Retraction Note: Forearm Bone Mineral Density in Postmenopausal Women with Rheumatoid Arthritis.

The Editors-in-Chief have retracted this article [1]. Serious concerns have been raised about the data presented [2], and after careful consideration and additional investigation the Editors-in-Chief no longer have confidence in this article.

Retraction Note: Urinary Cross-linked N-telopeptides of Type I Collagen Levels in Patients with Rheumatoid Arthritis.

The Editors-in-Chief have retracted this article [1]. Serious concerns have been raised about the data presented [2], and after careful consideration and additional investigation the Editors-in-Chief no longer have confidence in this article. All authors were contacted and did not respond to correspondence about this retraction.

Four subtypes of petroclival meningiomas: differences in symptoms and operative findings using the anterior transpetrosal approach.

BACKGROUND: Petroclival meningiomas are vaguely defined as tumours arising from the antero-medial zone to the internal auditory meatus. This report subclassifies petroclival meningiomas based on their origin determined by using radiological and intra-operative findings. METHOD: Ninety-one patients with petroclival meningioma underwent surgery via the anterior transpetrosal approach. The Meckel's cave was routinely opened. Tumour origin was classified into four subtypes according to the main attachment and trigeminal nerve deviation into, upper clivus (UC), cavernous sinus (CS), tentorium (TE), and petrous apex (PA). Their characteristic clinical symptoms and anatomical features were investigated. FINDINGS: The characteristic symptom was ataxia in the UC type (37.5%), abducens nerve palsy in the CS type (64.3%) and trigeminal neuropathy, mainly neuralgia in the PA type (80.0%) with a higher statistical difference from other subtypes. The rate of tumour invasion into Meckel's cave reached 70.3% in average, with the lowest rate in the PA type (25.0%). The rate of middle fossa extension was the highest in the TE type (59.5%). The middle fossa approach was considered to be ideal for UC and TE types because of easier access to the Meckel's cave. Radical dissection without complications was difficult in the CS type. Both the anterior transpetrosal approach and the lateral suboccipital approach could be indicated in the PA type due to the rare invasion of Meckel's cave and middle fossa, and frequent extension into the internal auditory meatus. CONCLUSIONS: This classification is useful to predict the relation between the tumour and the cranial nerves based on symptoms and images. The anterior transpetrosal approach could be used for all four subtypes and with an absolute indication in the UC and TE types showing middle fossa extension.

Regulation of the catalase gene promoter by Sp1, CCAAT-recognizing factors, and a WT1/Egr-related factor in hydrogen peroxide-resistant HP100 cells.

Reactive oxygen species play a critical role in the onset of apoptosis induced by various extracellular stimuli, including ionizing radiation. Therefore active regulation of reactive oxygen species-metabolizing enzymes may be one response to an apoptotic stimulus. In this regard, HP100 cells, H(2)O(2)-resistant variants derived from human leukemia HL60 cells, display an interesting phenotype in which the activity of catalase is constitutively high, whereas its mRNA is reduced after X-ray irradiation. In the present study, we investigated the molecular mechanisms underlying this phenomenon. By combining analyses from nuclear run-on, reporter gene transient transfection, genomic footprinting, site-directed mutagenesis, electrophoretic mobility shift analysis, and Western blotting experiments, we found that constitutively elevated catalase expression is strongly regulated at the transcriptional level by both Sp1 and CCAAT-recognizing factors and that much higher levels of nuclear Sp1 and NF-Y are present in HP100 nuclei as compared with HL60 nuclei. In addition, we demonstrated an X-ray-inducible association of a WT1/Egr-related factor with an overlapping Sp1/Egr-1 recognition sequence located within the core promoter of the catalase gene. This association may lead to inactivation of the promoter by disturbing or competing with the transactivating ability of Sp1.

Different effects of polylysine and polyarginine on the transition to a condensed state of DNA in polyethyleneglycol/salt solution.

Circular dichroism spectroscopy has been used to investigate the influence of polylysine and polyarginine on the transition to a condensed state of DNA brought about by high concentrations of polyethyleneglycol and salt. From the dependence on DNA concentration of the CD signals, the anomalous CD of free DNA in polyethyleneglycol/salt solution was attributed to the intermolecular association of DNA molecules. The CD spectral changes in polyethyleneglycol/salt solution of the DNA - polylysine complex were indistinguishable from those of free DNA while the DNA-polyarginine complex suffered much smaller spectral changes as compared with free DNA, at low DNA concentrations where time-independent CD spectra were observed in polyethyleneglycol/salt solution for both the complexed and free DNA. The repression of the spectral change by the latter complex was more remarkable at higher ratios of polyarginine to DNA. The facts indicate that, whereas polylysine binding has little influence on the intermolecular structural transition of double-stranded DNA into a compact molecular configuration in polyethyleneglycol/salt solution, polyarginine binding has an effect of inhibiting the transition.

