Structural stability in Aurivillius phases based on ab initio thermodynamics

The Aurivillius oxide family possessess various attractive physical properties and have been commercially applicable in many areas. The regular large-period phases of this family are believed to offer better flexibilities of performance optimization than the commercial ones. However, the experimental synthesis of them is still challenging and the physical mechanisms of their structural stability are not yet clear. We propose a quasi-binary solid solution approach to study the structural stability of Aurivillius phases based on ab initio calculations. Three typical homologous series, CaBi₂Na_m-2Nb_mO_3m+3 and M_m-3Bi₄Ti_mO_3m+3 (M=Ca, Sr) with different in-plane lattice mismatches and chemical compositions, are studied. Our results prove that all the three systems are thermodynamically stable up to m=7 phases. By decomposing the formation process into two separate steps and analyzing the contributions to Gibbs formation energy from different factors, the configurational entropy as well as chemical bond optimization is suggested to play a crucial role in stabilizing the final phases, together with the elastic effect that was solely considered as the dominant factor before.     

8-Hydroxyguanine: From its discovery in 1983 to the present status

8-Hydroxyguanine (8-OH-G) was discovered in 1983 in our laboratory at the National Cancer Center Research Institute, Tokyo. Since it could be formed in DNA not only in vitro but also in vivo by oxygen radical forming agents, we immediately hypothesized the importance of this discovery in connection with its biological consequence. Further intensive efforts by us from 1983 to 1990 confirmed that 8-OH-G is a highly significant oxidated DNA lesion involved in mutation and/or carcinogenesis in mammals, including humans. With the subsequent entry of many investigators to this research field the number of publications on 8-OH-G increased exponentially, reaching more than several thousands by the end of 2005. In this article, a summary is given of the important works carried out in the early days, and further notable contributions by many investigators are reviewed, focusing on 8-OH-G in the mammalian system. A special emphasis is given to research on knockout mice that are deficient in genes involved in the repair systems of the 8-OH-G lesion. Lastly, our own recent work is summarized involving a one-year carcinogenesis study of Ogg1 (the gene for 8-OH-G specific glycosylase/AP lyase^*1) knockout mice that have been exposed to oxidative stress.     

Functional Interdependence in Coupled Dissipative Structures: Physical Foundations of Biological Coordination

Coordination within and between organisms is one of the most complex abilities of living systems, requiring the concerted regulation of many physiological constituents, and this complexity can be particularly difficult to explain by appealing to physics. A valuable framework for understanding biological coordination is the coordinative structure, a self-organized assembly of physiological elements that collectively performs a specific function. Coordinative structures are characterized by three properties: (1) multiple coupled components, (2) soft-assembly, and (3) functional organization. Coordinative structures have been hypothesized to be specific instantiations of dissipative structures, non-equilibrium, self-organized, physical systems exhibiting complex pattern formation in structure and behaviors. We pursued this hypothesis by testing for these three properties of coordinative structures in an electrically-driven dissipative structure. Our system demonstrates dynamic reorganization in response to functional perturbation, a behavior of coordinative structures called reciprocal compensation. Reciprocal compensation is corroborated by a dynamical systems model of the underlying physics. This coordinated activity of the system appears to derive from the system’s intrinsic end-directed behavior to maximize the rate of entropy production. The paper includes three primary components: (1) empirical data on emergent coordinated phenomena in a physical system, (2) computational simulations of this physical system, and (3) theoretical evaluation of the empirical and simulated results in the context of physics and the life sciences. This study reveals similarities between an electrically-driven dissipative structure that exhibits end-directed behavior and the goal-oriented behaviors of more complex living systems.     

