PubMed Health⌕ Search

Biomedical subjects

K Yamane

Publications and source records attributed to K Yamane.

At least 19 recordsLinked to original sources
PubMed2003

Essential Bacillus subtilis genes.

To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among approximately 4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from bacteria with small genomes. Unexpectedly, most genes involved in the Embden-Meyerhof-Parnas pathway are essential. Identification of unknown and unexpected essential genes opens research avenues to better understanding of processes that sustain bacterial life.

Bacillus subtilis↗
PubMed2003

Elevated circulating soluble CD40 ligand in patients with mixed connective tissue disease.

Abnormalities of CD40 ligand have been demonstrated in various kinds of diseases. Our objective was to determine serum soluble CD40 ligand (sCD40L) levels in patients with mixed connective tissue disease (MCTD). Serum sCD40L levels of 23 patients with MCTD and 21 healthy individuals were measured with specific enzyme-linked immunosorbent assays. Serum levels of sCD40L were significantly higher in patients with MCTD than in healthy individuals (median 0.179 ng/ml vs 0.99 ng/ml, 25th-75th percentile; 0.117-0.296 ng/ml vs 0.82-1.70 ng/ml, P<0.005), whereas there were no significant correlation between elevated serum sCD40L levels and clinical or serological features in patients with MCTD. These results suggest that sCD40L plays a role in the pathogenesis of MCTD. Further studies are needed to clarify this.

Adult↗
PubMed2003

Plasma plasmin-alpha2-plasmin inhibitor complex levels are increased in systemic sclerosis patients with pulmonary hypertension.

OBJECTIVE: To determine the frequency and clinical significance of plasma plasmin-alpha(2)-plasmin inhibitor complex (PIC) in patients with systemic sclerosis (SSc). METHODS: Plasma samples from 74 patients with SSc and 32 healthy volunteers were examined by a specific enzyme-linked immunosorbent assay. RESULTS: Elevated plasma PIC levels were present in 35 of the 74 patients (47.3%) with SSc. The patients with elevated plasma PIC levels had pulmonary hypertension (PH) at a significantly higher incidence than those with normal PIC levels (31.4 vs 7.7%, P<0.01). When PH was classified into isolated PH (IPH) and secondary PH (SPH), the presence of IPH was significantly greater in patients with elevated PIC levels than in those with normal levels (25.7 vs 5.1%, P<0.02). CONCLUSIONS: These results suggest that plasma PIC levels may be a marker of PH, especially IPH, in patients with SSc.

Adult↗
PubMed2002

A case of linear scleroderma with muscle calcification.

We report a 21-year-old man with linear scleroderma with muscle calcification revealed by a computed tomographic (CT) scan. Levels of serum calcium and phosphorus were normal. This is the first report of localized scleroderma with muscle calcification. Muscle involvement may cause contracture or functional abnormalities of the extremities. Therefore, CT scans may be useful in evaluating muscle involvement in patients with localized scleroderma.

Biopsy↗
PubMed2002

Clinical significance of serum surfactant protein D (SP-D) in patients with polymyositis/dermatomyositis: correlation with interstitial lung disease.

OBJECTIVE: To determine the clinical significance of serum surfactant protein D (SP-D) levels in patients with polymyositis/dermatomyositis (PM/DM). METHODS: Serum SP-D levels were assayed using a sensitive enzyme-linked immunosorbent assay in 59 patients with PM/DM and in 29 healthy controls. RESULTS: The serum level of SP-D was significantly higher in patients with PM/DM than in healthy controls (mean+/-S.D. 61.7+/-122.6 vs 31.0+/-12.4 ng/ml, P < 0.01). The serum SP-D level in patients with interstitial lung disease (ILD) was significantly higher than in those without ILD (118.7+/-220.2 vs 38.7+/-21.0 ng/ml, P < 0.001). Serum level of SP-D was correlated with the presence of ILD. The incidences of decreased vital capacity (%VC) and of decreased diffusing capacity of carbon monoxidase (%DLCO) were also significantly greater in patients with an elevated SP-D level than in those with a normal level (64 vs 7%, P < 0.02; 73 vs 27%, P < 0.01). Moreover, the serum SP-D level was inversely correlated with %VC (r=-0.452, P < 0.01) and %DLCO (r=-0.349, P < 0.05). CONCLUSION: The serum SP-D level may be a useful marker for ILD in patients with PM/DM.

