BACKGROUND:Oxidative DNA damage is involved in the pathophysiology of essential hypertension (EH), which is a multifactorial disorder. Apurinic/apyrimidinic endonuclease 1/redox effector factor-1 (APE1/REF-1) is an essential endonuclease in the base excision repair pathway of oxidatively damaged DNA, in addition to having reducing properties that promote the binding of redox-sensitive transcription factors. Blood pressure in APE1/REF-1-knockout mice is reported to be significantly higher than in wild-type mice. The aim of this study was to investigate the relationship between EH and the human APE1/REF-1 gene through a haplotype-based case-control study using single-nucleotide polymorphisms (SNPs).METHODS:We selected five SNPs in the human APE1/REF-1 gene (rs1760944, rs3136814, rs17111967, rs3136817, and rs1130409), and performed case-control studies in 265 EH patients and 266 age-matched normotensive (NT) subjects.RESULTS:rs17111967 was found to show nonheterogeneity among Japanese subjects. There were no significant differences in the overall distribution of genotypes or alleles for each SNP between EH and NT groups. In the overall distribution of the haplotype-based case-control study constructed based on rs1760944, rs3136817, and rs1130409, the frequency of the G-T-T haplotype was significantly higher in the EH group than in the NT group (2.1% vs. 0.0%, P = 0.001). Multiple logistic regression analysis also revealed significant differences for the G-T-T haplotype, even after adjustment for confounding factors (OR = 8.600, 95% CI: 1.073-68.951, P = 0.043).CONCLUSIONS:Based on the present results, the G-T-T haplotype appears to be a genetic marker of EH, and the APE1/REF-1 gene appears to be a susceptibility gene for EH.

Objectives: The aim of this study was to investigate the relationship between cerebral infarction (CI) and the human apurinic/apyrimidinic endonuclease 1/redox effector factor-1 (APE1/REF-1) gene using single-nucleotide polymorphisms (SNPs) and a haplotype-based case-control study.Design and methods: We selected 5 SNPs in the human APE1/REF1 gene (rs1760944, rs3136814, rs17111967, rs3136817 and rs1130409), and performed case-control studies in 177 CI patients and 309 control subjects.Results: rs17111967 was found to have no heterogeneity in Japanese. The overall distribution of the haplotype-based case-control study constructed by rs1760944, rs3136814 and rs1130409 showed a significant difference. The frequency of the G-C-T haplotype was significantly higher in the CI group than in the control group (2.5% vs. 0.0%, p>0.001).Conclusions: Based on the results of the haplotype-based case-control-study, the G-C-T haplotype may be a genetic marker of CI, and the APE1/REF-1 gene may be a CI susceptibility gene. (C) 2009 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

It has been reported that oxidative stress is involved in the pathophysiology of essential hypertension (EH), which is a multifactorial disorder. Extracellular superoxide dismutase (EC-SOD) protects the human body from oxidative stress by converting the toxic superoxide anion (O2−) into less toxic hydrogen peroxide (H2O2). In EC-SOD knockout mice, blood pressure was reported to be significantly higher than that seen in wild-type mice. The aim of this study was thus to investigate the relationship between EH and the human EC-SOD gene by using single-nucleotide polymorphisms (SNPs) in a haplotype-based case-control study. We selected 6 SNPs within the human EC-SOD gene (rs13306703, rs699473, rs699474, rs17881426, rs2536512 and rs1799895), and then performed case-control studies in 243 EH patients and 251 age-matched normotensive (NT) subjects. In Japanese subjects, no heterogeneity was found for rs699474, and no significant differences were observed between the EH and NT groups for the overall distribution of the genotypes or the alleles for each of the SNPs. However, in the haplotype-based case-control study that used rs13306703 and rs2536512, significant differences were observed in the overall distribution (x 2 = 14.26, p =0.003). The frequency of the T-A haplotype was significantly higher in the EH group than in the NT group (2.4% vs 0.0 %, p <0.001). Based on the results of our haplotype-based case-control study, the T-A haplotype may be a genetic marker for EH, and thus the EC-SOD gene might be a susceptibility gene for EH.