Evolutionarily conserved structure of the 3' non-translated region of a Chinese hamster polyubiquitin gene.

From a V79 Chinese hamster genomic library, we isolated a clone containing a polyubiquitin gene (designated as CHUB1), and determined its nucleotide sequence. The coding region of the CHUB1 gene consisted of five direct repeats of the ubiquitin unit with no spacer, followed by a single tyrosine residue. Northern hybridization analysis with a synthesized probe specific to the 3' non-translated region of the CHUB1 gene revealed that it codes for a 1.8 kb mRNA. An evident homology to the human polyubiquitin gene UbB and the chicken UbI gene was observed in the region corresponding to the full extent of the mature mRNA sequence, suggesting that these three genes belong to a common polyubiquitin gene subfamily, and that the sequence in the 3' non-translated region of the CHUB1 gene is unique to this subfamily.

Conformation of the HMG17-nucleosome complex.

The nucleosome core binds more than two molecules of HMG17 at low ionic strength (8.9 mM Tris-HCl/8.9 mM boric acid/0.25 mM Na2EDTA, pH 8.3). Circular dichroism of the complexes showed only minor conformational changes of the nucleosome core DNA on binding of HMG17, with no detectable change in the histone secondary structure. The fluorescence of N-(3-pyrene) maleimide bound to -SH groups at Cys-110 of H3 histones in the core particle suggested that the structure of the histone octamer assembly changed little upon binding of HMG17 to the nucleosome. These observations support the idea that even a high level of HMG17 binding, e.g., four HMGs per nucleosome, alone, does not open up the core particle.

Phosphatidylinositol 3-kinase inhibitors, Wortmannin or LY294002, inhibited accumulation of p21 protein after gamma-irradiation by stabilization of the protein.

Expression of the cyclin kinase inhibitor, p21, is regulated both transcriptionally and posttranscriptionally by the ubiquitin-proteasome degradation pathway. Recently, we reported that DNA damage is required for efficient p21 expression by demonstrating that enhanced p21 mRNA expression induced by DNA damage results in increased p21 protein, but enhanced p21 mRNA without DNA damage does not. In addition, we demonstrated that DNA damage suppressed the ubiquitination of p21. In this study, we analyze the link between p21 stabilization and DNA damage. Enhanced p21 protein expression in ML-1 cells resulting from 15 Gy gamma-irradiation was diminished by Wortmannin or LY294002 pretreatment of cells. However, the levels of p21 mRNA were not affected by inhibitor pretreatment. Wortmannin or LY294002 pretreatment reduces p53 expression after gamma-irradiation to a lesser degree than that of p21. In addition, we examined the involvement of DNA-PK, whose activity is inhibited by Wortmannin or LY294002, in p21 stabilization using the SCID fibroblast cell line and a DNA-PK targeting ML-1 cell line. Accumulation of p21 protein by gamma-irradiation was similar to that of DNA-PK intact cells and was reduced by Wortmannin or LY294002 pretreatment. Involvement of another DNA damage detecting enzyme, the ATM gene product, whose activity is also inhibited by Wortmannin or LY294002, was evaluated. ATM deficient cells induced p21 after gamma-irradiation, gamma-irradiation-induced p21 protein was diminished by pretreatment of cells with Wortmannin or LY294002. We conclude that the p21 stabilization mechanism functions after gamma-irradiation, was sensitive to Wortmannin or LY294002, and required neither DNA-PK nor ATM gene product for activity.

Novel structure of a Chinese hamster polyubiquitin gene.

We isolated a polyubiquitin gene, CHUB2, from the V79 Chinese hamster genomic library, and determined its complete structure. Based on sequence homology to the human polyubiquitin gene UbC in the 5' and 3' untranslated region, the CHUB2 gene was characterized as the V79 Chinese hamster equivalent to the human UbC gene. However, the overall coding region structure of the CHUB2 gene was altered from the consensus structure of polyubiquitin genes, with the last ubiquitin coding unit being followed by 161 bp of partially deleted and mutated ubiquitin-like sequence. Although a similarly deleted and mutated polyubiquitin gene was recently reported in a partially sequenced cDNA of mouse (Finch et al. (1992) Cell Growth Differ. 3, 269-278), the present study describes the complete sequence of a polyubiquitin gene containing this unusual structure for the first time, and suggests that this structure is conserved in rodents. By employing both Southern and Northern analysis with a probe specific to the CHUB2 gene, it was found that a second, closely related gene is present in the Chinese hamster genome, and that both loci are transcriptionally active in V79 cells. The two genes, and their respective transcripts, differ in size because of variation in the relative number of repeating ubiquitin coding units.

