Rapid quantification of DNA methylation through dNMP analysis following bisulfite-PCR

We report a novel method for rapid quantification of the degree of DNA methylation of a specific gene. Our method combined bisulfite-mediated PCR and quantification of deoxyribonucleoside monophosphate (dNMP) contents in the PCR product through capillary electrophoresis. A specific bisulfite-PCR product was enzymatically hydrolyzed to dNMP monomers which were quantitatively analyzed through subsequent capillary electrophoresis. PCR following bisulfite treatment converts unmethylated cytosines to thymines while leaving methyl-cytosines unchanged. Then the ratio of cytosine to thymine determined by capillary electrophoresis represents the ratio of methyl-cytosine to cytosine in genomic locus of interest. Pure oligonucleotides with known sequences were processed in parallel as standards for normalization of dNMP peaks in capillary electrophoresis. Sources of quantification uncertainty such as carryovers of dNTPs or primers and incomplete hydrolysis were examined and ruled out. When the method was applied to samples with known methylation levels (by bisulfite-mediated sequencing) as a validation, deviations were within ±5%. After bisulfite-PCR, the analytical procedure can be completed within 1.5 h

Coordination tuning of cobalt phosphates towards efficient water oxidation catalyst

The development of efficient and stable water oxidation catalysts is necessary for the realization of practically viable water-splitting systems. Although extensive studies have focused on the metal-oxide catalysts, the effect of metal coordination on the catalytic ability remains still elusive. Here we select four cobalt-based phosphate catalysts with various cobalt-and phosphate-group coordination as a platform to better understand the catalytic activity of cobalt-based materials. Although they exhibit various catalytic activities and stabilities during water oxidation, Na2CoP2O7 with distorted cobalt tetrahedral geometry shows high activity comparable to that of amorphous cobalt phosphate under neutral conditions, along with high structural stability. First-principles calculations suggest that the surface reorganization by the pyrophosphate ligand induces a highly distorted tetrahedral geometry, where water molecules can favourably bind, resulting in a low overpotential (similar to 0.42 eV). Our findings emphasize the importance of local cobalt coordination in the catalysis and suggest the possible effect of polyanions on the water oxidation chemistry.

Unexpected discovery of low-cost maricite NaFePO_4 as a high-performance electrode for Na-ion batteries

Battery chemistry based on earth-abundant elements has great potential for the development of cost-effective, large-scale energy storage systems. Herein, we report, for the first time, that maricite NaFePO_4 can function as an excellent cathode material for Na ion batteries, an unexpected result since it has been regarded as an electrochemically inactive electrode for rechargeable batteries. Our investigation of the Na re-(de)intercalation mechanism reveals that all Na ions can be deintercalated from the nano-sized maricite NaFePO_4 with simultaneous transformation into amorphous FePO_4. Our quantum mechanics calculations show that the underlying reason for the remarkable electrochemical activity of NaFePO_4 is the significantly enhanced Na mobility in the transformed phase, which is ~ one fourth of the hopping activation barrier. Maricite NaFePO_4, fully sodiated amorphous FePO_4, delivered a capacity of 142 mA h g^(−1) (92% of the theoretical value) at the first cycle, and showed outstanding cyclability with a negligible capacity fade after 200 cycles (95% retention of the initial cycle)

Optical dispersion control in surfactant-free DNA thin films by vitamin B2 doping

A new route to systematically control the optical dispersion properties of surfactant-free deoxyribonucleic acid (DNA) thin solid films was developed by doping them with vitamin B2, also known as riboflavin. Surfactant-free DNA solid films of high optical quality were successfully deposited on various types of substrates by spin coating of aqueous solutions without additional chemical processes, with thicknesses ranging from 18 to 100 nm. Optical properties of the DNA films were investigated by measuring UV-visible-NIR transmission, and their refractive indices were measured using variable-angle spectroscopic ellipsometry. By doping DNA solid films with riboflavin, the refractive index was consistently increased with an index difference Δn ≥ 0.015 in the spectral range from 500 to 900 nm, which is sufficiently large to make an all-DNA optical waveguide. Detailed correlation between the optical dispersion and riboflavin concentration was experimentally investigated and thermo-optic coefficients of the DNA-riboflavin thin solid films were also experimentally measured in the temperature range from 20 to 85 °C, opening the potential to new bio-thermal sensing applications

The anti-aging gene KLOTHO is a novel target for epigenetic silencing in human cervical carcinoma

