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Intron retention (IR) is an important regulatory mechanism that affects gene expression and protein functions. Using klotho mice at the pre-symptomatic state, we discovered that retained-introns accumulated in several organs including the liver and that among these retained introns in the liver a subset was recovered to the normal state by a Japanese traditional herbal medicine. This is the first report of IR recovery by a medicine. IR-recovered genes fell into two categories: those involved in liver-specific metabolism and in splicing. Metabolome analysis of the liver showed that the klotho mice were under starvation stress. In addition, our differentially expressed gene analysis showed that liver metabolism was actually recovered by the herbal medicine at the transcriptional level. By analogy with the widespread accumulation of intron-retained pre-mRNAs induced by heat shock stress, we propose a model in which retained-introns in klotho mice were induced by an aging stress and in which this medicine-related IR recovery is indicative of the actual recovery of liver-specific metabolic function to the healthy state. Accumulation of retained-introns was also observed at the pre-symptomatic state of aging in wild-type mice and may be an excellent marker for this state in general.

[][1] Takashi Sugimura was a pioneer in cancer research and a figure recognized internationally for his seminal contributions to the understanding of mutagenicity and chemical carcinogenesis. Rather than focusing on the many accolades, honors, and influential positions that he held

During the maturation of transfer RNA (tRNA), a variety of chemical modifications can be introduced at specific nucleotide positions post-transcriptionally. 5-Methyluridine (m5U) is one of the most common and conserved modifications from eubacteria to eukaryotes. Although TrmA protein in Escherichia coli and Trm2p protein in Saccharomyces cerevisiae, which are responsible for the 5-methylation of uracil at position 54 (m5U54) on tRNA, are well characterized, the biological function of the U54 methylation responsible enzyme in mammalian species remains largely unexplored. Here, we show that the mammalian tRNA methyltransferase 2 homolog A (TRMT2A) protein harbors an RNA recognition motif in the N-terminus and the conserved uracil-C5-methyltransferase domain of the TrmA family in the C-terminus. TRMT2A predominantly localizes to the nucleus in HeLa cells. TRMT2A-overexpressing cells display decreased cell proliferation and altered DNA content, while TRMT2A-deficient cells exhibit increased growth. Thus, our results reveal the inhibitory role of TRMT2A on cell proliferation and cell cycle control, providing evidence that TRMT2A is a candidate cell cycle regulator in mammals.

We have imaged rock density distribution beneath Liwa fracture zone in the southern part of the the Sumatran Fault Zone by modelling and inverting Bouguer gravity data in two-and three-dimensional environments, respectively. The purpose of this study is aimed to figure out the subsurface distribution of rock densities associated with subsurface basement structure representing the evidence of trans-tensional tectonic product in the SF. In the gravity modeling, to eliminate distortions to the measured gravity values before modelling and inverting the data, Bouguer anomalies obtained in field measurements are reduced to the horizontal plane of z = +800 m as a representation of the average elevation in Liwa. For the inversion, we used algorithm implementing depth-and minimum volume weighting parameters in order to obtain a smooth model with better vertical resolution. The two-dimensional models show clearly surface topography of the basement rocks and the presence of normal faults. The reduced Bouguer anomaly of +800 m elevation shows the presence of structural lineaments extending primarily in a northwest-southeast direction, parallel to Sumatran Fault Zone and older graben faults showing a negative flower structure. From the three-dimensional inversion, the model illustrates an increase of density contrast, lower values being found near the surface and higher values in the deeper parts. The lower density contrast of 0.15 to 0.3 g/cm3 found in the rock groups at depths of 2 km and less is characteristic of relatively homogeneous and poorly compacted rocks. Rocks with moderate to high density contrast (>1.0 g/cm3) are recognized at depths of over 2 km. This model suggests a change of basement morphology as a function of depth, and delineates structural lineaments extending in northwest-southeast direction. This study supports the previous thought that Liwa area is underlain by graben structures, formed by trans-tensional tectonic events. Higher-density Tertiary volcanic breccia and lower-density Quaternary volcanic products of the Ranau Formation form the basement rocks and the overlying younger sediments, respectively.

When the average thickness of additional cover concrete in design phase and that in construction phase are separately analyzed for each type of member such as column, beam, etc., it showed an almost normal distribution, respectively. Furthermore, concerning the relationship between distribution of the average cover concrete thickness on each measuring face of any member and the deviation within a member, a tendency was found that the deviation within a member increases along with an increase in the average value while the former remains small as far as the latter is small.

