Single-Nucleotide Mutation Matrix: A New Model for Predicting the NF-κB DNA Binding Sites

<div><p>In this study, we established a single nucleotide mutation matrix (SNMM) model based on the relative binding affinities of NF-κB p50 homodimer to a wild-type binding site (GGGACTTTCC) and its all single-nucleotide mutants detected with the double-stranded DNA microarray. We evaluated this model by scoring different groups of 10-bp DNA sequences with this model and analyzing the correlations between the scores and the relative binding affinities detected with three wet experiments, including the electrophoresis mobility shift assay (EMSA), the protein-binding microarray (PBM) and the systematic evolution of ligands by exponential enrichment-sequencing (SELEX-Seq). The results revealed that the SNMM scores were strongly correlated with the detected binding affinities. We also scored the DNA sequences with other three models, including the principal coordinate (PC) model, the position weight matrix scoring algorithm (PWMSA) model and the Match model, and analyzed the correlations between the scores and the detected binding affinities. In comparison with these models, the SNMM model achieved reliable results. We finally determined 0.747 as the optimal threshold for predicting the NF-κB DNA-binding sites with the SNMM model. The SNMM model thus provides a new alternative model for scoring the relative binding affinities of NF-κB to the 10-bp DNA sequences and predicting the NF-κB DNA-binding sites.</p></div

The single-nucleotide mutant matrix (SNMM).

a<p>Base of the reference sequence (GGGACTTTCC). 1 to 10, base position in the 10-bp NF-κB DBS.</p

The relative binding affinities of the NF-κB p50 homodimer to four variant sequences.

<p>A, The binding affinities of the NF-κB p50 homodimer to four sequences detected with the radioactive EMSA (R-EMSA), NIRF-EMSA (N-EMSA) and SELEX-Seq (SELEX), respectively, and scored with the SNMM, PWMSA, Match and PC models, respectively. B, The correlation between the EMSA-detected values and the model scores. *, <i>p</i><0.05; no *, <i>p</i>>0.05. P value refers to the confidence interval of Pearson's <i>r</i>.</p

Correlation analysis.

<p>A, Correlations between the EMSA values and the scores of the PC, SNMM, PWMSA, and Match models, respectively. B, Correlations between the PBM <i>z</i> scores and the scores of the PC, SNMM, PWMSA, and Match models, respectively. C, Correlations between the SELEX-Seq values and the scores of the SNMM, PWMSA, Match, and PC models, respectively. Correlation between the SELEX-Seq values and the EMSA values. **, <i>p</i><0.01. P value refers to the confidence interval of Pearson's <i>r</i>. The number under the abscissa refers to the number of values or sequences used in the corresponding correlation analysis.</p

Iridium–Ruthenium Alloyed Nanoparticles for the Ethanol Oxidation Fuel Cell Reactions

In this study, carbon supported Ir–Ru nanoparticles with average sizes ranging from 2.9 to 3.7 nm were prepared using a polyol method. The combined characterization techniques, that is, scanning transmission electron microscopy equipped with electron energy loss spectroscopy, high resolution transmission electron microscopy, energy dispersive X-ray spectroscopy, and X-ray diffraction, were used to determine an Ir–Ru alloy nanostructure. Both cyclic voltammetry and chronoamperometry (CA) results demonstrate that Ir₇₇Ru₂₃/C bears superior catalytic activities for the ethanol oxidation reaction compared to Ir/C and commercial Pt/C catalysts. In particular, the Ir₇₇Ru₂₃/C catalyst shows more than 21 times higher mass current density than that of Pt/C after 2 h reaction at a potential of 0.2 V vs Ag/AgCl in CA measurement. Density functional theory simulations also demonstrate the superiority of Ir–Ru alloys compared to Ir for the ethanol oxidation reaction

Detection of the DNA-binding affinities of the NF-κB p50 homodimer to four sequences with NIRF-EMSA.