Adult↗
PubMed2002

Anti-U5 snRNP antibody as a possible serological marker for scleroderma-polymyositis overlap.

OBJECTIVE: To determine the prevalence of the anti-U5 small nuclear ribonucleoprotein (snRNP) antibody in patients with systemic sclerosis. METHODS: Sera from 281 patients with systemic sclerosis, including 10 patients with overlapping polymyositis, were assayed using RNA immunoprecipitation and protein immunoprecipitation. RESULTS: Only one serum sample showed precipitation of U5 snRNA with scarce precipitation of U2, U1, U4 and U6 snRNAs. In addition, the serum precipitated a 200 kDa protein. The serum was from a 35-yr-old Japanese male patient with overlapping systemic sclerosis and polymyositis accompanied by large-cell lung carcinoma. The clinical appearance was similar to that of a case reported previously. CONCLUSION: The presence of the anti-U5 snRNP antibody in serum may be specific for scleroderma-polymyositis overlap syndrome.

Adult↗
PubMed2001

A novel SOD1 gene mutation in familial ALS with low penetrance in females.

We identified a novel missense mutation in the Cu/Zn superoxide dismutase gene in a family with amyotrophic lateral sclerosis (ALS). The mutation was a transition of T to C, resulting in a substitution of leucine 126 to serine in exon 5. The family had very unique clinical features of extremely mild severity only in the legs of two male patients with onset of 42 and 52 years old, and their mothers did not develop any symptom even after reaching the age of 80 and carrying the same mutation. The present study suggests that there are other factors that delay or prevent the disease.

Adult↗
PubMed2001

p53 contains a DNA break-binding motif similar to the functional part of BRCT-related region of Rb.

The BRCT regions are two repeating structures at BRCA1 carboxyl-terminus and are ubiquitous in some proteins involved in DNA repair and cell cycle checkpoints. It was shown that BRCTs of TopBP1, BRCA1, and BRCT-Ws of Rb bound DNA ends and breaks. We indicate here that the C-terminus of p53 tumor suppressor contains a DNA binding motif (residues 327-333 in human), whose features are similar to those of the part of BRCT-W in Rb with DNA binding activity. The short motif was required for the gel retardation activity of DNA fragments, since residues 311-333 showed the activity while residues 311-326 showed no activity. Significant numbers of total p53 and its fragments with the motif formed multimerizing complexes and associated with DNA ends and breaks. These results suggest the common presence of DNA binding motifs that can recognize DNA ends or damages in major tumor suppressors, Rb, BRCA1 and p53. The oncogenic activity of p53 C-terminus (residues 311-393) required both the DNA damage recognition motif and the repair enzyme-associating domain.

Amino Acid Motifs↗
PubMed2001

Minimal functional structure of Escherichia coli 4.5 S RNA required for binding to elongation factor G.

Escherichia coli cells contain abundant amounts of metabolically stable 4.5 S RNA. Consisting of 114 nucleotides, 4.5 S RNA is structurally homologous to mammalian 7 S RNA, and it plays an essential role in targeting proteins containing signal peptide to the secretory apparatus by forming an signal recognition-like particle with Ffh protein. It also binds independently to protein elongation factor G (EF-G) and functions in the translation process. This RNA contains a phylogenetically conserved RNA domain, the predicted secondary structure of which consists of a hairpin motif with two bulges. We examined the binding activity of mutants with systematic deletions to define the minimal functional interaction domain of 4.5 S RNA that interacts with EF-G. This domain consisted of 35-nucleotides extending from 36 to 70 nucleotides of mature 4.5 S RNA and contained two conserved bulges in which mutations of A47, A60, G61, C62, A63, and A67 diminished binding to EF-G, whereas those at A39, C40, C41, A42, G48, and G49 did not affect binding. These data suggested that the 10 nucleotides in 4.5 S RNA, which are conserved between 4.5 S RNA and 23 S rRNA, have a key role for EF-G binding. Based on the NMR-derived structure of mutant A47U, we further verified that substituting U at A47 causes striking structural changes and the loss of the symmetrical bulge. These results indicate the mechanism by which EF-G interacts with 4.5 S RNA and the importance of the bulge structure for EF-G binding.

