsbZ and Psb27 for Photosystem II were missing, and those for PsaF, PsbO, PsbU, and PsbV were poorly conserved. cpcG for a rod core linker peptide for phycobilisomes and nblA related to the degradation of phycobilisomes were also missing. Potential signal peptides of the presumptive products of petJ and petE for soluble electron transfer catalysts were less conserved than the remaining portions. These observations may be related to the fact that photosynthesis in G. violaceus takes place not in thylakoid membranes but in the cytoplasmic membrane. A large number of genes for sigma factors and transcription factors in the LuxR, LysR, PadR, TetR, and MarR families could be identified, while those for major elements for circadian clock, kaiABC were not found. These differences may reflect the phylogenetic distance between G. violaceus and other cyanobacteria.

Base Sequence↗
PubMed2003

Hyena disease (premature physeal closure) in calves due to overdose of vitamins A, D3, E.

Holstein suckling calves on a farm manifested severe emaciation, generalized alopecia, dome-like cranial deformation, and high mortality (Case 1). Metaphyseal growth plates of the femur were achondroplastic; segmented, partially resorped, and replaced with immature bony trabeculae containing degenerated chondrocytes. The skull was thin and partially replaced with connective tissue. Diffuse and severe fatty degeneration was observed in the hepatic stellate (Ito') cells. After 6 mo, surviving calves manifested unthrifty with short and irregular hindquarters (Case 2). The metaphyseal growth plates were poorly formed, irregular, partially disappeared centrally, and often sealed with thin bony trabeculae. The cartilage matrix was not homogeneous but was finely fibrous, and chondrocytes were flat and degenerated. The bone lesion was diagnosed as chondrodysplasia due to premature physeal closure. These calves had been administered excessive amounts of vitamins A, D3 and E, and blood chemistry of acute case showed hypervitaminosis A and E. Case I demonstrated acute disease, while Case 2 demonstrated chronic sequelae. Hypervitaminosis A was the suspected cause.

Animals↗
PubMed2002

Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110.

The complete nucleotide sequence of the genome of a symbiotic bacterium Bradyrhizobium japonicum USDA110 was determined. The genome of B. japonicum was a single circular chromosome 9,105,828 bp in length with an average GC content of 64.1%. No plasmid was detected. The chromosome comprises 8317 potential protein-coding genes, one set of rRNA genes and 50 tRNA genes. Fifty-two percent of the potential protein genes showed sequence similarity to genes of known function and 30% to hypothetical genes. The remaining 18% had no apparent similarity to reported genes. Thirty-four percent of the B. japonicum genes showed significant sequence similarity to those of both Mesorhizobium loti and Sinorhizobium meliloti, while 23% were unique to this species. A presumptive symbiosis island 681 kb in length, which includes a 410-kb symbiotic region previously reported by Göttfert et al., was identified. Six hundred fifty-five putative protein-coding genes were assigned in this region, and the functions of 301 genes, including those related to symbiotic nitrogen fixation and DNA transmission, were deduced. A total of 167 genes for transposases/104 copies of insertion sequences were identified in the genome. It was remarkable that 100 out of 167 transposase genes are located in the presumptive symbiotic island. DNA segments of 4 to 97 kb inserted into tRNA genes were found at 14 locations in the genome, which generates partial duplication of the target tRNA genes. These observations suggest plasticity of the B. japonicum genome, which is probably due to complex genome rearrangements such as horizontal transfer and insertion of various DNA elements, and to homologous recombination.

Bradyrhizobium↗
PubMed2002

Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1.

The entire genome of a thermophilic unicellular cyanobacterium, Thermosynechococcus elongatus BP-1, was sequenced. The genome consisted of a circular chromosome 2,593,857 bp long, and no plasmid was detected. A total of 2475 potential protein-encoding genes, one set of rRNA genes, 42 tRNA genes representing 42 tRNA species and 4 genes for small structural RNAs were assigned to the chromosome by similarity search and computer prediction. The translated products of 56% of the potential protein-encoding genes showed sequence similarity to experimentally identified and predicted proteins of known function, and the products of 34% of these genes showed sequence similarity to the translated products of hypothetical genes. The remaining 10% lacked significant similarity to genes for predicted proteins in the public DNA databases. Sixty-three percent of the T. elongatus genes showed significant sequence similarity to those of both Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120, while 22% of the genes were unique to this species, indicating a high degree of divergence of the gene information among cyanobacterial strains. The lack of genes for typical fatty acid desaturases and the presence of more genes for heat-shock proteins in comparison with other mesophilic cyanobacteria may be genomic features of thermophilic strains. A remarkable feature of the genome is the presence of 28 copies of group II introns, 8 of which contained a presumptive gene for maturase/reverse transcriptase. A trace of genome rearrangement mediated by the group II introns was also observed.

Cyanobacteria↗
PubMed2002

Distinct lymphatic spread of endometrial carcinoma in comparison with cervical and ovarian carcinomas.