The 40th International Symposium of the Princess Takamatsu Cancer Research Fund, entitled “DNA Repair and Human Cancers,” was held on November 10–12, 2009 at Hotel Grand Palace, Tokyo, Japan. The meeting focused on the role of DNA repair in preventing mutations by endogenous and exogenous DNA damage and increasing the efficacy of chemotherapeutic agents by interfering with DNA repair. The 14 presentations by the speakers from the United States, four from the United Kingdom, one each from Italy, The Netherlands, and France, and 13 from Japan, covered most aspects of DNA repair, spanning DNA damage, molecular structures of repair enzymes, and clinical studies on inhibition of DNA repair processes. Extensive time was reserved for discussions with the active participation of the 150 invited Japanese scientists. The choice of a symposium on DNA repair in human cancers resulted in part from the excellent basic and clinical studies that have been carried out for many years in Japan, and the general lack of recognition versus the importance of DNA repair in understanding carcinogenesis. Cancer Res; 70(11); 4269–73. ©2010 AACR.

We experienced a very rare case, simultaneous intra- and extra-uterine pregnancy without ovulation induction, and performed left salpingo-oophorectomy including luteectomy at 7 weeks and 5 days gestation as a treatment after exploratory laparotomy. One week later, spontaneous abortion occurred in of progestin supplement therapy. After the operation, serum progesterone (P), estrogens (E: E1, E2, E3), luteining hormone (LH), follicle-stimulating hormone (FSH), and urinary human chorionic gonadotropin (hCG) were measured. Serum P levels were under 7 ng/ml throughout the period studied, and decreased around the abortion. Serum E2 maintained normal range and dropped more rapidly than P just before the abortion. In contrast LH, FSH and urinary hCG showed relatively high levels after luteectomy and even at miscarriage.

This report concerns a research on cover concrete thickness implemented for a number of members at 18 completed reinforced concrete buildings through non-destructive inspection and an analysis of the distribution and fluctuation of cover thickness. On the basis of the disclosed actual state of deviation within a member and among members, it has become obvious that the smaller deviation within a member on one hand and the larger deviation among members on the other hand lead to the large cover thickness fluctuation within a building as a whole.

This paper reports on the investigation of thickness of cover concrete through nondestructive test for a quantity of member samples from 18 buildings of reinforced concrete structure constructed actually in standard methods as well as on the analysis of its distribution and fluctuations. While the preceding paper reported on the actual state of deviation within a member and that among members, this paper analyzes the influences of “additional cover concrete in design phase” and “that in construction phase”. As a result of this, it has been disclosed that any free movement of reinforcing bars due to the said influences leads to increase in deviation within a member as well as that among members.

This paper develops a new framework for fusion that is designed for eliminating the intermediate data structures involved in the composition of functions that have one accumulating parameter. The new fusion framework comprises two steps:algebraic fusionand its subsequentimprovementprocess. The key idea in our development is to regard functions with an accumulating parameter as functions that operate over the monoid ofdata contexts. Algebraic fusion composes each such function with a monoid homomorphism that is derived from the definition of the consumer function to obtain a higher-order function that computes over the monoid of endofunctions. The transformation result may be further refined by an improvement process, which replaces the operation over the monoid of endofunctions (i.e., function closures) with another monoid operation over a monoid structure other than function closures.Using our framework, one can formulate a particular solution to the fusion problem by devising appropriate monoids and monoid homomorphisms. This provides a unified exposition of a variety of fusion methods that have been developed so far in different formalisms. Furthermore, the cleaner formulation makes it possible to argue about some delicate issues on a firm mathematical basis. We demonstrate that algebraic fusion and improvement in the world of complete pointed partial orders (CPOs) and continuous functions can correctly fuse functions that operate on partial and infinite data structures. We also show that subtle differences in termination behaviours of transformed programmes caused by certain different fusion methods can be cleanly explained by corresponding improvement processes that have different underlying monoid structures.

Transcription factor Nrf2 regulates production of antioxidants and protects cells from oxidative/electrophilic stresses. Paradoxically, glutathione, one of the Nrf2-regulated antioxidants, has been assumed to promote genotoxicity of KBrO3. To address this glutathione hypothesis, we examined roles Nrf2 plays in the cellular defense against KBrO3-induced oxidative damage using Nrf2-/-, Ogg1-/- and Nrf2::Ogg1 double knockout mice. We found that upon KBrO3 treatment Nrf2::Ogg1 double knockout animals suffered from severe kidney damage, but unexpectedly the double knockout mice accumulated lower level of 8-hydroxyguanine than Ogg1-/- mice. Thus, KBrO3-induced nephrotoxicity appears not to depend on the formation of 8-hydroxyguanine. Our data also indicate that both the KBrO3-induced nephrotoxicity and formation of 8-hydroxyguanine are Nrf2-controlled processes, but the changes of the glutathione level are Nrf2-independent. Based on these results we conclude that glutathione is a minor part of the mechanism promoting genotoxicity of KBrO3 in Ogg1 knockout mice.

