Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain.

BACKGROUND: The purine repressor (PurR) regulates genes that encode enzymes for purine biosynthesis. PurR has a two domain structure with an N-terminal DNA-binding domain (DBD) and a C-terminal corepressor-binding domain (CBD). The three dimensional structure of a ternary complex of PurR bound to both corepressor and a specific DNA sequence has recently been determined by X-ray crystallography. RESULTS: We have determined the solution structure of the PurR DBD by NMR. It contains three helices, with the first and second helices forming a helix-turn-helix motif. The tertiary structure of the three helices is very similar to that of the corresponding region in the ternary complex. The structure of the hinge helical region, however, which makes specific base contacts in the minor groove of DNA, is disordered in the DNA-free form. CONCLUSION: The stable formation of PurR hinge helices requires PurR dimerization, which brings the hinge regions proximal to each other. The dimerization of the hinge helices is likely to be controlled by the CBD dimerization interface, but is induced by specific-DNA binding.

Evolution of the replication regions of IncI alpha and IncFII plasmids by exchanging their replication control systems.

The basic replicons of bacterial plasmids consist of two sets of genetic systems, the replication-structural system and the replication control system. Comparison of nucleotide sequences suggested that the basic replicons of plasmids P307 (IncFI) and pMU2200 (IncZ) were generated by reciprocal recombination between ancestors of R100 (IncFII) and ColIb-P9 (IncI alpha), or vice versa. The plasmids of each pair, P307/pMU2200 and R100/ColIb-P9, are structurally unrelated to each other. Based on this information, we constructed in vitro and analyzed P307-like chimeric replicons from ColIb-P9 and R100. When the replication-structural region of ColIb-P9 was combined with the whole replication control region of R100, the resultant replicon replicated stably as R100 did. These results revealed that the basic replicons of the plasmids diverged by exchanging their replication control systems. Thus, we propose that the replication control systems of plasmids, in some cases, evolved independently of their structural systems, although these two systems work together to maintain the replication functions. We also showed that the reciprocal recombination was specified by the unique secondary structures of RNA involved in the control of expression of the genes encoding the replication initiator proteins.

Construction of a contiguous 874-kb sequence of the Escherichia coli -K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features.

The contiguous 874.423 base pair sequence corresponding to the 50.0-68.8 min region on the genetic map of the Escherichia coli K-12 (W3110) was constructed by the determination of DNA sequences in the 50.0-57.9 min region (360 kb) and two large (100 kb in all) and five short gaps in the 57.9-68.8 min region whose sequences had been registered in the DNA databases. We analyzed its sequence features and found that this region contained at least 894 potential open reading frames (ORFs), of which 346 (38.7%) were previously reported, 158 (17.7%) were homologous to other known genes, 232 (26.0%) were identical or similar to hypothetical genes registered in databases, and the remaining 158 (17.7%) showed no significant similarity to any other genes. A homology search of the ORFs also identified several new gene clusters. Those include two clusters of fimbrial genes, a gene cluster of three genes encoding homologues of the human long chain fatty acid degradation enzyme complex in the mitochondrial membrane, a cluster of at least nine genes involved in the utilization of ethanolamine, a cluster of the secondary set of 11 hyc genes participating in the formate hydrogenlyase reaction and a cluster of five genes coding for the homologues of degradation enzymes for aromatic hydrocarbons in Pseudomonas putida. We also noted a variety of novel genes, including two ORFs, which were homologous to the putative genes encoding xanthine dehydrogenase in the fly and a protein responsible for axonal guidance and outgrowth of the rat, mouse and nematode. An isoleucine tRNA gene, designated ileY, was also newly identified at 60.0 min.

A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map.

The 718,122 base pair sequence of the Escherichia coli K-12 genome corresponding to the region from 12.7 to 28.0 minutes on the genetic map is described. This region contains at least 681 potential open reading frames, of which 277 (41%) have been previously identified, 147 (22%) are homologous to other known genes, 139 (20%) are identical or similar to the hypothetical genes registered in databases, and the remaining 118 (17%) do not show a significant similarity to any other gene. In this region, we assigned a cluster of cit genes encoding multienzyme citrate lyase, two clusters of fimbrial genes and a set of lysogenic phage genes encoding integrase, excisionase and repressor in the e14 genetic element. In addition, a new valine tRNA gene, designated valZ, and a family of long directly repeated sequences, LDR-A, -B and -C, were found.

A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map.