It has been reported that oxidative stress is a factor in cerebral infarction (CI). Extracellular superoxide dismutase (EC-SOD) is important in preventing oxidative stress, and the cerebral infarct size of EC-SOD knockout mice is significantly larger than that in wild-type controls. The aim of this study was to investigate the relationship between CI and the human EC-SOD gene using single-nucleotide polymorphism (SNP) in Japanese individuals. We selected five single-nucleotide polymorphisms of the human EC-SOD gene (rs13306703, rs699473, rs17881426, rs2536512 and rs1799895) and performed a case-control study using each SNP and haplotype in 175 CI patients (103 men, 72 women) and 299 controls (144 men and 155 women). Among women, there were significant differences between the CI and control group in overall distribution of alleles for rs699473 (men: OR=1.031, 95% CI: 0.705-1.506, women: OR=1.916, 95% CI: 1.196-3.071) and rs2536512 (men: OR=0.774, 95% CI: 0.523-1.146, women: OR=2.107, 95% CI: 1.227-3.462). In a haplotype-based case control on rs13306703, rs699473 and rs1799895 in women, the frequency of the C-C-C haplotype was significantly higher in the CI group than in the control group (men; 51.5% vs 51.4% p=0.9865, women; 62.5% vs 49.7% p=0.0108). Multiple logistic regression analysis also revealed a significant difference in C-C-C haplotype in women, even after adjustment for confounding factors (OR=2.205, 95% CI: 1.069-4.552 p=0.032). The C-C-C haplotypes could be genetic markers for CI, and the EC-SOD gene may be a susceptibility gene for CI in women.

To understand the physiological role of the ykoN gene of Bacillus subtilis, the gene was expressed from the IPTG-inducible spac promoter in B. subtilis cells. When lipid composition of the cells induced for ykoN expression was examined, a new spot of phospholipid was found on the thin layer chromatogram. Induction of ykoN in Escherichia coli cells produced a similar new spot. The new spot was produced in mutant E. coli cells lacking cardiolipin or phosphatidylethanolamine, but not in the cells lacking phosphatidylglycerol. The result suggests an involvement of phosphatidylglycerol in production of the new spot. Examination of the lipid composition during the stages of B. subtilis growth revealed that the new phospholipid was produced four hours after cessation of logarithmic growth, consistent with an increase in the promoter activity of ykoN in the late stage in sporulation. YkoN has the pentapeptide lipase/esterase motif (Gly-X-Ser-X-Gly), and shows a lipolytic activity (Matsuura et al., in press). The mutant YkoN (S205A) in which the central serine residue of the motif is replaced with alanine produced the new phospholipid in the amount as small as only 1/10 of the wild type, suggesting that the lipolytic activity of YkoN is involved in the new phospholipid production.

The product YkoN of the gene of unknown function, ykoN, of Bacillus subtilis Marburg has the pentapeptide lipase/esterase motif (Gly-X-Ser-X-Gly), and thus YkoN is expected to have a lipase or esterase activity. To characterize the expected enzyme activity the plasmid having a modified ykoN that include the sequence for His(x6) tag at its C-terminus of YkoN, which has 373 amino acid residues, was constructed. His-tagged YkoN protein of 39 kDa was induced in Escherichia coli BL21 (DE3) cells harboring chaperon plasmid pGro7 and purified to near homogeneity by using gel filtration and Ni-agarose. When p-nitrophenyl-esters of different fatty acid chain length were examined, the purified YkoN hydrolyzed the esters of fatty acid with short chain length (4-6 carbon atoms) preferentially. The esters of fatty acid with longer chain (C ≥ 10) were hydrolyzed inefficiently. The activity required no divalent cations and was not affected by addition of EDTA. The optimal pH for the activity was from pH 7.4 to pH 8.6. These results indicate that YkoN is a novel esterase which hydrolyzes the esters of fatty acid with short chain length.

