A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs

The programmability of RNA–RNA interactions through intermolecular base-pairing has been successfully exploited to design a variety of RNA devices that artificially regulate gene expression. An in silico design for interacting structured RNA sequences that satisfies multiple design criteria becomes a complex multi-objective problem. Although multi-objective optimization is a powerful technique that explores a vast solution space without empirical weights between design objectives, to date, no web service for multi-objective design of RNA switches that utilizes RNA–RNA interaction has been proposed. We developed a web server, which is based on a multi-objective design algorithm called MODENA, to design two interacting RNAs that form a complex in silico. By predicting the secondary structures with RactIP during the design process, we can design RNAs that form a joint secondary structure with an external pseudoknot. The energy barrier upon the complex formation is modeled by an interaction seed that is optimized in the design algorithm. We benchmarked the RNA switch design approaches (MODENA+RactIP and MODENA+RNAcofold) for the target structures based on natural RNA-RNA interactions. As a result, MODENA+RactIP showed high design performance for the benchmark datasets.     

Molecular Mechanisms and Tumor Biological Aspects of 5-Fluorouracil Resistance in HCT116 Human Colorectal Cancer Cells

5-Fluorouracil (5-FU) is a cornerstone drug used in the treatment of colorectal cancer (CRC). However, the development of resistance to 5-FU and its analogs remain an unsolved problem in CRC treatment. In this study, we investigated the molecular mechanisms and tumor biological aspects of 5-FU resistance in CRC HCT116 cells. We established an acquired 5-FU-resistant cell line, HCT116R^F10. HCT116R^F10 cells were cross-resistant to the 5-FU analog, fluorodeoxyuridine. In contrast, HCT116R^F10 cells were collaterally sensitive to SN-38 and CDDP compared with the parental HCT16 cells. Whole-exome sequencing revealed that a cluster of genes associated with the 5-FU metabolic pathway were not significantly mutated in HCT116 or HCT116R^F10 cells. Interestingly, HCT116R^F10 cells were regulated by the function of thymidylate synthase (TS), a 5-FU active metabolite 5-fluorodeoxyuridine monophosphate (FdUMP) inhibiting enzyme. Half of the TS was in an active form, whereas the other half was in an inactive form. This finding indicates that 5-FU-resistant cells exhibited increased TS expression, and the TS enzyme is used to trap FdUMP, resulting in resistance to 5-FU and its analogs.     

An Engineered Biliverdin-Compatible Cyanobacteriochrome Enables a Unique Ultrafast Reversible Photoswitching Pathway

Cyanobacteriochromes (CBCRs) are promising optogenetic tools for their diverse absorption properties with a single compact cofactor-binding domain. We previously uncovered the ultrafast reversible photoswitching dynamics of a red/green photoreceptor AnPixJg2, which binds phycocyanobilin (PCB) that is unavailable in mammalian cells. Biliverdin (BV) is a mammalian cofactor with a similar structure to PCB but exhibits redder absorption. To improve the AnPixJg2 feasibility in mammalian applications, AnPixJg2_BV4 with only four mutations has been engineered to incorporate BV. Herein, we implemented femtosecond transient absorption (fs-TA) and ground state femtosecond stimulated Raman spectroscopy (GS-FSRS) to uncover transient electronic dynamics on molecular time scales and key structural motions responsible for the photoconversion of AnPixJg2_BV4 with PCB (Bpcb) and BV (Bbv) cofactors in comparison with the parent AnPixJg2 (Apcb). Bpcb adopts the same photoconversion scheme as Apcb, while BV4 mutations create a less bulky environment around the cofactor D ring that promotes a faster twist. The engineered Bbv employs a reversible clockwise/counterclockwise photoswitching that requires a two-step twist on ~5 and 35 picosecond (ps) time scales. The primary forward P_fr → P_o transition displays equal amplitude weights between the two processes before reaching a conical intersection. In contrast, the primary reverse P_o → P_fr transition shows a 2:1 weight ratio of the ~35 ps over 5 ps component, implying notable changes to the D-ring-twisting pathway. Moreover, we performed pre-resonance GS-FSRS and quantum calculations to identify the Bbv vibrational marker bands at ~659,797, and 1225 cm⁻¹. These modes reveal a stronger H-bonding network around the BV cofactor A ring with BV4 mutations, corroborating the D-ring-dominant reversible photoswitching pathway in the excited state. Implementation of BV4 mutations in other PCB-binding GAF domains like AnPixJg4, AM1_1870g3, and NpF2164g5 could promote similar efficient reversible photoswitching for more directional bioimaging and optogenetic applications, and inspire other bioengineering advances.     

Stability of protective oxide films in waste incineration environment—solubility measurement of oxides in molten chlorides

Solubility measurements of several oxides in molten NaCl-KCl and NaCl-KCl-Na₂SO₄-K₂SO₄ were conducted in three different levels of basicity. The dissolution behavior of the oxides showed almost the same tendency as that shown by the dissolution behavior of the oxides in molten Na₂SO₄ in literature. In a waste incineration environment, a protective Cr₂O₃ film easily dissolves in molten chlorides as CrO₄²⁻ because pO²⁻ of the molten chlorides tends to have a small value due to the effect of water vapor contained in the combustion gas. From the result of the solubility measurement, the addition of molybdenum and/or silicon was expected to improve the corrosion resistance of alloys. Laboratory corrosion tests confirmed this expectation. However, the scale analysis suggested that the effect of molybdenum could not be explained completely by only the mechanism derived from the result of the solubility measurement.     

