Thermal stability of crown-motif [Au9(PPh3)8]3+ and [MAu8(PPh3)8]2+ (M = Pd, Pt) clusters: Effects of gas composition, single-atom doping, and counter anions.

The thermal behaviors of ligand-protected metal clusters, [Au9(PPh3)8]3+ and [MAu8(PPh3)8]2+ (M = Pd, Pt) with a crown-motif structure, were investigated to determine the effects of the gas composition, single-atom doping, and counter anions on the thermal stability of these clusters. We successfully synthesized crown-motif [PdAu8(PPh3)8][HPMo12O40] (PdAu8-PMo12) and [PtAu8(PPh3)8][HPMo12O40] (PtAu8-PMo12) salts with a cesium-chloride-type structure, which is the same as the [Au9(PPh3)8][PMo12O40] (Au9-PMo12) structure. Thermogravimetry-differential thermal analysis/mass spectrometry analysis revealed that the crown-motif structure of Au9-PMo12 was decomposed at ∼475 K without weight loss to form Au nanoparticles. After structural decomposition, the ligands were desorbed from the sample. The ligand desorption temperature of Au9-PMo12 increased under 20% O2 conditions because of the formation of Au nanoparticles and stronger interaction of the formed O=PPh3 than PPh3. The Pd and Pt single-atom doping improved the thermal stability of the clusters. This improvement was due to the formation of a large bonding index of M-Au and a change in Au-PPh3 bonding energy by heteroatom doping. Moreover, we found that the ligand desorption temperatures were also affected by the type of counter anions, whose charge and size influence the localized Coulomb interaction and cluster packing between the cationic ligand-protected metal clusters and counter anions.

Counteranion-induced structural isomerization of phosphine-protected PdAu8 and PtAu8 clusters.

Controlling the geometric structures of metal clusters through structural isomerization allows for tuning of their electronic state. In this study, we successfully synthesized butterfly-motif [PdAu8(PPh3)8]2+ (PdAu8-B, B means butterfly-motif) and [PtAu8(PPh3)8]2+ (PtAu8-B) by the structural isomerization from crown-motif [PdAu8(PPh3)8]2+ (PdAu8-C, C means crown-motif) and [PtAu8(PPh3)8]2+ (PtAu8-C), induced by association with anionic polyoxometalate, [Mo6O19]2- (Mo6) respectively, whereas their structural isomerization was suppressed by the use of [NO3]- and [PMo12O40]3- as counter anions. DR-UV-vis-NIR and XAFS analyses and density functional theory calculations revealed that the synthesized [PdAu8(PPh3)8][Mo6O19] (PdAu8-Mo6) and [PtAu8(PPh3)8][Mo6O19] (PtAu8-Mo6) had PdAu8-B and PtAu8-B respectively because PdAu8-Mo6 and PtAu8-Mo6 had bands in optical absorption at the longer wavelength region and different structural parameters characteristic of the butterfly-motif structure obtained by XAFS analysis. Single-crystal and powder X-ray diffraction analyses revealed that PdAu8-B and PtAu8-B were surrounded by six Mo6 with rock salt-type packing, which stabilizes the semi-stable butterfly-motif structure to overcome high activation energy for structural isomerization.

Non-destructive mid-IR spectroscopy with quantum cascade laser can detect ethylene gas dynamics of apple cultivar 'Fuji' in real time.

Many plants, including fruits and vegetables, release biogenic gases containing various volatile organic compounds such as ethylene (C2H4), which is a gaseous phytohormone. Non-destructive and in-situ gas sampling technology to detect trace C2H4 released from plants in real time would be attractive for visualising the ageing, ripening, and defence reactions of plants. In this study, we developed a C2H4 detection system with a detection limit of 0.8 ppb (3σ) using laser absorption spectroscopy. The C2H4 detection system consists of a mid-infrared quantum cascade laser oscillated at 10.5 µm, a multi-pass gas cell, a mid-IR photodetector, and a gas sampling system. Using non-destructive and in-situ gas sampling, while maintaining the internal pressure of the multi-pass gas cell at low pressure, the change in trace C2H4 concentration released from apples (Malus domestica Borkh.) can be observed in real time. We succeeded in observing C2H4 concentration changes with a time resolution of 1 s, while changing the atmospheric gas and surface temperature of apples from the 'Fuji' cultivar. This technique allows the visualisation of detailed C2H4 dynamics in plant environmental response, which may be promising for further progress in plant physiology, agriculture, and food science.