Uroguanylin (gene name: guanylate cyclase activator 2B, GUCA2B) is a peptide regulator of intestinal salt and water transport. It has been reported that the uroguanylin knockout mouse exhibits elevated blood pressure. Therefore, the GUCA2B gene is thought to be a susceptibility gene for essential hypertension (EH). Despite extensive studies, however, the relationship between the GUCA2B gene and EH has not yet been defined. The aim of this study was to assess the association between the human GUCA2B gene and EH. Using four single nucleotide polymorphisms (SNPs), we conducted a genetic association study in 281 EH patients and 279 age-matched normotensive (NT1) individuals. To derive more reliable data, we performed a duplicate case-control study in which we recruited another normotensive group (NT2). There was no significant difference in the overall distribution of alleles for any of the SNPs between the EH and NT1 groups, or between the EH and NT2 groups. Therefore, these four SNPs cannot be the genetic markers for EH. The occurrences of the C-A haplotype (rs883062-rs1047047) and the C-A-G haplotype (rs883062-rs1047047-rs2297566) were significantly higher in the EH group than in the NT1 group (p<0.0001) or the NT2 group (p<0.0001). These results suggest that the C-A haplotype and the C-A-G haplotype of the GUCA2B gene are the genetic markers for EH, and that GUCA2B or a neighboring gene might be a susceptibility gene for EH.

Metal electrodes for chemical sensors have been fabricated on an overhead-transparency film using the Line Patterning Method. This method comprises i) laser-printing of toner with negative pattern of the electrodes, ii) vapor-deposition of metal layers, and iii) removal of the toner and the upper metal layers. The resolution of the pattern was ca. 0.1–0.2 mm. We found that multilayered electrodes such as Au/Cr/film, Pt/Au/Cr/film, and Ag/Pt/Au/Cr/film satisfied conductivity, adhesiveness, and flexibility. Furthermore, a glucose sensor using the film electrode was fabricated.

Deep-sea yeast strains were isolated from mud samples collected in Sagami Bay (1,100-1,400 m) and the Japan Trench (4,500-6,500 m). All of the 46 yeast isolates were capable of growth at 24°C and atmospheric pressure, suggesting that these strains might originate neritic regions or land but survived in deep sea. Based on sequencing of 26S rRNA gene, 15 strains were classified into basidiomycetous yeasts including Cryptococcus liquefaciens, Kondoa aeria, Rhodosporidium diobovatum, Rhodosporidium sphaerocarpum, Rhodotorula mucilaginosa, Rhodotorula dairenensis and Rhodotorula slooffiae, and 8 strains were classified into ascomycetous yeasts including Aureobasidium pullulans, Candida zeylanoides, Kluyveromyces nonfermentans, Metschnikowia bicuspidate and Williopsis saturnus. Screening of the 46 isolates appeared to yield a high frequency of polygalacturonase (PGase) producers capable of degrading pectin. We suggest that deep-sea yeasts are new sources of PGase producers.

Ischemic stroke (IS) is thought to be a multifactorial disorder associated with genetic backgrounds and environmental factors. In the circulating plasma, tissue plasminogen activator (tPA) catalyzes the reaction from plasminogen to plasmin. If there is a functional disability of tPA, induction of thrombosis and infarction disorders can occur. The aim of this study was to perform a haplotype-based case-control study using single nucleotide polymorphisms (SNPs) in the human tPA gene, and to assess the association between the tPA gene and IS. We genotyped 182 IS individuals and 403 controls for five SNPs in the human tPA gene, rs7007329, rs732612, rs8178750, rs2020922, and rs4471024. Using these five SNPs, a haplotype-based case control study was performed. There were seven SNP combinations that exhibited significant differences in the overall distribution between the IS and control groups. Linkage disequilibrium analysis showed that the combination of rs7007329 and rs8178750 was useful in identification of the susceptibility haplotype. The frequency of the G-T haplotype at rs7007329-rs8178750 was significantly higher in the IS group (1.2%) as compared to the control group (0.0%) (p = 0.003). Diplotype analysis also showed a significant association of the diplotype with the G-T haplotype at rs7007329-rs8178750 (OR:11.4, 95%CI:1.32-97.9, p = 0.013). These results suggest that the G-T haplotype at rs7007329-rs8178750 of the tPA gene is a genetic marker for IS, and that tPA or a neighboring gene is a susceptibility gene for IS.