Rather than to attempt to summarize the vast contributions made to the field of modified nucleosides over the past 40 years, this review aims to present a chronological and somewhat personal account of how this area has developed to the present state. From 1965 onwards, one of the authors, Susumu Nishimura, has been involved in studying modified nucleosides in tRNA. Given that before this time little was known about the principal players of protein synthesis, such as the ribosomes, mRNA, tRNA and RNA polymerase, it seems fitting to recount how the author, like many other researchers from disparate disciplines, found himself drawn into this fascinating research area after graduating from the Department of Chemistry, Faculty of Science, University of Tokyo in 1955.Upon entering a graduate course within the Department of Biochemistry and Biophysics, Faculty of Science, University of Tokyo, his research project, under the direction of the late Shiro Akabori, focused on the mechanism of protein biosynthesis through studying the secretion of large amounts of amylase by Bacillus subtilis. During this time, many Japanese laboratories were deprived of important instruments and biochemicals such as preparative ultracentrifuges, liquid scintillation counters, spectrophotometers, ATP and radioactive amino acids etc. Understandably, these conditions made exploring the mechanism of protein biosynthesis difficult within Akabori’s laboratory during the period 1955 to 1960. Notwithstanding this, the motivation and determination of researchers in the Akabori laboratory remained unabated as they tackled this important and fascinating research area. Incidentally, an Assistant Professor in the laboratory, Masayasu Nomura greatly influenced Nishimura’s work at that time and indeed afterwards. Over the course of his PhD studies, Nishimura discovered a B. subtlis purine-specific extracellular RNase, similar to RNase T

In order to assess the effect of potassium bromate (KBrO3) on the induction of tumor formation, a 1-year carcinogenesis study was performed using Ogg1 knockout mice (Ogg1(-/-)) and wild-type mice (Ogg1(+/+)). The mice were chronically exposed to KBrO3 by putting it in the drinking water for 29 weeks, at 2 g/l for the first 18 weeks, and then at 1 g/l for another 11 weeks. After termination of treatment the mice were kept for an additional 23 weeks. The amount of 8-hydroxydeoxyguanosine (8-OH-dG) in kidney DNA after 29 weeks of KBrO3 exposure reached 500 8-OH-dG/10(6) dG, almost 250-fold that of untreated wild-type mice. During the course of study the mice appeared normal, although a decrease of body weight gain in both Ogg1(-/-) and Ogg1(+/+) mice exposed to KBrO3, and some kidney malfunction in KBrO3 treated Ogg1(-/-) mice was observed. Surprisingly, when Ogg1(-/-) and Ogg1(+/+) mice were sacrificed at 52 weeks, no tumor formation could be found in kidney or other organs such as lung, liver, spleen, thymus, stomach and intestine. Microscopic examination also showed the absence of precancerous foci in all tissues of both Ogg1(-/-) and Ogg1(+/+) mice. A possible explanation is presented to reconcile these results with those of others which showed an increased incidence of tumor formation in untreated Ogg1(-/-) mice.

High-resolution mass spectrometry has been investigated as a technique for identification of modified nucleosides in unfractionated hydrolysates of transfer RNA. The method is based on recognition of predetermined sets of exact mass values which are characteristic of individual nucleoside components. Mass spectra are photographically recorded in a non-time-resolved fashion, so that differing rates of nucleoside vaporization are of no consequence. Experimental parameters of sensitivity, spectrometer resolution and rates of vaporization were studied. Under typical conditions, 1-4 micrograms of tRNA are hydrolyzed, converted to volatile trimethylsilyl derivatives, and mass spectra of the resulting mixture recorded during 3 min at resolution 20 000; 75-100% of the minor nucleosides are usually identified in a single recording. The method is complementary to conventional methods of identification which rely on chromatographic mobilities, and can in principle be generally applied to recognition of biologically or chemically modified bases in nucleic acid.