<p>Abstract</p> <p>Background</p> <p><it>Klotho </it>was originally characterized as an anti-aging gene that predisposed Klotho-deficient mice to a premature aging-like syndrome. Recently, KLOTHO was reported to function as a secreted Wnt antagonist and as a tumor suppressor. Epigenetic gene silencing of secreted Wnt antagonists is considered a common event in a wide range of human malignancies. Abnormal activation of the canonical Wnt pathway due to epigenetic deregulation of Wnt antagonists is thought to play a crucial role in cervical tumorigenesis. In this study, we examined epigenetic silencing of <it>KLOTHO </it>in human cervical carcinoma.</p> <p>Results</p> <p>Loss of <it>KLOTHO </it>mRNA was observed in several cervical cancer cell lines and in invasive carcinoma samples, but not during the early, preinvasive phase of primary cervical tumorigenesis. <it>KLOTHO </it>mRNA was restored after treatment with either the DNA demethylating agent 2'-deoxy-5-azacytidine or histone deacetylase inhibitor trichostatin A. Methylation-specific PCR and bisulfite genomic sequencing analysis of the promoter region of <it>KLOTHO </it>revealed CpG hypermethylation in non-<it>KLOTHO</it>-expressing cervical cancer cell lines and in 41% (9/22) of invasive carcinoma cases. Histone deacetylation was also found to be the major epigenetic silencing mechanism for <it>KLOTHO </it>in the SiHa cell line. Ectopic expression of the secreted form of KLOTHO restored anti-Wnt signaling and anti-clonogenic activity in the CaSki cell line including decreased active β-catenin levels, suppression of T-cell factor/β-catenin target genes, such as <it>c-MYC </it>and <it>CCND1</it>, and inhibition of colony growth.</p> <p>Conclusions</p> <p>Epigenetic silencing of <it>KLOTHO </it>may occur during the late phase of cervical tumorigenesis, and consequent functional loss of KLOTHO as the secreted Wnt antagonist may contribute to aberrant activation of the canonical Wnt pathway in cervical carcinoma.</p

Design and synthesis of multigrain nanocrystals via geometric misfit strain.

The impact of topological defects associated with grain boundaries (GB defects) on the electrical, optical, magnetic, mechanical and chemical properties of nanocrystalline materials1,2 is well known. However, elucidating this influence experimentally is difficult because grains typically exhibit a large range of sizes, shapes and random relative orientations3-5. Here we demonstrate that precise control of the heteroepitaxy of colloidal polyhedral nanocrystals enables ordered grain growth and can thereby produce material samples with uniform GB defects. We illustrate our approach with a multigrain nanocrystal comprising a Co3O4 nanocube core that carries a Mn3O4 shell on each facet. The individual shells are symmetry-related interconnected grains6, and the large geometric misfit between adjacent tetragonal Mn3O4 grains results in tilt boundaries at the sharp edges of the Co3O4 nanocube core that join via disclinations. We identify four design principles that govern the production of these highly ordered multigrain nanostructures. First, the shape of the substrate nanocrystal must guide the crystallographic orientation of the overgrowth phase7. Second, the size of the substrate must be smaller than the characteristic distance between the dislocations. Third, the incompatible symmetry between the overgrowth phase and the substrate increases the geometric misfit strain between the grains. Fourth, for GB formation under near-equilibrium conditions, the surface energy of the shell needs to be balanced by the increasing elastic energy through ligand passivation8-10. With these principles, we can produce a range of multigrain nanocrystals containing distinct GB defects

Quantification of Trace-Level DNA by Real-Time Whole Genome Amplification

Quantification of trace amounts of DNA is a challenge in analytical applications where the concentration of a target DNA is very low or only limited amounts of samples are available for analysis. PCR-based methods including real-time PCR are highly sensitive and widely used for quantification of low-level DNA samples. However, ordinary PCR methods require at least one copy of a specific gene sequence for amplification and may not work for a sub-genomic amount of DNA. We suggest a real-time whole genome amplification method adopting the degenerate oligonucleotide primed PCR (DOP-PCR) for quantification of sub-genomic amounts of DNA. This approach enabled quantification of sub-picogram amounts of DNA independently of their sequences. When the method was applied to the human placental DNA of which amount was accurately determined by inductively coupled plasma-optical emission spectroscopy (ICP-OES), an accurate and stable quantification capability for DNA samples ranging from 80 fg to 8 ng was obtained. In blind tests of laboratory-prepared DNA samples, measurement accuracies of 7.4%, −2.1%, and −13.9% with analytical precisions around 15% were achieved for 400-pg, 4-pg, and 400-fg DNA samples, respectively. A similar quantification capability was also observed for other DNA species from calf, E. coli, and lambda phage. Therefore, when provided with an appropriate standard DNA, the suggested real-time DOP-PCR method can be used as a universal method for quantification of trace amounts of DNA

Conditions for Reversible Na Intercalation in Graphite: Theoretical Studies on the Interplay Among Guest Ions, Solvent, and Graphite Host

Graphite is the most widely used anode material for Li-ion batteries and is also considered a promising anode for K-ion batteries. However, Na+, a similar alkali ion to Li+ or K+, is incapable of being intercalated into graphite and thus, graphite is not considered a potential electrode for Na-ion batteries. This atypical behavior of Na has drawn considerable attention; however, a clear explanation of its origin has not yet been provided. Herein, through a systematic investigation of alkali metal graphite intercalation compounds (AM-GICs, AM = Li, Na, K, Rb, Cs) in various solvent environments, it is demonstrated that the unfavorable local Na-graphene interaction primarily leads to the instability of Na-GIC formation but can be effectively modulated by screening Na ions with solvent molecules. Moreover, it is shown that the reversible Na intercalation into graphite is possible only for specific conditions of electrolytes with respect to the Na-solvent solvation energy and the lowest unoccupied molecular orbital level of the complexes. It is believed that these conditions are applicable to other electrochemical systems involving guest ions and an intercalation host and hint at a general strategy to tailor the electrochemical intercalation between pure guest ion intercalation and cointercalation.