Ceftriaxone-associated Pseudolithiasis in Elderly People: Frequency and Risk Factors.

Objective Ceftriaxone (CTRX) is a widely used antibiotic because of its long plasma half-life and good tissue transmission. Many of the reported studies on CTRX-associated pseudolithiasis were performed in children. Although some studies have been published in adults, there are no studies limited to elderly people. The present study investigated CTRX-associated pseudolithiasis and explored its risk factors in the elderly. Methods We retrospectively reviewed 133 elderly patients (≥65 years old) treated with CTRX. Pseudolithiasis was defined as stones or sludge newly appearing in the gallbladder, as detected by computed tomography after the administration of CTRX. We evaluated the risk factors for pseudolithiasis using multivariate regression and inverse probability of treatment weighting analyses. Results Among the 133 patients, 24 (18%) developed CTRX-associated pseudolithiasis. In a multivariate analysis, the CTRX dose [odds ratio (OR) 4.54, 95% confidence interval (CI) 1.36-15.07, p=0.012] and CTRX treatment duration (OR 2.80, 95% CI 1.06-8.04, p=0.043) were significantly associated with pseudolithiasis formation. The cut-off value of the total CTRX dose associated with pseudolithiasis formation was 19 g. A propensity analysis determined that the frequency of pseudolithiasis was increased in patients treated with >19 g total CTRX compared with those who received ≤19 g in total (OR 4.06, 95% CI 1.45-11.32, p=0.008). Conclusion The incidence rate of CTRX-induced pseudolithiasis is high in elderly people, and the CTRX dose and CTRX treatment duration are significant risk factors for pseudolithiasis. A total dose of >19 g increases the likelihood of pseudolithiasis formation in elderly people treated with CTRX.

Epigenetics: application of virtual image restriction landmark genomic scanning (Vi-RLGS).

Restriction landmark genomic scanning (RLGS) is a powerful method for the systematic detection of genetic mutations in DNA length and epigenetic alteration due to DNA methylation. However, the identification of polymorphic spots is difficult because the resulting RLGS spots contain very little target DNA and many non-labeled DNA fragments. To overcome this, we developed a virtual image restriction landmark genomic scanning (Vi-RLGS) system to compare actual RLGS patterns with computer-simulated RLGS patterns (virtual RLGS patterns). Here, we demonstrate in detail the contents of the simulation program (rlgssim), based on the linear relationship between the reciprocal of mobility plotted against DNA fragment length and Vi-RLGS profiling of Arabidopsis thaliana.

Molecular characterization of microbial mutations induced by ion beam irradiation.

A positive selection system for gene disruption using a sucrose-sensitive transgenic rhizobium was established and used for the molecular characterization of mutations induced by ion beam irradiations. Single nucleotide substitutions, insertions, and deletions were found to occur in the sucrose sensitivity gene, sacB, when the reporter line was irradiated with highly accelerated carbon and iron ion beams. In all of the insertion lines, fragments of essentially the same sequence and of approximately 1188bp in size were identified in the sacB regions. In the deletion lines, iron ions showed a tendency to induce larger deletions than carbon ions, suggesting that higher LET beams cause larger deletions. We found also that ion beams, particularly "heavier" ion beams, can produce single gene disruptions and may present an effective alternative to transgenic approaches.

DNA adenine methylation changes dramatically during establishment of symbiosis.

The DNA adenine methylation status on specific 5'-GANTC-3' sites and its change during the establishment of plant-microbe interactions was demonstrated in several species of alpha-proteobacteria. Restriction landmark genome scanning (RLGS), which is a high-resolution two dimensional DNA electrophoresis method, was used to monitor the genomewide change in methylation. In the case of Mesorhizobium loti MAFF303099, real RLGS images obtained with the restriction enzyme MboI, which digests at GATC sites, almost perfectly matched the virtual RLGS images generated based on genome sequences. However, only a few spots were observed when the restriction enzyme HinfI was used, suggesting that most GANTC (HinfI) sites were tightly methylated and specific sites were unmethylated. DNA gel blot analysis with the cloned specifically unmethylated regions (SUMs) showed that some SUMs were methylated differentially in bacteroids compared to free-living bacteria. SUMs have also been identified in other symbiotic and parasitic bacteria. These results suggest that DNA adenine methylation may contribute to the establishment and/or maintenance of symbiotic and parasitic relationships.