The 569,750 base pair sequence corresponding to the 28.0-40.1 min region on the genetic map of Escherichia coli K-12 (W3110) was determined. This region includes the replication terminus region and contained at least 549 potential open reading frames. Among them, 160 (29%) were previously reported, 174 (32%) were homologous to other known genes, 102 (18%) were identical or similar to hypothetical genes registered in databases, and the remaining 113 (21%) did not show a significant similarity to any other gene. Of interest was the finding of a large number of genes and gene clusters in and near the replication termination region which had been thought to be genetically silent. Those included a cluster of genes for fatty acid beta-oxidation, the third copy of the pot (spermidine/putrescine transport system) gene cluster, the second dpp (dipeptide transport system) operon, the second dsm (anaerobic dimethyl sulfoxide reductase) operon, a cluster of fim (fimbrial) genes and a DNA helicase-like gene with a high molecular weight. In addition, we found the dnaC- and dnaT-like genes in the cryptic prophage, Rac, and a number of genes originated probably from plasmids.

A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map.

The 465,813 base pair sequence corresponding to the 40.1-50.0 min region on the genetic map of Escherichia coli K-12 (W3110) was determined. Analysis of the sequence revealed that this region contained at least 466 potential open reading frames, of which 187 (40%) were previously reported, 105 (23%) were homologous to other known genes, 103 (22%) were identical or similar to hypothetical genes registered in databases, and the remaining 71 (15%) did not show a significant similarity to any other gene. At the 45.2-46.0 min region, we found a very large cluster of about 30 genes, whose functions are involved in the biosynthesis of polysaccharides as the components of outer membranes. In addition, we identified a new asn-tRNA gene, designated asnW, between the asnT and asnU genes and a new lysogenic phage attachment site as the cis-element.

The plasmid F OmpP protease, a homologue of OmpT, as a potential obstacle to E. coli-based protein production.

OmpT, an outer membrane-localized protease of Escherichia coli, cleaves a number of exogenous and endogenous proteins during their purification. SecY, an endogenous membrane protein, is a target of this artificial proteolysis in vitro. Here we report that SecY cleavage occurs even in cell extracts from ompT-disrupted cells, if they carry an F plasmid derivative. A gene, ompP, on the F plasmid was shown to be responsible for this proteolysis. These results indicate that the absence of an F-like plasmid should be checked when choosing a host strain for E. coli-based protein production.

"Tactile" sensory nerve potentials elicited by air-puff stimulation: a microneurographic study.

To investigate the sensory nerve responses to selective touch stimulation, sensory nerve action potentials after brief air-puffs were recorded with a microelectrode. In patients with peripheral neuropathy, those with impairment of tactile sensations had significantly smaller responses than did those without tactile impairment, suggesting receptor activation failure as well as nerve conduction failure. Brief air-puff stimulation, when combined with microneurography, could be used for evaluating the tactile receptor properties in humans.

Solid-pseudopapillary tumor of the pancreas: immunohistochemical localization of neuroendocrine markers and CD10.

To clarify the neuroendocrine differentiation and CD10 expression in solid-pseudopapillary tumors (SPTs) of the pancreas, we performed immunohistochemical analysis in 19 such tumors, including one solid-pseudopapillary carcinoma (SPC), along with 20 pancreatic neuroendocrine tumors (PNTs), six acinar cell carcinomas (ACCs), and one pancreatoblastoma (PB). We used antisera directed against CD56, synaptophysin, protein gene product 9.5, the alpha-subunit of Go protein, chromogranin A, CD10, trypsin, chymotrypsin, various cytokeratins (CKs), CA19-9, vimentin, and alpha-1-antitrypsin (AAT). All SPTs exhibited immunoreactivity for CD56 and CD10, and 15 expressed other neuroendocrine markers focally with the exception of chromogranin A. Frequent clustering of synaptophysin-positive cells was noted. Two cases contained a peculiar nodule that cytomorphologically and immunohistochemically resembled PNT. CD10-positive cells were scarce in one SPC. PNTs were CD56-positive, but often with faint intensity, and staining for other neuroendocrine markers, including chromogranin A, was diffusely positive. CD10 was detected, mostly in a focal pattern, in five PNTs. Pan-CK, CK8, CK18, and CK19 were more frequently demonstrated in PNT than SPT. Vimentin and AAT were often identified in PNT as well and were not specific for SPT. ACCs were CD56-negative, with the exception of one case designated as a mixed acinar-endocrine carcinoma. PB was focally positive for CD56 at the periphery of the tumor nests. Four ACCs and one PB exhibited focal CD10 reactivity. This study demonstrated the unique immunohistochemical features of SPT. Our results also suggest that SPT exhibits, at least focally, neuroendocrine differentiation, and that these neuroendocrine markers and CD10 are diagnostically useful.

