Comparative study of synonymous codon usage variations between the nucleocapsid and spike genes of coronavirus, and C-type lectin domain genes of human and mouse

Coronaviruses (CoVs) are single-stranded RNA viruses which contain the largest RNA genomes, and severe acute respiratory syndrome coronavirus (SARS-CoV), a newly found group 2 CoV, emerged as infectious disease with high mortality rate. In this study, we compared the synonymous codon usage patterns between the nucleocapsid and spike genes of CoVs, and C-type lectin domain (CTLD) genes of human and mouse on the codon basis. Findings indicate that the nucleocapsid genes of CoVs were affected from the synonymous codon usage bias than spike genes, and the CTLDs of human and mouse partially overlapped with the nucleocapsid genes of CoVs. In addition, we observed that CTLDs which showed the similar relative synonymous codon usage (RSCU) patterns with CoVs were commonly derived from the human chromosome 12, and mouse chromosome 6 and 12, suggesting that there might be a specific genomic region or chromosomes which show a more similar synonymous codon usage pattern with viral genes. Our findings contribute to developing the codon-optimization method in DNA vaccines, and further study is needed to determine a specific correlation between the codon usage patterns and the chromosomal locations in higher organisms.     

Hall viscosity and electromagnetic response

We show that, for Galilean invariant quantum Hall states, the Hall viscosity appears in the electromagnetic response at finite wave numbers q. In particular, the leading q dependence of the Hall conductivity at small q receives a contribution from the Hall viscosity. The coefficient of the q(2) term in the Hall conductivity is universal in the limit of strong magnetic field.     

'q-Titration' of long-chain and short-chain lipids differentiates between structured and mobile residues of membrane proteins studied in bicelles by solution NMR spectroscopy

'q-Titration' refers to the systematic comparison of signal intensities in solution NMR spectra of uniformly (15)N labeled membrane proteins solubilized in micelles and isotropic bicelles as a function of the molar ratios (q) of the long-chain lipids (typically DMPC) to short-chain lipids (typically DHPC). In general, as q increases, the protein resonances broaden and correspondingly have reduced intensities due to the overall slowing of protein reorientation. Since the protein backbone signals do not broaden uniformly, the differences in line widths (and intensities) enable the narrower (more intense) signals associated with mobile residues to be differentiated from the broader (less intense) signals associated with "structured" residues. For membrane proteins with between one and seven trans-membrane helices in isotropic bicelles, we have been able to find a value of q between 0.1 and 1.0 where only signals from mobile residues are observed in the spectra. The signals from the structured residues are broadened so much that they cannot be observed under standard solution NMR conditions. This q value corresponds to the ratio of DMPC:DHPC where the signals from the structured residues are "titrated out" of the spectrum. This q value is unique for each protein. In magnetically aligned bilayers (q>2.5) no signals are observed in solution NMR spectra of membrane proteins because the polypeptides are "immobilized" by their interactions with the phospholipid bilayers on the relevant NMR timescale (～10(5)Hz). No signals are observed from proteins in liposomes (only long-chain lipids) either. We show that it is feasible to obtain complementary solution NMR and solid-state NMR spectra of the same membrane protein, where signals from the mobile residues are present in the solution NMR spectra, and signals from the structured residues are present in the solid-state NMR spectra. With assigned backbone amide resonances, these data are sufficient to describe major features of the secondary structure and basic topology of the protein. Even in the absence of assignments, this information can be used to help establish optimal experimental conditions.     

Comparison of energy consumptions between ultrasonic, mechanical, and combined soil washing processes

Vigorous physical effects including micro-jet and micro-streaming can be induced in heterogeneous systems by acoustic cavitation. This can be useful for the removal of pollutants from contaminated soil particles. In this study, the diesel removal efficiencies in ultrasonic, mechanical, and combined soil washing processes have been compared considering the electrical energy consumptions for these processes. The combined process showed synergistic effects for both removal efficiency and effective volume also has the advantage of a short operation time compared to the sequential processes. Thus the ultrasonic soil washing process with mechanical mixing is considered a promising technology for industrial use.     

Effects of Ti addition on sol-gel derived InO and InZnO thin film transistors

In this study, we have newly developed titanium-indium oxide (TiInO) and titanium-indium zinc oxide (TiInZnO) thin films as the active channel layer in thin film transistors (TFTs) by the sol-gel process. The effects of adding Ti on TiInO and TiInZnO TFTs were investigated. The addition of Ti elements can suppress formation of oxygen vacancies because of the stronger oxidation tendency of Ti relative to that of Zn or In. TiInO and TiInZnO TFTs showed lower off currents and higher on/off current ratios than pure InO and InZnO TFTs. A TiInO TFT doped with 10.31 mol% Ti showed good performance with an on/off current ratio greater than 10⁷, and a field-effect mobility of 1.91 cm² V^?1 S^?1. A TiInZnO TFT doped with 2.92 mol % Ti showed an on/off current ratio greater than 10⁶, and a field-effect mobility of 0.45 cm² V^?1 S^?1.     