<p>A, A representative image of the NIRF-EMSA detections. B, The quantified signal intensities of the shifted bands (labeled as DNA/p50 complex in Image A). a, GGGGATTCCC; b, GGGATCTCCC; c, GGGATACCCC; d, GGGAGGCCCC.</p

Highly Efficient K_0.15MnO₂ Birnessite Nanosheets for Stable Pseudocapacitive Cathodes

In this paper, we reported a facile synthesis of Birnessite K_0.15MnO₂·0.43H₂O nanosheets in a solution phase. The structural and electrochemical properties of the K_0.15MnO₂ nanosheets for supercapacitor (SC) reactions were studied, and a gravimetric capacitance of 303 F/g was obtained at a charge/discharge current of 0.2 A/g. Electrochemical kinetics showed that a non-Faradaic (electrical double layer) current existed throughout the charging potential range, while a dominant Faradaic (pseudocapacitive) current was observed at high and low potentials during anodic and cathodic scans, respectively. Asymmetric pseudocapacitive full-cells were constructed with both anodic and cathodic K_0.15MnO₂ composite materials and subjected to long-term galvanostatic charge/discharge analyses. A specific capacitance of 67.8 F/g was obtained for the cathodic K_0.15MnO₂ full-cells after 1000 cycles, with a capacitive retention of 87.8% and Coulombic and energy efficiencies of ∼100 and ∼90%, respectively. <i>In situ</i> X-ray absorption near edge spectroscopy further corroborated the potential-dependent Faradaic reactions, suggesting a predominant change in valence state of K_0.15MnO₂ to occur between 0.3 and 0.6 V (vs Ag/AgCl). The present study not only underscores the structure–function relationship of MnO₂-based electrode materials for SC reactions but also provides a new approach in fabricating advanced pseudocapacitors by utilizing cost-effective transition metal oxide materials

Palladium–Tin Alloyed Catalysts for the Ethanol Oxidation Reaction in an Alkaline Medium

In this paper, we present a study of a series of carbon-supported Pd–Sn binary alloyed catalysts prepared through a modified Polyol method as anode electrocatalysts for direct ethanol fuel cell reactions in an alkaline medium. Transmission electron microscopy, energy-dispersive X-ray spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy, and aberration-corrected scanning transmission electron microscopy equipped with electron energy loss spectroscopy were used to characterize the Pd–Sn/C catalysts, where homogeneous Pd–Sn alloys were determined to be present with the surface Sn being partially oxidized. Among various Pd–Sn catalysts, Pd₈₆Sn₁₄/C catalysts showed much enhanced current densities in cyclic voltammetric and chronoamperometric measurements, compared to commercial Pd/C (Johnson Matthey). The overall rate law of ethanol oxidation reaction for both Pd₈₆Sn₁₄/C and commercial Pd/C were also determined, which clearly showed that Pd₈₆Sn₁₄/C was more favorable in high ethanol concentration and/or high pH environment. Density functional theory calculations also confirmed Pd–Sn alloy structures would result in lower reaction energies for the dehydrogenation of ethanol, compared to the pure Pd crystal

Platinum-Tin Oxide Core–Shell Catalysts for Efficient Electro-Oxidation of Ethanol

Platinum-tin (Pt/Sn) binary nanoparticles are active electrocatalysts for the ethanol oxidation reaction (EOR), but inactive for splitting the C-C bond of ethanol to CO₂. Here we studied detailed structure properties of Pt/Sn catalysts for the EOR, especially CO₂ generation in situ using a CO₂ microelectrode. We found that composition and crystalline structure of the tin element played important roles in the CO₂ generation: non-alloyed Pt₄₆-(SnO₂)₅₄ core–shell particles demonstrated a strong capability for C-C bond breaking of ethanol than pure Pt and intermetallic Pt/Sn, showing 4.1 times higher CO₂ peak partial pressure generated from EOR than commercial Pt/C