Recent advances in rice genome and chromosome structure research by fluorescence in situ hybridization (FISH)

Fluorescence in situ hybridization (FISH) is an effective method for the physical mapping of genes and repetitive DNA sequences on chromosomes. Physical mapping of unique nucleotide sequences on specific rice chromosome regions was performed using a combination of chromosome identification and highly sensitive FISH. Increases in the detection sensitivity of smaller DNA sequences and improvements in spatial resolution have ushered in a new phase in FISH technology. Thus, it is now possible to perform in situ hybridization on somatic chromosomes, pachytene chromosomes, and even on extended DNA fibers (EDFs). Pachytene-FISH allows the integration of genetic linkage maps and quantitative chromosome maps. Visualization methods using FISH can reveal the spatial organization of the centromere, heterochromatin/euchromatin, and the terminal structures of rice chromosomes. Furthermore, EDF-FISH and the DNA combing technique can resolve a spatial distance of 1 kb between adjacent DNA sequences, and the detection of even a 300-bp target is now feasible. The copy numbers of various repetitive sequences and the sizes of various DNA molecules were quantitatively measured using the molecular combing technique. This review describes the significance of these advances in molecular cytology in rice and discusses future applications in plant studies using visualization techniques.     

Detection of polymorphism in the methlyenetetrahydrofolate reductase gene by Raman spectroscopy

A novel approach using micro‐Raman spectroscopy for the detection of alteration of global DNA methylation levels in human individuals with polymorphism in the methlyenetetrahydrofolate reductase (MTHFR) gene was tested. Comparison of measured Raman spectra from samples with wild type genotype to those with polymorphism (homozygous and heterozygous ) in the MTHFR gene revealed that the intensity of the ~ 2945 cm^–1 peak, representing C–H stretches in the DNA constituents and in the methyl group is sample dependent. The intensity ratios between the area of these peaks in the different samples and the peaks at 1667 cm^–1 were used to assess the extent of methylation, allowing classification of the DNA samples for the common MTHFR polymorphism, MTHFR 677 C > T. These results suggest that improvement of the identification capabilities of Raman spectroscopy for DNA methylation can contribute to disease diagnosis and to a better understanding of the physical and biomolecular processes related to epigenetic regulation of the genome. Copyright © 2012 John Wiley & Sons, Ltd.     

An investigation of a genomewide supported psychosis variant in ZNF804A and white matter integrity in the human brain

ZNF804A, a genomewide supported susceptibility gene for schizophrenia and bipolar disorder, has been associated with task-independent functional connectivity between the left and right dorsolateral prefrontal cortices. Several lines of evidence have converged on the hypothesis that this effect may be mediated by structural connectivity. We tested this hypothesis using diffusion tensor magnetic resonance imaging in three samples: one German sample of 50 healthy individuals, one Scottish sample of 83 healthy individuals and one Scottish sample of 84 unaffected relatives of bipolar patients. Voxel-based analysis and tract-based spatial statistics did not detect any fractional anisotropy (FA) differences between minor allele carriers and individuals homozygous for the major allele at rs1344706. Similarly, region-of-interest analyses and quantitative tractography of the genu of the corpus callosum revealed no significant FA differences between the genotype groups. Examination of effect sizes and confidence intervals indicated that this negative finding is very unlikely to be due to a lack of statistical power. In summary, despite using various analysis techniques in three different samples, our results were strikingly and consistently negative. These data therefore suggest that it is unlikely that the effects of genetic variation at rs1344706 on functional connectivity are mediated by structural integrity differences in large, long-range white matter fiber connections.     

Separation of PCR-ready DNA from dairy products using magnetic hydrophilic microspheres and poly(ethylene glycol)-NaCl water solutions

Carboxyl group-containing magnetic nonporous poly(2-hydroxyethyl methacrylate-co-glycidyl methacrylate) (P(HEMA-co-GMA)) and magnetic glass microspheres were used for the isolation of bacterial DNA. P(HEMA-co-GMA) microspheres were prepared by the dispersion polymerization in toluene/2-methylpropan-1-ol mixture in the presence of magnetite nanoparticles obtained by coprecipitation of Fe(II) and Fe(III) salts with ammonium hydroxide. Carboxyl groups were then introduced by oxidation of the microspheres with potassium permanganate. The most extensive DNA recovery was achieved at PEG 6000 concentrations of 12% or 16% and 2 M NaCl. The method proposed was used for bacterial DNA isolation from different dairy products containing Bifidobacterium and Lactobacillus cells. The presence of target DNA and the quality of isolated DNA were checked by polymerase chain reaction (PCR) amplification with specific primers.