Self-supported organometallic rhodium quinonoid nanocatalysts for stereoselective polymerization of phenylacetylene

Heterogeneous self-supported organometallic nanocatalysts (ONs) were synthesized by treatment of the eta6-pi-hydroquinone rhodium complex [(1,4-hydroquinone)Rh(COD)]+ with Al(Oi-Pr)3. The organometallic nanocatalysts, the size of which can be controlled by alteration of the reaction conditions, show high catalytic activities in the stereoselective polymerization of phenylacetylene to produce cis-poly(phenylacetylene). A key feature of the ON catalyst synthesis is a facile eta6 to eta4 hapticity change occurring in the quinonoid ring, which is triggered by deprotonation of the -OH groups by Al(Oi-Pr)3, with concomitant coordination of the quinone oxygen atoms to the aluminum.     

Flavusides A and B, antibacterial cerebrosides from the marine-derived fungus Aspergillus flavus

Flavusides A (1) and B (2), two new antibacterial cerebroside derivatives, and the previously described phomaligol A (3), kojic acid (4), methyl kojic acid (5), and dimethyl kojic acid (6) have been isolated from the extract of a marine isolate of the fungus Aspergillus flavus. The structure and absolute stereochemistry of two cerebrosides were assigned on the basis of NMR and Tandem FAB-MS/MS experiments. Compounds 1, 2, and 3 exhibited a mild antibacterial activity against Staphylococcus aureus, methicillin-resistant S. aureus, and multidrug-resistant S. aureus. The minimum inhibitory concentration (MIC) values for each strain are as follows: compounds 1 and 2 showed 15.6 μg/ml for S. aureus and 31.2 μg/ml for methicillin-resistant S. aureus and multidrug-resistant S. aureus, and compound 3 exhibited 31.2 μg/ml for S. aureus and methicillin-resistant S. aureus and 62.5 μg/ml for multidrug-resistant S. aureus.     

Simply supported elastic beams under parametric excitation

In this paper, the nonlinear characteristics of the parametric resonance of simply supported elastic beams are investigated. Considering a geometrically exact formulation for unsharable and inextensible elastic beams subject to support motions, the integral-partial-differential equation of motion is obtained. The third-order perturbation of the equation of motion is then determined in a form amenable to an asymptotic treatment. The method of multiple scales is used to obtain the equations that describe the modulation of the amplitude and phase of parametric-resonance motions. The stability and bifurcations of the system are investigated considering, in particular, the frequency-response function. Furthermore, experimental results are shown to confirm the theoretically predicted stability and bifurcations.     

Liquid Chromatography-Tandem Mass Spectrometry for the Simultaneous Analysis of 353 Pesticides in the Edible Insect Tenebrio molitor Larvae (Mealworms)

Tenebrio molitor larvae (mealworm) is an edible insect and is considered a future food. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), a novel method for simultaneous analysis of 353 target analytes was developed and validated. Various sample preparation steps including “quick, easy, cheap, effective, rugged, and safe” (QuEChERS) extraction conditions, number of acetonitrile-hexane partitions, and dispersive-solid phase extraction (dSPE) sorbents were compared, and the optimal conditions were determined. In the established method, 5 g of homogenized mealworms was extracted with acetonitrile and treated with QuEChERS EN 15662 salts. The crude extract was subjected to three rounds of acetonitrile-hexane partitioning, and the acetonitrile layer was cleaned with C18 dSPE. The final solution was matrix-matched and injected into LC-MS/MS (2 μL). For target analytes, the limits of quantitation (LOQs) were ≤10 μg/kg, and the correlation coefficient (r²) of calibration was >0.990. In recovery tests, more than 90% of the pesticides showed an excellent recovery range (70–120%) with relative standard deviation (RSD) ≤20%. For more than 94% of pesticides, a negligible matrix effect (within ±20%) was observed. The analytical method was successfully applied and used for the detection of three urea pesticides in 4 of 11 mealworm samples.     

Semi-fluorinated polyarylenes: Microwave-assisted synthesis and structure–property relationships

A series of three fluorine containing and three non-fluorinated Diels–Alder step-growth polyarylene polymers and copolymers was synthesized via conventional oil bath heating (days/weeks). A drastic time reduction was realized with a microwave-assisted polymerization (hours). The polymers were characterized by multinuclear (¹H, ¹³C, and ¹⁹F) NMR and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, thermal analysis (thermogravimetric analysis [TGA], differential scanning calorimetry [DSC], and dynamic mechanical analysis [DMA]), gel permeation chromatography, X-ray diffraction (XRD), water contact analysis, and refractive index (RI) measurements. The NMR spectra indicated a mixture of para and meta conformations through the polymer backbone increasing to more para with greater fluorine content. TGA revealed the fluorine-containing polyarylenes possessed the highest char yields at almost 80% at 1000°C under nitrogen, and all the polyarylenes possessed onset of degradation temperatures above 550°C under nitrogen and air atmospheres. XRD analysis indicated more ordering for the fluorine-containing polyarylenes which afforded the high char yields. DMA gave storage moduli values in the range of 1–10 GPa for the polyarylenes. Molecular weights for all samples were above 100 kg/mol. Water contact angles did not change with fluorine content due to the shielding effect of the pendant phenyl groups. However, the RI decreased to 1.6497 at 632.8 nm for the polyarylene with the highest fluorine content.