Tyrosyl-tRNA synthetase (TyrRS) has been studied extensively by mutational and structural analyses to elucidate its catalytic mechanism. TyrRS has the HIGH and KMSKS motifs that catalyze the amino acid activation with ATP. In the present study, the crystal structures of the Escherichia coli TyrRS catalytic domain, in complexes with l-tyrosine and a l-tyrosyladenylate analogue, Tyr-AMS, were solved at 2.0A and 2.7A resolution, respectively. In the Tyr-AMS-bound structure, the 2'-OH group and adenine ring of the Tyr-AMS are strictly recognized by hydrogen bonds. This manner of hydrogen-bond recognition is conserved among the class I synthetases. Moreover, a comparison between the two structures revealed that the KMSKS loop is rearranged in response to adenine moiety binding and hydrogen-bond formation, and the KMSKS loop adopts the more compact ("semi-open") form, rather than the flexible, open form. The HIGH motif initially recognizes the gamma-phosphate, and then the alpha and gamma-phosphates of ATP, with a slight rearrangement of the residues. The other residues around the substrate also accommodate the Tyr-AMS. This induced-fit form presents a novel "snapshot" of the amino acid activation step in the aminoacylation reaction by TyrRS. The present structures and the T.thermophilus TyrRS ATP-free and bound structures revealed that the extensive induced-fit conformational changes of the KMSKS loop and the local conformational changes within the substrate binding site form the basis for driving the amino acid activation step: the KMSKS loop adopts the open form, transiently shifts to the semi-open conformation according to the adenosyl moiety binding, and finally assumes the rigid ATP-bound, closed form. After the amino acid activation, the KMSKS loop adopts the semi-open form again to accept the CCA end of tRNA for the aminoacyl transfer reaction.

A 64-year-old woman was diagnosed as having rheumatoid arthritis in 1999 at a nearby hospital. She had been treated with etodolac, actarit, mizoribine (MZ) and prednisolone. On May 25, 2001, she noticed fever and nausea and was treated with diclofenac sodium and clindamycin. On May 31, a nasal bleeding, tarry stool, hyperuricemia, renal dysfunction and thrombocytopenia developed and she was admitted to our hospital. Administration of drugs except prednisolone was stopped and hemodialysis was carried out on June 1. Fever and nausea improved during several days. Hyperuricemia and renal dysfunction disappeared on June 11. The platelet count became normal after platelet transfusion and she was discharged from our hospital on July 2. She was also diagnosed as having Sjogren's syndrome. In our case, a delay in MZ discharge by transient renal dysfunction might have caused a hyperuricemia, following an aggravation of renal dysfunction. So, care should be taken about latent renal dysfunction during the use of MZ. Moreover, it may be necessary to consider a discontinuation of MZ and administration of hemodialysis in the case of transient renal dysfunction.

A 69-year-old man visiting our hospital with an epigastralgia and tarry stool was diagnosed as having Behçet's disease on the basis of repetitious aphthous stomatitis, erythema nodosum and arthralgia in 1991. The next year, he suffered from double active ulcers in the antrum of the stomach, and he had been operated on for intestinal perforation. In 1994, endoscopic examination revealed the gastric mucosal bridge between the double ulcers. The double ulcer healed after an eradication therapy of H. pylori, but the gastric mucosal bridge has remained there on the gastrointestinal endoscopy. The gastric mucosal bridge with Behçet's disease has not been reported in Japan, being considered to be very rare.

Mutations in particular codons of c-Ha-ras have a strong activating potential, and an activated ras oncogene has been found in a number of human cancers. Using fragments of the human c-Ha-ras gene containing 8-hydroxyguanine (8-OH-G) in codon 12, we provide evidence for highly complex biochemical events leading to activation of the oncogene. Replication with DNA polymerases alpha (Pol(alpha)) and beta (Pol(beta)) led to misincorporation of dAMP, while DNA polymerase eta (Pol(eta)) caused additional insertion of dGMP. For the first time we report an 'action-at-a-distance' mutagenic effect for Pol(eta). Replication catalyzed by this enzyme resulted in misincorporating dAMP, dTMP and dGMP opposite non-oxidized guanine 3'-flanked by 8-OH-G. Interestingly, two adjacent 8-OH-G residues greatly relaxed the specificity of Pol(eta), which in this system was able to incorporate all four nucleotides. Moreover, two adjacent 8-OH-G residues completely blocked Pol(alpha) and strongly inhibited Pol(beta), whereas Pol(eta) was entirely resistant to this inhibition. These results suggest an important role for Pol(eta) in inducing hypermutability in codon 12. Our observations are important for understanding the consequences of 8-OH-G being positioned within the mutational hot spots of oncogenes, the outcome of which appears to be relatively complex even in minimal in vitro systems.

A 68-year-old female had been treated for chronic type C hepatitis at our department since June, 1992. In August of the same year, swelling of the right eyelid developed and she was diagnosed as having sarcoidosis on the basis of uveitis, skin lesions, and bilateral hilar lymphadenopathy (BHL) on chest X-ray. With steroid therapy, the symptom improved and BHL disappeared. In July, 2001, dryness of the mouth and dry eyes developed, and she was diagnosed as having Sjögren's syndrome (SjS). This case may be precious in discussing the pathophysiology of sarcoidosis and SjS including the association with hepatitis C virus infection.