Deep-sea sediment samples were collected at a depth of 3,064 m in the Japan Sea. Microorganisms in the sediment sample were cultivated under several pressure conditions, and the high-pressure adapted microbes were isolated. Two of the isolates exhibited piezophilic growth profiles. This is the first report to show the presence of piezophiles in the Japan Sea.

A deep-sea yeast, Cryptococcus liquefaciens strain N6, produces two polygalacturonases, p36 and p40 (N6-PGases). These N6-PGases were highly active at 0-10 degrees C in comparison to a PGase from Aspergillus japonicus. The hydrolytic activity of these N6-PGases remained almost unchanged up to a hydrostatic pressure of 100 MPa at 24 degrees C with a very small activation volume of -1.1 ml/mol. At 10 degrees C, however, the activation volume increased to 3.3 or 5.4 ml/mol (p36 and p40, respectively), suggesting that the enzyme-substrate complexes can expand at their transition states. We speculate that such a volume expansion upon forming the enzyme-substrate complexes contributes to decreasing the activation energy for hydrolysis. This can account for the high activity of N6-PGases at low-temperature.

ABSTRACT The human phosphoglycerate kinase (PGK1) gene is located within Xq11–Xq13 and is closely linked to the androgen receptor gene within a region implicated in a number of X-chromosome-linked urologic disorders. A polymorphism of a TATC short tandem repeat (STR) is present downstream from the PGK1 3′ nuclease-sensitive site. We present the PGK1 flanking STR sequence and population genetic data for 190 Japanese males and 83 Japanese females. Ten STR alleles and 29 genotypes were identified in the population. Five alleles—*10, *11, *12, *13, and *14—were common in the Japanese with frequencies greater than 10%. No significant deviations from Hardy-Weinberg equilibrium were established. The power of discrimination was 0.993 for females and 0.819 for males; heterozygosity was 0.759 for females; and the polymorphic information content was 0.936. These data indicate that this STR locus shows a high degree of polymorphism in this Japanese population and may prove to be a useful genetic marker in forensic medicine, in determining the clonality of neoplasms, and potentially in studying predisposition to prostate cancer and other urologic diseases.

The microbial community adherent directly or indirectly to the gut wall of termites is distinct from that of the other habitats in the gut. The bacterial 16S rRNA genes were identified from the fractionated gut walls of two termite species, Hodotermopsis sjoestedti and Neotermes koshunensis, and compared with those previously identified from Reticulitermes speratus. Surprisingly, the bacterial constituents were almost entirely different among the termites at the phylotype level (the criterion of the phylotype was >97% nucleotide identity). Bacteria in the order Bacteroidales, which were commonly abundant symbionts on gut walls, were phylogenetically analyzed. They were dispersed in a number of clusters formed by phylotypes from the guts of various termites. In situ hybridization with probes specific for some phylotypes and a phylogenetic cluster detected the cells of several Bacteroidales members with a significant variety of cell morphology in the gut wall fractions, which reflects the phylogenetic diversity of this order.

Several previous studies have shown that essential hypertension (EH) is associated with fibrinolysis. Tissue plasminogen activator (t-PA) plays a key role in fibrinolysis. Thus, it is possible that the t-PA gene is a susceptibility gene of EH. However, there have been no reported studies of association between EH and the t-PA gene using single nucleotide polymorphisms (SNPs). The aim of the present haplotype-based case-control study was to investigate whether SNPs in the human t-PA gene are associated with EH. We performed a genetic association study using 3 SNPs (rs7007329, rs8178750, rs4471024). The subjects were 276 EH patients and 283 age-matched normotensive (NT) individuals. There were no significant differences in overall distribution of genotypes or alleles between EH patients and NT subjects. Also, there were no significant differences in the haplotype-based case-control study. The present results do not indicate an association between the t-PA gene and EH.