Specific codon usage pattern and its implications on the secondary structure of silk fibroin mRNA.

We have identified two distinctive regions of the repetitive unit nucleotide sequence of fibroin mRNA of Bombyx mori. The codon usage for the major amino acids, glycine, alanine and serine is distinctly different in these two regions, indicating that it is determined by the fibroin mRNA or gene structure but not by the tRNA population. Comparative computer analyses of nucleotide substitutions in the unit sequence suggest that selection has operated on the codon usage to optimize the secondary structure characteristic of the fibroin mRNA.

Higher frequency of concerted evolutionary events in rodents than in man at the polyubiquitin gene VNTR locus.

The polyubiquitin gene is an evolutionarily conserved eukaryotic gene, encoding tandemly repeated multiple ubiquitins, and is considered to be subject to concerted evolution. Here, we present the nucleotide sequences of new alleles of the polyubiquitin gene UbC in humans and CHUB2 in Chinese hamster, which encode a different number of ubiquitin units from those of previously reported genes. And we analyze the concerted evolution of these genes on the basis of their orthologous relationship. That the mean of the synonymous sequence difference Ks which is defined as the number of synonymous substitution relative to the total number of synonymous sites, within the UbC and CHUB2 genes (0.192 +/- 0.096) is significantly less than Ks between these genes (0.602 +/- 0.057) provides direct evidence for concerted evolution. Moreover, it also appears that concerted evolutionary events have been much more frequent in CHUB2 than in UbC, because Ks within CHUB2 (0.022 +/- 0.018) is much less than that within UbC (0.362 +/- 0.192). By a numerical simulation, postulating that the major mechanism of concerted evolution in polyubiquitin genes is unequal crossing over, we estimated the frequency of concerted evolutionary events of CHUB2 at 3.3 x 10(-5) per year and that of UbC at no more than 5.0 x 10(-7) per year.

Prevalence of Smqnr and plasmid-mediated quinolone resistance determinants in clinical isolates of Stenotrophomonas maltophilia from Japan: novel variants of Smqnr.

Stenotrophomonas maltophilia is an important pathogen in healthcare-associated infections. S. maltophilia may contain Smqnr, a quinolone resistance gene encoding the pentapeptide repeat protein, which confers low-level quinolone resistance upon expression in a heterologous host. We investigated the prevalence of Smqnr and plasmid-mediated quinolone resistance (PMQR) determinants in S. maltophilia isolates from Japan. A total of 181 consecutive and nonduplicate clinical isolates of S. maltophilia were collected from four areas of Japan. The antimicrobial susceptibility profiles for these strains were determined. PCR was conducted for Smqnr and PMQR genes, including qnrA, qnrB, qnrC, qnrS, aac(6')-Ib and qepA. PCR products for Smqnr and aac(6')-Ib were sequenced. For the S. maltophilia isolates containing Smqnr, pulsed-field gel electrophoresis (PFGE) was performed using XbaI. Resistance rates to ceftazidime, levofloxacin, trimethoprim-sulfamethoxazole, chloramphenicol and minocycline were 67.4%, 6.1%, 17.7%, 8.8% and 0%, respectively. The minimum inhibitory concentration required to inhibit the growth of 50% and 90% of organisms were 0.5 and 2 mg/L for moxifloxacin but 1 and 4 mg/L for levofloxacin, respectively. Smqnr was detected in 104 of the 181 S. maltophilia isolates (57.5%), and the most frequent was Smqnr6, followed by Smqnr8 and Smqnr11. Eleven novel variants from Smqnr48 to Smqnr58 were detected. The 24 Smqnr-containing S. maltophilia isolates were typed by PFGE and divided into 21 unique types. Nine S. maltophilia isolates (5.0%) carried aac(6')-Ib-cr. No qnr or qepA genes were detected. This study describes a high prevalence of Smqnr and novel variants of Smqnr among S. maltophilia from Japan. Continuous antimicrobial surveillance and further molecular epidemiological studies on quinolone resistance in S. maltophilia are needed.

Effects of exercise on bone mineral density in mature osteopenic rats.