Base Sequence↗
PubMed2001

Structural characterization of n-butyl-isocyanide complexes of cytochromes P450nor and P450cam.

Alkyl-isocyanides are able to bind to both ferric and ferrous iron of the heme in cytochrome P450, and the resulting complexes exhibit characteristic optical absorption spectra. While the ferric complex gives a single Soret band at 430 nm, the ferrous complex shows double Soret bands at 430 and 450 nm. The ratio of intensities of the double Soret bands in the ferrous isocyanide complex of P450 varies, as a function of pH, ionic strength, and the origin of the enzyme. To understand the structural origin of these characteristic spectral features, we examined the crystallographic and spectrophotometric properties of the isocyanide complexes of Pseudomonas putida cytochrome P450cam and Fusarium oxysporum cytochorme P450nor, since ferrous isocyanide complex of P450cam gives a single Soret band at 453 nm, while that of P450nor gives one at 427 nm. Corresponding to the optical spectra, we observed C-N stretching of a ferrous iron-bound isocyanide at 2145 and 2116 cm(-1) for P450nor and P450cam, respectively. The crystal structures of the ferric and ferrous n-butyl isocyanide complexes of P450cam and P450nor were determined. The coordination structure of the fifth Cys thiolate was indistinguishable for the two P450s, but the coordination geometry of the isocyanide was different for the case of P450cam [d(Fe-C) = 1.86 A, angleFe-C-N = 159 degrees ] versus P450nor [d(Fe-C) = 1.85 A, angleFe-C-N = 175 degrees ]. Another difference in the structures was the chemical environment of the heme pocket. In the case of P450cam, the iron-bound isocyanide is surrounded by some hydrophobic side chains, while, for P450nor, it is surrounded by polar groups including several water molecules. On the basis of these observations, we proposed that the steric factors and/or the polarity of the environment surrounding the iron-bound isocyanide significantly effect on the resonance structure of the heme(Fe)-isocyanide moiety and that differences in these two factors are responsible for the spectral characteristics for P450s.

Camphor 5-Monooxygenase↗
PubMed2001

Effect of depletion of FtsY on spore morphology and the protein composition of the spore coat layer in Bacillus subtilis.

Bacillus subtilis FtsY is a homolog of the alpha-subunit of mammalian signal recognition particle (SRP) receptor, and is essential for protein translocation and vegetative cell growth. An FtsY conditional null mutant (strain ISR39) can express ftsY during the vegetative stage but not during spore formation. Spores of ISR39 have the same resistance to heat and chloroform as the wild-type, while their resistance to lysozyme is reduced. Electron microscopy showed that the outer coat of spores was incompletely assembled. The coat protein profile of the ftsY mutant spores was different from that of wild-type spores. The amounts of CotA, and CotE were reduced in spore coat proteins of ftsY mutant spores and the molecular mass of CotB was reduced. In addition, CotA, CotB, and CotE are present in normal form at T(8) of sporulation in ftsY mutant cells. These results suggest that FtsY has a pivotal role in assembling coat proteins onto the coat layer during spore morphogenesis.

Bacillus subtilis↗
PubMed2001

Blockade of endogenous transforming growth factor beta signaling prevents up-regulated collagen synthesis in scleroderma fibroblasts: association with increased expression of transforming growth factor beta receptors.

OBJECTIVE: To elucidate the role of transforming growth factor beta (TGFbeta) in the increased expression of the collagen gene in scleroderma fibroblasts. METHODS: Dermal fibroblasts from 10 patients with diffuse systemic sclerosis (SSc) of recent onset and from 10 healthy individuals were studied. The production of active and total (active + latent) TGFbeta1 levels from cultured dermal fibroblasts was measured using a TGFbeta1 enzyme-linked immunosorbent assay system. Expression of the TGFbeta type I and type II receptor proteins in dermal fibroblasts was determined by immunoblotting, and the level of expression of human alpha2(I) collagen messenger RNA (mRNA) was evaluated by Northern blot analysis. The transcriptional activity of the human alpha2(I) collagen gene was examined with chloramphenicol acetyltransferase (CAT) assays using the -772 COL1A2/CAT construct. RESULTS: SSc fibroblasts expressed increased levels of TGFbeta type I and type II receptors but secreted amounts of TGFbeta similar to those secreted by normal fibroblasts. The blockade of TGFbeta signaling with anti-TGFbeta antibodies or a TGFbeta1 antisense oligonucleotide abolished the increased mRNA expression, as well as the up-regulated transcriptional activity of the human alpha2(I) collagen gene in SSc fibroblasts. CONCLUSION: These results suggest that TGFbeta plays a crucial role in the pathogenesis of SSc and raise the possibility of a therapeutic approach with anti-TGFbeta antibodies or a TGF11 antisense oligonucleotide.