The distribution of metastatic pelvic lymph nodes (PLNs) and aortic lymph nodes (ALNs) in 27 node-positive endometrial carcinomas (ECs) was analyzed in comparison with that in 25 node-positive cervical carcinomas (CCs) and 58 node-positive ovarian carcinomas (OCs). All patients underwent systematic pelvic and aortic lymphadenectomy. Lymph nodes were classified into the five subgroups: ALN above the inferior mesenteric artery (IMA; A1), ALN below the IMA (A2), the common iliac and sacral LNs (P1), the internal and external iliac LNs and obturator LNs (P2) and the suprainguinal LNs (P3). EC was similar to CC in that metastases to P2 were more frequent compared to A1 or A2, whereas EC and OC shared a common feature in that A1, A2 and P2 were involved at high rates. ALN metastases were significantly associated with P1 positivity in both EC and CC (P<0.05), but not in OC. However, the incidence of both ALN and PLN metastases in EC (67%) was similar to that in OC (61%), being much higher than that in CC (36%). ALN involvement alone was observed in 7% for EC, 0% for CC and 21% for OC. Based on the distribution of LN metastases, it appears that CC metastasizes primarily to PLN, whereas OC metastasizes almost equally to both PLN and ALN. Interestingly, EC can directly metastasize to both PLN and ALN with PLN metastases being dominant, a distinct lymphatic spread pattern better viewed as being somewhere between CC and OC.

Adult↗
PubMed2002

A comparative study of the conversion of 7-hydroxycholesterol in rabbit, guinea pig, rat, hamster, and chicken.

The metabolism of epimeric 7-hydroxycholesterol was studied in vitro. 7Alpha-hydroxycholesterol or 7beta-hydroxycholesterol were incubated with rabbit, guinea pig, rat, hamster, and chicken microsomal suspensions and then extracted and analyzed using high-performance liquid chromatography (HPLC). 7Alpha-hydroxy-4-cholesten-3-one was the main product from 7alpha-hydroxycholesterol in the rabbit, guinea pig, and rat. A considerable amount of 7-ketocholesterol was also produced in the hamster and chicken. In all vertebrates, 7beta-hydroxycholesterol was converted only to 7-ketocholesterol in all vertebrates. 7Beta-hydroxy-4-cholesten-3-one was not detected. Reduction of 7-ketocholesterol was also studied in the rat and hamster. Whereas 7-ketocholesterol was converted to 7beta-hydroxycholesterol in the rat, it was converted to both 7alpha- and 7beta-hydroxycholesterol in the hamster. These results suggest that 7alpha-hydroxycholesterol is converted not only to 7alpha-hydroxy-4-cholesten-3-one but also to 7-ketocholesterol in the hamster and chicken. 7Beta-hydroxycholesterol was converted to 7-ketocholesterol in all vertebrates tested. The interconversion between 7alpha- and 7beta-hydroxycholesterol via 7-ketocholesterol was observed in the hamster in this in vitro study.

Animals↗
PubMedDate not supplied

Parovarian cystadenoma: sonographic features associated with magnetic resonance and histopathologic findings.

Differentiation between malignant and benign parovarian tumors is necessary before any surgery is planned, because the postoperative spread of ovarian cancers is well documented. Both malignant and benign parovarian tumors may contain intracystic projections, so their presence is not a differentiating factor. We describe the cases of 2 patients with parovarian cystadenomas that were evaluated using sonography, MRI, and histopathology in an attempt to begin to identify the sonographic characteristics of such lesions and correlate them with MRI and histopathologic findings. In both cases, sonography revealed a cystic mass that contained multiple small intracystic mural nodules, most of which were associated with the "Chinese hat" artifact. MRI findings confirmed the presence of the cystic masses and the nodules. Histopathologic findings confirmed the diagnosis of serous cystadenoma arising in a parovarian cyst; the intracystic nodules consisted of fibrotic tissue covered with a single layer of epithelium. Thus, the results of all 3 evaluations correlated well. This characteristic sonographic appearance may be useful in making an accurate preoperative diagnosis of parovarian cystadenomas.

Adult↗
PubMedDate not supplied

Diagnostic usefulness of endometrial aspiration cytology for endometrial cancer cases with normal curettage findings.

OBJECTIVE: To determine whether endometrial aspiration cytology is useful for endometrial cancer cases with normal endometrial curettage findings. STUDY DESIGN: Eleven cases in which endometrial cancer could be detected by endometrial aspiration cytology but not endometrial curettage were classified into 2 groups by cancer locus, on the endometrial surface (A) or in the myometrium (B). A clinicopathologic and cytologic analysis was performed to compare the 2 groups. RESULTS: Five cases had cancer lesions localized at the fundus and one at the isthmus (group A). The other 5 had lesions localized in the myometrium (group B). The myometrium invasion was beyond half the myometrium in group B and within half in group A. It required > 2 cytologic examinations for a definitive diagnosis in 33.3% of group A and 80.0% of group B. The endometrial cytology differed clearly between the groups: large clusters of malignant cells with a dirty background (group A) vs. small clusters with a clean background (group B). The log-rank test revealed that group B had significantly poorer prognoses than did group A despite nearly the same rate of stage I/II cases in the 2 groups (p = 0.004). CONCLUSION: Endometrial aspiration cytology was useful for endometrial cancer cases with normal curettage findings as part of early detection. However, the cytologic diagnosis did not indicate good prognoses in the cases of cancer localized in the myometrium.