An effective method for detection and analysis of DNA damage induced by heavy-ion beams.

We have developed an efficient system to detect and analyze DNA mutations induced by heavy-ion beams in Arabiopsis thaliana. In this system, a stable transgenic Arabidopsis line that constitutively expresses a yellow fluorescent protein (YFP) by a single-copy gene at a genomic locus was constructed and irradiated with heavy-ion beams. The YFP gene is a target of mutagenesis, and its loss of function or expression can easily be detected by the disappearance of YFP signals in planta under microscopy. With this system, a (12)C(6+)-induced mutant with single deletion and multiple base changes was isolated.

Global methylation screening in the Arabidopsis thaliana and Mus musculus genome: applications of virtual image restriction landmark genomic scanning (Vi-RLGS).

Understanding the role of 'epigenetic' changes such as DNA methylation and chromatin remodeling has now become critical in understanding many biological processes. In order to delineate the global methylation pattern in a given genomic DNA, computer software has been developed to create a virtual image of restriction landmark genomic scanning (Vi-RLGS). When using a methylation- sensitive enzyme such as NotI as the restriction landmark, the comparison between real and in silico RLGS profiles of the genome provides a methylation map of genomic NotI sites. A methylation map of the Arabidopsis genome was created that could be confirmed by a methylation-sensitive PCR assay. The method has also been applied to the mouse genome. Although a complete methylation map has not been completed, a region of methylation difference between two tissues has been tested and confirmed by bisulfite sequencing. Vi-RLGS in conjunction with real RLGS will make it possible to develop a more complete map of genomic sites that are methylated or demethylated as a consequence of normal or abnormal development.

Chlorophyll-deficient mutants of rice demonstrated the deletion of a DNA fragment by heavy-ion irradiation.

Heavy-ion irradiation is a new method of mutation breeding to produce new cultivars. We established the application of this method in rice plants to obtain mutants. Rice seeds were irradiated by C or Ne ions (135MeV/u) with a LET (linear energy transfer) of 22.7 or 64.2 keV/microm, respectively. Chlorophyll-deficient mutants (CDM) segregated in M2 progeny were albino, pale-green, yellow or striped-leave phenotypes. The highest rate of CDM with C-ion irradiation, 7.31%, was obtained at 40 Gy among the doses examined. Ne-ion irradiation gave the highest rate, 11.6%, at 20 Gy. We used the RLGS (Restriction Landmark Genomic Scanning) method to analyze DNA deletion in an albino mutant genome. Not I-landmark RLGS profiles detected about 2000 spots in rice. We found that one of the polymorphic spots was strongly linked to the albino phenotypic mutant derived from deleting of a DNA fragment, and demonstrated the high ability to detect of polymorphic regions by the RLGS method.

In silico restriction landmark genome scanning analysis of Xanthomonas oryzae pathovar oryzae MAFF 311018.

We have developed a restriction landmark genome scanning (RLGS) system in silico, involving two-dimensional electrophoretic analysis of DNA by computer simulation that is based on the availability of whole-genome sequences for specific organisms. We applied the technique to the analysis of the Xanthomonas oryzae pathovar oryzae (Xoo) MAFF 311018, which causes bacterial blight in rice. The coverage that was found to be achievable using RLGS in silico, as a percentage of the genomic regions that could be detected, ranged from 44.5% to 72.7% per image. However, this reached a value of 96.7% using four images that were obtained with different combinations of landmark restriction enzymes. Interestingly, the signal intensity of some of the specific spots obtained was significantly lower than that of other surrounding spots when MboI, which cleaves unmethylated 5'-GATC-3' sites, was used. DNA gel blot analysis with both DNA adenine methylase (Dam)-sensitive and -insensitive isoschizomers (MboI and Sau3AI) revealed that Dam-mediated DNA adenine methylation had indeed occurred at these particular sites. These results suggest that a significant portion of the 5'-GATC-3' sites within the Xoo genome is stably methylated by Dam.