SOME PROPERTIES OF THE MAXIMUM LIKELIHOOD ESTIMATOR IN THE SIMULTANEOUS SWITCHING AUTOREGRESSIVE MODEL

Abstract. The simultaneous switching autoregressive (SSAR) model proposed by Kunitomo and Sato (A non-linearity in economic time series and disequilibrium econometric models. In Theory and Application of Mathematical Statistics (ed. A. Takemura). Tokyo:University of Tokyo Press (in Japanese), 1994; Asymmetry in economic time series and simultaneous switching autoregressive model. Struct. Change Econ. Dyn. , forthcoming (1994).) is a Markovian non-linear time series model. We investigate the finite sample as well as the asymptotic properties of the least squares estimator and the maximum likelihood (ML) estimator. Due to a specific simultaneity involved in the SSAR model, the least squares estimator is badly biased. However, the ML estimator under the assumption of Gaussian disturbances gives reasonable estimates.     

Continuous emulsion polymerization of vinyl acetate. II Operation in a single Couette–Taylor vortex flow reactor using sodium lauryl sulfate as emulsifier

Continuous emulsion polymerizations of vinyl acetate were conducted at 50°C in a single continuous Couette–Taylor vortex flow reactor (CCTVFR) using sodium lauryl sulfate as emulsifier and potassium persulfate as initiator. The polymerization can be carried out very smoothly and stably, but the steady‐state monomer conversion attained in a CCTVFR is not as high as that in a plug flow reactor (PFR), but only slightly higher than that in a continuous stirred tank reactor (CSTR), even if the Taylor number is adjusted to an optimum value. Also, the effects of operating variables, such as the emulsifier, initiator, and monomer concentrations in the feed and the mean residence time on the kinetic behaviors were almost the same as those observed in a CSTR. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 2755–2762, 2002     

Production of Ceramic Green Bodies Using a Microwave-Reactive Organic Binder

Because the pyrolysis of organic substances can result in the emission of harmful pollutant gases, a reduction in the use of organic binders is one aim of today's ceramics industry. A novel ceramic-forming process was developed that requires considerably less organic binder than conventional techniques. The process involves immobilizing reactive molecules on the surfaces of the particles, which on subsequent irradiation with microwaves, form bridges that bind the entire particle assembly together. The chemical forces involved produce strong bonds, resulting in a significant reduction in the amount of organic binder that is required to maintain the shape of the ceramic green body. This method will help to decrease emissions of harmful gases produced from pyrolysis of the binder.     

Binary phase behavior of 1,3-distearoyl-2-oleoyl-sn-glycerol (SOS) and 1,3-distearoyl-2-linoleoyl-sn-glycerol (SLS)

The binary phase behavior of SOS (1,3-distearoyl-2-oleoyl-sn-glycerol) and SLS (1,3-distearoyl-2-linoleoyl-sn-glycerol) was examined by using DSC and conventional and synchrotron radiation X-ray diffraction. The solid-solution phases were observed in the metastable α and γ forms in all concentration ranges. Results indicated that the miscible γ form did not transform to the β′ form when the mixtures were subjected to simple cooling from a high-temperature liquid to a low-temperature solid phase. However, and α-melt-mediated transformation into β′ and β₂ resulted in the formation of immiscible phases in concentration ranges of SLS below 30%. By contrast, at SLS concentration ranges above 30%, the α-melt-mediated transformation caused crystallization of only the γ form, and β′ and β₂ crystals did not appear. These results show that the specific interactions between SOS and SLS are operative in the phase behavior of the mixture states of SOS and SLS.     

High-Temperature Fracture Mechanism of Low-Ca-Doped Silicon Nitride

High-purity Si₃N₄ (with 2.5 wt% glassy SiO₂) doped with 0 to 450 at.ppm of Ca was prepared as a model system to investigate the effects of grain-boundary segregants on fracture phenomenology at 1400°C. Subcritical crack-growth (SCG) resistance as well as creep resistance was degraded significantly by the presence of a small amount of Ca. The internal friction of the doped materials exhibited the superposition of a grain-boundary relaxation peak and a high-temperature background, and the apparent viscosity of the grain-boundary film was determined from the peak. Based on these experimental data, the fracture mechanism at 1400°C was divided into three regions: "brittle," SCG, and creep failure as a function of both external strain rate and Ca concentration, C _Ca. From the investigation of the C _Ca dependence of the critical strain rate for the transition from "brittle" to SCG fractures, the SCG phenomenon is suggested to be triggered by small-scale, grain-boundary sliding. The C _Ca dependence of "steady-state" creep rate was far from the theoretical dependence of diffusional creep via a solution-precipitation mechanism. The discrepancy was interpreted to be due to the presence of an impurity-insensitive creep component. This component may correspond to the lowest limit of the tensile creep rate in Si₃N₄ polycrystalline materials containing intergranular glassy-SiO₂ film.     

Ring hydrogenation of naphthalene and 1-naphthol over supported metal catalysts in supercritical carbon dioxide solvent

Catalytic ring hydrogenations of naphthalene and 1-naphthol were studied over several supported metal catalysts in supercritical carbon dioxide solvent at low temperature. Higher concentration of hydrogen in supercritical carbon dioxide and lower reaction temperature were responsible for higher catalyst activity and selectivities to the desired partial ring hydrogenated products as compared with those observed in organic solvent for the same catalyst.