Adult↗
PubMedDate not supplied

Experimental gizzard erosions in specific-pathogen-free chicks by serotype 1 group I avian adenoviruses from broilers.

The pathogenicity of serotype 1 group I avian adenovirus (GIAAV) strains isolated from gizzard erosions for 1-wk-old specific-pathogen-free (SPF) chickens was investigated. In Experiment 1, SPF chickens inoculated orally with a serotype 1 strain (Tokushima2000/GE) of GIAAV isolated from gizzard erosion in broilers were euthanatized and necropsied from 3 to 12 days after inoculation. Clinically, there were no significant signs in the chickens inoculated with Tokushima strain. The gizzards were found macroscopically to be dilated with liquefied contents. The koilin layer of the gizzard exhibited multifocal white lesions with occasional erosions. Gross lesions of the koilin layer (white foci and erosion) appeared at 3 days after inoculation and persisted until 12 days after inoculation. The gross lesions were most severe at 9 days after inoculation. Histologically, multifocal degeneration, necrosis, and loss of the glandular epithelial cells with intranuclear inclusions, liquefactive change of koilin substance, and erosive lesions of koilin layers and surface epithelium of the gizzards were observed. Macrophages increased in the focal areas of the lamina propriabelow the liquefactive koilin substances. Immunohistochemically, intranudear inclusions were positive against GIAAV antigen. Histologic lesions of gizzards were most severe at 7 and 9 days after inoculation, but the frequency of intranuclear inclusions was greatest at 5 days after inoculation. In Experiment 2, the pathogenicities of four strains of serotype 1 GIAAV for 1-wk-old SPF chickens were compared. Three strains isolated from gizzard erosion had similar pathogenicities but one strain from a normal chicken was not pathogenic for chickens. These results suggest that gizzard erosions by serotype 1 GIAAV infection may occur in broiler chickens in Japan.

Adenoviridae Infections↗
PubMedDate not supplied

Reproduction of hydropericardium syndrome in three-week-old cyclophosphamide-treated specific-pathogen-free chickens by adenoviruses from inclusion body hepatitis.

The pathogenicity of serotype 8 group I avian adenovirus (GIAAV) strains (TR630 and Saga97 strains) from inclusion body hepatitis (IBH) against cyclophosphamide (CY)-treated 3-wk-old specific-pathogen-free (SPF) chickens was examined. SPF chickens were inoculated intramuscularly with 10(7) plaque-forming units of viruses. Both strains from IBH could produce hydropericardium and mortality in CY-treated chickens as hydropericardium syndrome (HPS) that serotype 4 GIAAV strains cause, although they could not induce either hydropericardium or mortality in nontreated chickens. Histologically, hepatocytic necrosis with intranuclear inclusions, pancreatic acinar necrosis with intranuclear inclusions, and epicardial edema were seen in CY-treated chickens inoculated with GIAAV from IBH. Immunohistochemically, these inclusions were positive against GIAAV antigen. There were neither histologic lesions nor positive reactions against GIAAV antigen in nontreated chickens inoculated with GIAAV from IBH. From the present findings, pathogenic characteristics of IBH strains and HPS strains in the chickens were essentially the same.

Adenoviridae Infections↗
PubMedDate not supplied

Pathology of listerial encephalitis in chickens in Japan.

Neural signs (torticollis, drowsiness) and mortality were observed in five chickens of a native chicken flock (reared for meat) that included 450 male birds on a farm that had 2300 native chickens and 1120 layers. Histologic lesions were observed in the medulla oblongata, optic lobe, cerebellum, and spinal cord of the affected birds. The lesions, which were most severe in the medulla oblongata, were massive abscesses with rarefaction (demyelination and malacia) of the parenchyma with gram-positive bacteria. The degenerative and necrotic areas were characterized by fibrin thrombosis, hemorrhages, and congestion in the blood vessels. Immunohistochemically, the bacteria positive for L. monocytogenes antigen were observed in the medulla oblongata, cerebellum, and spinal cord. Ultrastructurally, the small rod-shaped and thin-cell-walled bacteria were observed in the parenchyma of the medulla oblongata. Listeria monocytogenes (serotype 4b) was isolated from the medulla oblongata and spinal cord. The pathogenesis of listerial encephalitis in chickens was discussed.

Animals↗