Single unit responses of human cutaneous mechanoreceptors to air-puff stimulation.

OBJECTIVE: To investigate responsiveness of human cutaneous mechanoreceptor to selective tactile stimuli produced by brief air-puff stimulation. METHODS: Using percutaneous microneurography, activities of single sensory units innervating glabrous skin of the hand were recorded, and air-puff stimuli with a short rise time (0.5 ms), generated by a high-speed air control system, were applied to the receptive field. Receptor activation time was estimated as the latency difference between electrically and air-puff evoked responses. RESULTS: Thirty units were analyzed: all 4 kinds of mechanoreceptors of human glabrous skin (fast adapting type 1 [FA I, n=7], fast adapting type 2 [FA II, n=4], slowly adapting 1 [SA I, n=5] and slowly adapting 2 [SA II, n=14]) were activated by air-puff stimulation. Estimated receptor activation times were 0.6-6.2 ms (mean 2.2 ms). FA II units occasionally responded twice or more to a single air-puff stimulus. CONCLUSIONS: Brief air-puffs can activate all 4 human cutaneous mechanoreceptors, and the receptor transduction time is estimated as approximately 2.0 ms. Properties of human mechanoreceptors can be studied using air-puff stimulation and microneurography.

Properties of human skin mechanoreceptors in peripheral neuropathy.

OBJECTIVES: To investigate the properties of mechanoreceptors in patients with peripheral neuropathy. The skin mechanoreceptor is a terminal organ of the primary sensory neuron, which is likely to be affected earlier and more severely than is the nerve trunk by peripheral neuropathies. METHODS: Single sensory unit responses to air-puff and electric stimulation were recorded using the microneurographic technique in the glabrous skin of the hand. Receptor transduction time was estimated by a latency difference between electric- and air-puff-induced responses. RESULTS: A total of 38 mechanoreceptive units were obtained from 14 normal subjects. All the units responded to air-puff stimuli irrespective of the receptor type, and receptor transduction time was approximately 2 ms. A total of 32 units were recorded from 11 patients with neuropathy of variable causes. Seven (22%) of the 32 neuropathic units did not respond to air-puffs despite their ability to respond to electric stimulation. Compared to normal ones, units from patients with peripheral neuropathy had significantly higher mechanical thresholds, but receptor transduction times did not differ significantly. CONCLUSIONS: Changes in receptor properties in human neuropathy are characterized by increased mechanical threshold without prolongation of receptor transduction time, possibly due to a high threshold for generating receptor potentials.

Clinical features of three fatal cases of non-specific interstitial pneumonia.

We describe the clinical courses of the 3 fatal patients (2 females and 1 male) with idiopathic non-specific interstitial pneumonia (NSIP) among 24 patients with NSIP. Lung biopsies were diagnosed to be NSIP group II in all patients. The clinical courses from onset to death of these 3 patients were 41 months, 46 months, and 91 months. A follow-up chest CT demonstrated no apparent honey-comb formation. We found that i) about 20% of patients with NSIP died of respiratory failure, ii) in the chest CT findings, apparent honey-comb formation was rare even just before death, iii) prediction of the prognosis based on the histological findings was difficult. This is the first report to describe the clinical features of deceased patients with idiopathic NSIP; the incidence of fatal cases was considered to range from 10 to 20%.

[Effect of imipenem/cilastatin combined with vancomycin for MRSA infection].

Therapeutic efficacy of the combined regimen, imipenem/cilastatin (IPM/CS) plus vancomycin (VCM), was examined in a total of 13 patients infected with MRSA (10 patients with pneumonia, 2 with sepsis and 1 with urinary tract infection). Based on the results of determination of FIC indices, in vitro combined effects were synergistic in 4 strains and additive in 3 strains. There was, however, no apparent correlation between the in vitro combined effect in terms of FIC index and clinical outcome. No side effects or abnormal laboratory findings were observed. The average daily doses of IPM/CS and VCM were 1.2 g and 1.25 g and the average administration periods were 17.5 and 14.9 days, respectively. The present results suggested that simultaneous use of IPM/CS and VCM at the standard doses could yield an enhancement of both bacteriological and clinical efficacies in treatment of the patients with MRSA infection.

[Primary intracranial T cell type malignant lymphoma: a case report].