Antibodies↗
PubMed2001

Clinical significance of surfactant protein D as a serum marker for evaluating pulmonary fibrosis in patients with systemic sclerosis.

OBJECTIVE: To determine the clinical significance of surfactant protein D (SP-D), a useful marker for evaluating various lung diseases, in patients with systemic sclerosis (SSc) and to clarify any clinical significance between SP-D and KL-6, which is known to be correlated with pulmonary fibrosis (PF) in SSc patients. METHODS: We used a specific enzyme-linked immunosorbent assay to measure serum SP-D levels in 83 patients with SSc and 31 healthy control subjects. RESULTS: The serum levels of SP-D were significantly higher in patients with SSc than in healthy controls (mean +/- SD 81.9+/-59.2 versus 34.8+/-13.7 ng/ml). Serum SP-D levels in patients with diffuse cutaneous SSc were significantly higher than those in patients with limited cutaneous SSc (98.8+/-72.1 versus 66.8+/-40.0 ng/ml). Serum SP-D levels in patients with PF were significantly elevated compared with those in patients without PF (99.7+/-64.1 versus 65.3+/-49.4 ng/ml). Moreover, the incidences of decreased percentage diffusing capacity for carbon monoxide and decreased percentage vital capacity were also significantly greater in patients with elevated SP-D levels than in those with normal levels (67% versus 43% and 36% versus 17%, respectively). There was a significant positive correlation between serum levels of SP-D and KL-6. Serum SP-D and KL-6 levels showed almost the same sensitivities and specificities in the diagnosis of PF (68% versus 73% and 70% versus 74%, respectively). These two markers also predicted PF to almost the same degree (31% versus 33%, respectively). CONCLUSION: These results suggest that SP-D, as well as KL-6, may be a useful serum marker for evaluating PF in patients with SSc.

Antibodies, Antinuclear↗
PubMed2001

Immunohistochemical and ultrastructural study of basophilic inclusions in adult-onset motor neuron disease.

We immunohistochemically and ultrastructurally studied basophilic inclusions (BI) in a patient with adult-onset sporadic motor neuron disease (MND). BI were frequently observed not only in degenerated anterior horn cells, such as central chromatolytic neurons, but also in normal-appearing large anterior horn neurons. They had various shapes, round, elliptical or irregular, and occasionally they had distinct basophilic rims. They also varied in size. There were no halos around them nor core in their centers. Immunohistochemically, some BI were immunostained for ubiquitin or SOD1, but BI were not immunoreactive with anti-phosphorylated neurofilament (SMI 31), phosphorylated tau, cystatin C or Golgi (MG-160) antibodies. Ubiquitin-positive skein-like inclusions (SI) were occasionally observed in the somata of anterior horn neurons. Ultrastructurally, BI consisted of filamentous structures associated with granules, which were attached to thick filaments. The thick filaments were straight without constriction or side arms and their diameter was twice that of the neurofilaments. BI occasionally contained tubular structures among the granule-associated filaments. The granulo-filamentous profiles varied from being compactly arranged to being more loosely packed. The structure of BI resembles that of the Lewy body-like hyaline inclusions (LBHI) observed in sporadic MND patients. Bundles of filaments resembling SI, which were composed of compactly packed filaments without fine granules running parallel to the longitudinal axis, were frequently observed inside or at the periphery of BI, and occasionally clustered in the perikarya. Each filament measured approximately 15-25 nm in diameter, and a bundle of these grouped filaments was sometimes surrounded by a unit membrane. We also occasionally observed in-between structures of BI and bundles of filaments resembling SI. These findings suggest a certain relationship between BI, SI and LBHI in the pathomechanism of BI development. Further studies are needed to elucidate whether sporadic adult-onset MND characterized by BI forms a different subtype of MND.

Anterior Horn Cells↗