Polymerase chain reaction (PCR) amplification using formalin-fixed material is very limited. In the present study the use of 6 week formalin-fixed placenta for individual identification was examined based on DNA analyses. The objective of the examination was to prove whether the placenta was from a woman who had just given birth. DNA extraction was carried out from the maternal blood sample and from the formalin-fixed placental samples composed of three parts: maternal side, infant side and umbilical cord. One minisatellite (D1S80), 12 short tandem repeat (STR) polymorphisms and amelogenin X, Y were investigated. All the polymorphic systems were detected in the maternal blood sample. The majority of the DNA isolated from the placental tissues had molecular weights of approximately 500 bp, and only two to four STR loci were amplified using the DNA. In order to amplify more DNA polymorphic markers from the formalin-fixed tissues, whole genome amplification was performed. After amplification by degenerate oligonucleotide-primed PCR (DOP-PCR), the products contained DNA with increased molecular weight up to > 10 kbp. More DNA loci were typed using the DOP-PCR products. Furthermore, large molecular size fragments were purified from the DOP-PCR products by agarose electrophoresis, and then the D1S80 locus and 12 STR loci were successfully amplified using these fragments.

The rpoE gene encoding an RNA polymerase sigmaE subunit was isolated from a gamma-phage library of the deep-sea piezophilic and psychrophilic bacterium Shewanella violacea strain DSS12. Structual analysis showed that the gene organization of the fragment containing S. violacearpoE was the l-aspartate oxidase-coding gene, rpoE, rseA, rseB and rseC in that order, the same as in the case of Photobacterium profundum SS9 and Escherichia coli K-12. The cloned gene, 576 bp in length, was found to encode a protein consisting of 192 amino acid residues with a molecular mass of 21,806 Da. Amino acid alignment of the RpoE protein showed that the functional domains responsible for DNA recognition, DNA melting, core binding, and RseA interaction were highly conserved. We purified hexahistidine-fused RpoE protein by constructing an overexpression plasmid. Core-binding analysis revealed that the cloned RpoE protein has the ability to bind with core RNA polymerase as a sigma factor.

RNA polymerase from cells of the deep-sea bacterium Shewanella violacea DSS12 was purified using three chromatographic steps. An in vitro transcription assay indicated that the purified enzyme was sigma(70) containing RNA polymerase. The enzyme activity was inhibited in the presence of rifampicin when the sensitive domain was targeted. The rpoBC genes encoding for the beta and beta' subunits of RNA polymerase were cloned and their nucleotide sequences determined. Expression plasmids, designated pQSVB and pQSVC, to overproduce these proteins were constructed, and the proteins were purified using a Ni2+ affinity column. In vitro reconstitution using all proteins for the holoenzyme (alpha, beta, beta', sigma(70)) was carried out and the activity of the recombinant RNA polymerase was detected.

More than 80% of residual halophilic α-amylase (crude and purified) activity from strain S-1 was observed in the presence of various organic solvents. More than 78% remaining activity was detected after incubation for 120 hr in the presence of styrene, toluene, benzene or chloroform. Enzyme activity and stability with chloroform were higher than that without chloroform at the low or high temperature, and enzyme activity was higher in the presence of chloroform than one without chloroform when EDTA (5-15 mM) was added.

Strains of halophilic archaea, Haloarcula vallismortis and two Haloarcula strains OHF-1 and OHF-2, showed high tolerance to organic solvents at high media NaCl concentrations. For example, the lowest log Pow of the solvent which allowed growth (log Pow is the common logarithm of the partition coefficient of a given solvent in a mixture of n-octanol and water) for H. vallismortis was 5.1 at 20% NaCl and 4.4 at 30% NaCl. The solvent tolerance of Haloarcula argentinensis, on the other hand, was not affected by the NaCl concentration. Cells of strains OHF-1 and OHF-2 were of triangular or irregular morphology but became spherical in cultures in NaCl media overlaid with cyclohexane (log Pow=3.4), but returned to the triangular shape when the organic solvent evaporated from the medium. When cells of strains OHF-1, OHF-2, and H. argentinensis were grown in NaCl media in the presence of n-decane, they contained less phosphatidylglycerol and more phosphatidylglycerosulfate and phosphatidylglycerophosphate methyl ester than when grown without added n-decane. When the solvent was removed from the media after cultivation, the levels of these compounds returned to their initial ones.