Exploring the Minimal RNA Substrate of Flexizymes

Flexizymes are tRNA acylation ribozymes that have been successfully used to facilitate genetic code reprogramming. They are capable of charging acid substrates onto various tRNAs and tRNA analogues. However, their minimal RNA substrate has not been investigated. Here we have designed fluorescently labeled short RNAs corresponding to the four, three, and two bases (4bRNA, 3bRNA, 2bRNA) at the tRNA 3′-end and explored the minimal RNA substrate of flexizymes, dFx and eFx. 3bRNA was the observed minimal RNA substrate of the flexizymes, but the efficiency of acylation of this short RNA was two to three times lower than that of 4bRNA. The efficiency of acylation of 4bRNA was comparable with that of the microhelix, a 22-base RNA conventionally used as a tRNA analogue for analyzing acylation efficiency. We also compared the efficiencies of acylation of the microhelix and 4bRNA with various acid substrates. Thanks to the short length of 4bRNA, its acyl-4bRNA products exhibited larger mobility shifts in gel electrophoresis than those exhibited by acyl-microhelix products with every substrate tested. This indicated that 4bRNA was an ideal RNA substrate for analyzing the efficiency of acylation by flexizymes.     

Determination of atomistic deformation of tricalcium silicate paste with high-volume fly ash

We examined the effect of incorporating high-volume fly ash on the atomic arrangement and interatomic deformation behavior of calcium silicate hydrates in tricalcium silicate paste upon exposure to external forces. The interatomic structural changes and strains under compressive load were assessed using synchrotron in situ high-energy X-ray scattering-based atomic pair distribution function analysis. Three different types of strains, which were (a) macroscopic strains from gauges on the surfaces of specimen, (b) strains in a reciprocal space (Bragg peak shift), and (c) strains in real space (PDF peak shift), were compared to each other. All monitored and calculated strains for tricalcium silicate-fly ash (50 wt% fly ash) paste were compared with the counterparts of the pure tricalcium silicate paste. Pair distribution function analysis in the range of r < 10 Å indicated that the atomic arrangement of tricalcium silicate-fly ash was similar to that of synthetic calcium silicate hydrates followed by that of pure tricalcium silicate paste. Moreover, the pair distribution function refinement results revealed that the calcium silicate hydrate structure in tricalcium silicate-fly ash paste was similar to tobermorite 11 Å, unlike that in pure tricalcium silicate paste. The interatomic strain of tricalcium silicate-fly ash in the real space (r < 20 Å) was smaller than that of tricalcium silicate under compression, which suggested that the incompressibility of calcium silicate hydrates at atomistic scale was enhanced by the incorporation of fly ash into it. This was likely to be caused by the increased silicate polymerization of calcium silicate hydrates, which was attributed to the increase in the amount of silicate in their structure via the addition of fly ash.     

Study of Cuprate Superconductivity Using the Particle Number Conserving Bogoliubov-de Gennes Equations: ARPES and STS Images From Surface Plus Bulk Layers Model

Journal of Superconductivity and Novel Magnetism - We theoretically study the superconductivity in hole-doped cuprate superconductors by employing a model composed of surface and bulk CuO $$_2$$...     

Physics‐based model of lithium‐ion batteries running on a circuit simulator

The authors developed a physics‐based equivalent circuit model of a lithium‐ion battery (LIB) whose parameters are continually updated, reflecting the theoretical calculation results of the Butler‐Volmer equation, diffusion equations of the lithium‐ion and lithium, and Nernst equations of the liquid and solid phases. The developed model was applied to the charge/discharge simulations of an LIB, and the experimental and simulated results of constant current discharges and pulsed‐charge/discharge were found to be in excellent agreement. In particular, using the developed model, analyzing transient responses of the LIB derived from the transition of the electric double layer charging to the electrode reaction is possible. These results demonstrate that the electrochemical performance of an LIB can be calculated on a circuit simulator using the developed model.     

Combinatorial Measurement of CDKN1A/p21 and KIF20A Expression for Discrimination of DNA Damage-Induced Clastogenicity

In vitro mammalian cytogenetic tests detect chromosomal aberrations and are used for testing the genotoxicity of compounds. This study aimed to identify a supportive genomic biomarker could minimize the risk of misjudgments and aid appropriate decision making in genotoxicity testing. Human lymphoblastoid TK6 cells were treated with each of six DNA damage-inducing genotoxins (clastogens) or two genotoxins that do not cause DNA damage. Cells were exposed to each compound for 4 h, and gene expression was comprehensively examined using Affymetrix U133A microarrays. Toxicogenomic analysis revealed characteristic alterations in the expression of genes included in cyclin-dependent kinase inhibitor 1A (CDKN1A/p21)-centered network. The majority of genes included in this network were upregulated on treatment with DNA damage-inducing clastogens. The network, however, also included kinesin family member 20A (KIF20A) downregulated by treatment with all the DNA damage-inducing clastogens. Downregulation of KIF20A expression was successfully confirmed using additional DNA damage-inducing clastogens. Our analysis also demonstrated that nucleic acid constituents falsely downregulated the expression of KIF20A, possibly via p16 activation, independently of the CDKN1A signaling pathway. Our results indicate the potential of KIF20A as a supportive biomarker for clastogenicity judgment and possible mechanisms involved in KIF20A downregulation in DNA damage and non-DNA damage signaling networks.