Dual-energy X-ray absorptiometry (DXA) was used to examine the effects of quantitative application of treadmill running exercise on bone mineral density (BMD) of the tibia and the fourth and fifth lumbar (L4 + L5) vertebrae in mature osteopenic rats. Twenty 37-week-old rats with bone loss, resulting from feeding a relatively low calcium diet for 14 weeks after ovariectomy at the age of 23 weeks, were divided into four groups of five rats each according to the intensity and duration of the exercise: 12 m/minute, 1 h/day in group EX1; 18 m/minute, 1 h/day in group EX2; 12 m/minute, 2 h/day in group EX3; and sedentary control in group CON. With a standard calcium diet, the exercise was performed 5 days a week for 12 weeks, and the BMD of both the right tibia and the L4 + L5 vertebrae was measured using DXA at weeks 0, 4, 8, and 12. At the end of 12 weeks of exercise, the right femur and the L5 vertebra were dissected and the mechanical strength was measured using a three-point bending test and a compression test, respectively. After 12 weeks of exercise, a significant increase in the tibial BMD was observed in only group EX1 compared with that in group CON (p = 0.0039, by two-way analysis of variance). However, any significant increase in the L4 + L5 vertebral BMD was not observed in any exercise groups compared with that in the control group. While a maximum breaking force of the femoral shaft in group EX1 was significantly greater than that in group CON (p < 0.05, by Mann-Whitney's U-test), that in groups EX2 and EX3 did not significantly differ from that in group CON. However, there was no significant difference in a maximum breaking force of the L5 vertebral body among all the exercise and control groups. These results indicated that the beneficial effects of treadmill running exercise under a standard calcium diet were recognized only in the weight-bearing bones of the mature osteopenic rats resulting from estrogen deficiency and inadequate calcium intake only when an optimal level of exercise was applied.

Comparison of the 5' upstream region of the evolutionarily equivalent polyubiquitin gene of humans and Chinese hamsters.

The 5' upstream region of the Chinese hamster polyubiquitin gene CHUB2 was determined, and compared to that of the evolutionarily equivalent polyubiquitin gene UbC of humans. The 5' upstream region of the CHUB2 gene is distinct from that of the UbC gene in containing fewer recognition sequences for binding of transcription factors, which are quite sparsely distributed in this region. It seemed probable that the absence of AP-1 sites in the promoter of the CHUB2 gene was likely to be responsible for the very dissimilar regulation of the two genes by UV light and TPA, despite the fact that these genes are evolutionarily equivalent.

Expression of the Bombyx mori beta-tubulin-encoding gene in testis.

We have isolated a beta-tubulin-encoding cDNA clone of Bombyx mori from testes and determined the nucleotide sequence. Northern analyses showed that its expression is testis-specific and most active in the pupal stage.

Heterogeneous structure of the polyubiquitin gene UbC of HeLa S3 cells.

The nucleotide sequence of the polyubiquitin gene UbC of HeLa S3 cells and its upstream region was determined and characterized. Recognition sequences for the transcription factors HSF, NF kappa B, AP-1(c-jun), NF-IL6 and Sp1 were found in the upstream control region, a result consistent with the observation of a distinct regulatory response for the UbC gene compared with that of another polyubiquitin gene UbB. Employing a PCR procedure to amplify the entire coding region from genomic DNA, we found a heterogeneity in the repeat number (eight and nine repeats) of the ubiquitin coding units, which resulted from an apparent deletion of either the seventh or the eighth unit in the predominant nine-ubiquitin-unit coding gene. In addition, by comparison with the nucleotide sequence of the UbC gene of human leukocytes previously determined, we found a significant number of nucleotide discrepancies. However, these discrepancies could be substantially reduced by realigning the units so that the first and second ubiquitin units of the sequence determined here are translocated to the boundary between the eighth and the ninth units.

The methyl viologen-resistance-encoding gene smvA of Salmonella typhimurium.

The complete nucleotide sequence of the gene encoding the Salmonella typhimurium methyl viologen-resistant protein, SmvA, similar to QacA (resistance to quaternary ammonium ion) of Staphylococcus aureus, and the surrounding sequences were determined. This indicated that the gene arrangement of S. typhimurium is different from that of Escherichia coli in this region.

The human gene encoding the largest subunit of RNA polymerase II.

The nucleotide sequence of a large portion of the human RNA polymerase II large subunit (RpII LS)-encoding gene and its whole gene structure were determined. The RpIILS gene consists of 29 exons. The sequence of the 5' flanking region is highly conserved as compared with that of the mouse RpIILS and contains several SP1-binding sites, a CCAAT sequence and a sequence homologous to a heat-shock element. In addition, several inverted repeats and palindrome sequences were involved in the 5' upstream region. Those suggest that the 5' flanking domain of RpIILS would be highly structured which may be responsible for transcriptional regulation.

Isolation of deuterated histones from yeast grown on media dissolved in 2H2O.

We have succeeded in growing Saccharomyces cerevisiae (baker's yeast) on media containing 2H2O and isolating the core histones highly deuterated in the non-exchangeable positions. The deuterated histones obtained here are of great value for their possible widespread use for structural studies of chromatin.