RAPD markers encoding retrotransposable elements are linked to the male sex in Cannabis sativa L.

Male-associated DNA sequences were analyzed in Cannabis sativa L. (hemp), a dioecious plant with heteromorphic sex chromosomes. DNA was isolated from male and female plants and subjected to random amplified polymorphic DNA analysis. Of 120 primers, 17 yielded 400 to 1500-bp fragments detectable in male, but not female, plants. These fragments were cloned and used as probes in gel-blot analysis of genomic DNA. When male and female DNA was hybridized with 2 of these male-specific fragments, MADC(male-associated DNA sequences in C. sativa)3 and MADC4, particularly intense bands specific to male plants were detected in addition to bands common to both sexes. The MADC3 and MADC4 sequences were shown to encode gag/pol polyproteins of copia-like retrotransposons. Fluorescence in situ hybridization with MADC3 and MADC4 as probes revealed a number of intense signals on the Y chromosome as well as dispersed signals on all chromosomes. The gel-blot analysis and fluorescence in situ hybridization results presented here support the hypothesis that accumulation of retrotransposable elements on the Y chromosome might be 1 cause of heteromorphism of sex chromosomes.

Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression.

Early studies proposed that DNA methylation could have a role in regulating gene expression during development [Riggs, A.D. (1975) Cytogenet. Cell Genet. 14, 9-25]. However, some studies of DNA methylation in known tissue-specific genes during development do not support a major role for DNA methylation. In the results presented here, tissue-specific differentially methylated regions (TDMs) were first identified, and then expression of genes associated with these regions correlated with methylation status. Restriction landmark genomic scanning (RLGS) was used in conjunction with virtual RLGS to identify 150 TDMs [Matsuyama, T., Kimura, M.T., Koike, K., Abe, T., Nakao, T., Asami, T., Ebisuzaki, T., Held, W.A., Yoshida, S. & Nagase, H. (2003) Nucleic Acids Res. 31, 4490-4496]. Analysis of 14 TDMs by methylation-specific PCR and by bisulfite genomic sequencing confirms that the regions identified by RLGS are differentially methylated in a tissue-specific manner. The results indicate that 5% or more of the CpG islands are TDMs, disputing the general notion that all CpG islands are unmethylated. Some of the TDMs are within 5' promoter CpG islands of genes, which exhibit a tissue-specific expression pattern that is consistent with methylation status and a role in tissue differentiation.

Preference of DNA methyltransferases for CpG islands in mouse embryonic stem cells.

Many CpG islands have tissue-dependent and differentially methylated regions (T-DMRs) in normal cells and tissues. To elucidate how DNA methyltransferases (Dnmts) participate in methylation of the genomic components, we investigated the genome-wide DNA methylation pattern of the T-DMRs with Dnmt1-, Dnmt3a-, and/or Dnmt3b-deficient ES cells by restriction landmark genomic scanning (RLGS). Approximately 1300 spots were detected in wild-type ES cells. In Dnmt1(-/-) ES cells, additional 236 spots emerged, indicating that the corresponding loci are methylated by Dnmt1 in wild-type ES cells. Intriguingly, in Dnmt3a(-/-)Dnmt3b(-/-) ES cells, the same 236 spots also emerged, and no additional spots appeared differentially. Therefore, Dnmt1 and Dnmt3a/3b share targets in CpG islands. Cloning and virtual image RLGS revealed that 81% of the RLGS spots were associated with genes, and 62% of the loci were in CpG islands. By contrast to the previous reports that demethylation at repeated sequences was severe in Dnmt1(-/-) cells compared with Dnmt3a(-/-)Dnmt3b(-/-) cells, a complete loss of methylation was observed at RLGS loci in Dnmt3a(-/-)Dnmt3b(-/-) cells, whereas methylation levels only decreased to 16% to 48% in the Dnmt1(-/-) cells. We concluded that there are CpG islands with T-DMR as targets shared by Dnmt1 and Dnmt3a/3b and that each Dnmt has target preferences depending on the genomic components.