Primary intracranial T cell type malignant lymphoma is extremely rare. Only 8 cases are reported in the literature so far. In this paper, a case with this type of malignant lymphoma is reported. A 41-year-old man was admitted because of abnormal behavior. Enhanced CT scan demonstrated high density mass and perifocal low-density area in the right frontal lobe, the right basal ganglia and the periventricular region. Specimen biopsied from right frontal lobe was submitted for histological examination. An immunohistochemical technique using monoclonal surface markers confirmed reactivity for LCA, MT-1, OKT-4 and OKT-8, while there was no reactivity for MB-1 and OKB-2. Pathological diagnosis was diffuse medium T cell type malignant lymphoma. Postoperatively, after 60 Gy irradiation, the tumor disappeared. There is no difference on CT findings between B cell type and T cell type malignant lymphoma.

[A case of vacuolated meningioma].

A rare case of falx meningioma with extensive vacuolization was reported. A 57-year-old woman was admitted to Okayama University Hospital because of numbness in her left lower limb. A plain CT scan showed a hypodense mass in the right frontal region with marked enhancement after contrast medium injection. MRI on T1 weighted images showed low intense mass with the so-called "peritumoral band" of low intensity at the periphery of the mass. Angiogram showed a mass effect and a tumor stain fed by the right pericallosal artery and left middle meningeal artery. The mass was excised en bloc. Microscopic examination demonstrated tumor cells with varied sized vacuoles, which were mostly fat-negative, except for small islands with typical meningothelial cells in the periphery of the tumor. Ultrastructurally, there were two kinds of vacuole in the tumor cells. The smaller, round vacuoles were in the cytoplasm, while the larger ones were in the extracellular space. The cell processes had developed junctional complex, and numerous cytoplasmic filaments were evident. With these findings, this mass was diagnosed as vacuolated meningioma. It is important especially in frozen section not to misdiagnose the tumor as liposarcoma, chordoma, metastatic brain tumor and so on.

[An elderly case of squamous cell lung cancer showing partial response by daily administration of oral etoposide].

We report an elderly case of squamous cell lung cancer showing partial response by daily administration of oral etoposide. The 86-year-old man had been diagnosed as squamous cell lung cancer (Stage II, T2N1M0) in September 1992. He had received no active treatment, because he was too old and had pulmonary emphysema. Dyspnea became gradually worse due to complete atelectasis of right lung in December 1994. After treatment with oral etoposide (50 mg/day) for 10 days, atelectasis was reduced and a partial response was obtained. No severe side effect except leukopenia was noted.

[Swyer-James syndrome with pneumothorax].

We report a case of Swyer-James syndrome with pneumothorax. A 20 year-old man was admitted to our hospital with dyspnea. Right pneumothorax was diagnosed by chest X-ray. He had a history of current pneumonia in childhood. After improvement of the pneumothorax, chest X-ray revealed hyperlucency of the right upper lung. Chest-CT revealed a low attenuation area and a cystic space in the right upper lobe. Xenon-133 clearance was delayed in ventilation scintigraphy. Bronchography showed cylindrical bronchiectasis in the proximal bronchi and poor filling of the peripheral bronchi in the right upper lobe. Pulmonary angiography showed a small right upper pulmonary artery. Swyer-James syndrome was diagnosed. The pneumothorax was probably caused by weakness of the cystic spaces.

[Role of neutrophils in acute lung injury induced by Candida sepsis].

To evaluate the role of inflammatory cells in acute lung injury induced by Candida sepsis, we investigated the time course of cell counts in bronchoalveolar lavage (BAL) fluid, the lung wet-to-dry weight (W/D) ratio and the CFU of Candida after a Candida infection. Male BALB/c mice were injected intravenously with 107 CFU of Candida albicans. They were sacrificed by exsanguination 0, 6, 12, 18, and 24 h after infection. The lung W/D ratio was determined in order to assess the severity of pulmonary edema. BAL was performed 3 times with 0.5 ml of sterile saline. The lung W/D ratio increased significantly 24 h after the injection of Candida, and the neutrophil counts in the BAL fluid increased significantly 12, 18, and 24 h after Candida injection. To assess the effect of neutrophils on Candida-induced acute lung injury, we investigated that of neutrocytosis and neutropenia on cell counts in BAL fluid, of the W/D ratio, and of the CFU of Candida in the lung 24 h after infection. We created neutrocytotic mice using G-CSF, and neutropenic mice with cyclophosphamide. Peripheral neutrophil counts decreased significantly in cyclophosphamide-treated mice, and increased significantly in G-CSF-treated mice. The lung W/D ratio increased significantly in cyclophosphamide-treated mice. Neutrophil counts in BAL fluid increased significantly in G-CSF-treated mice, and decreased significantly in cyclophosphamide-treated mice. The CFU of Candida in the lung decreased significantly in G-CSF-treated mice, and increased significantly in cyclophosphamide-treated mice. We concluded that neutrophils play a protective role in Candida albicans-induced acute lung injury.