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.     

Polystyrene‐graft‐poly(ethylene oxide) copolymers prepared by macromonomer technique in dispersion. I. Liquid chromatographic separation of product mixtures

Products of the radical dispersion copolymerization of methacryloyl‐terminated poly(ethylene oxide) (PEO) macromonomer and styrene were separated and characterized by size exclusion chromatography (SEC), full adsorption‐desorption (FAD)/SEC coupling and eluent gradient liquid adsorption chromatography (LAC). In dimethylformamide, which is a good solvent for PEO side chains but a poor solvent for polystyrene (PS), amphiphilic PS‐graft‐PEO copolymers formed aggregates, which were very stable at room temperature even upon substantial dilution. The aggregates disappeared at high temperature or in tetrahydrofuran (THF), which is a good solvent for both homopolymers and for PS‐graft‐PEO. FAD/SEC procedure allowed separation of homo‐PS from graft‐copolymer and determination of both its amount and molar mass. Effective molar mass of graft‐copolymer was estimated directly from the SEC calibration curve determined with PS standards. Presence of larger amount of the homo‐PS in the final graft‐copolymer products was also confirmed with LAC measurements. The results indicate that there are at least two or maybe three polymerization loci; namely the continuous phase, the particle surface layer and the particle core. The graft copolymers are produced mainly in the continuous phase while PS or copolymer rich in styrene units is formed mostly in the core of monomer‐swollen particles. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 2284–2291, 2000     

Generation and Rearrangement of N,O‐Dialkenylhydroxylamines for the Synthesis of 2‐Aminotetrahydrofurans

A new diastereoselective route to 2‐aminotetrahydrofurans has been developed from N,O‐dialkenylhydroxylamines. These intermediates undergo a spontaneous C?C bond‐forming [3,3]‐sigmatropic rearrangement followed by a C?O bond‐forming cyclization. A copper‐catalyzed N‐alkenylation of an N‐Boc‐hydroxylamine with alkenyl iodides, and a base‐promoted addition of the resulting N‐hydroxyenamines to an electron‐deficient allene, provide modular access to these novel rearrangement precursors. The scope of this de novo synthesis of simple nucleoside analogues has been explored to reveal trends in diastereoselectivity and reactivity. In addition, a base‐promoted ring‐opening and Mannich reaction has been discovered to covert 2‐aminotetrahydrofurans to cyclopentyl β‐aminoacid derivatives or cyclopentenones.     

QCD at a Finite isospin density: From the pion to quark-antiquark condensation

QCD at a finite isospin chemical potential μ _I is studied. This theory has no fermion-sign problem and can be simulated on a lattice by using present-day techniques. We solve this theory analytically in two limits: low μ _I, where chiral perturbation theory is applicable, and asymptotically high μ _I, where perturbative QCD is at work. At a low isospin density, the ground state is a superfluid pion condensate. At a very high density, it is a Fermi liquid with Cooper pairing. The pairs carry the same quantum numbers as the pions. Motivated by this observation, we put forward a conjecture that the transition from hadron to quark matter is smooth. The conjecture passes several nontrivial tests. Our results imply a nontrivial phase diagram in the space of the temperature and chemical potentials of isospin and baryon number. At asymptotically large values of μ _I and small values of the baryon chemical potential, the ground state is in a phase similar to the Fulde-Ferrell-Larkin-Ovchinnikov phase. It is characterized by a spatially modulated superfluid order parameter 〈ūγ ₅ d〉 and may be the asymptotic limit of the inhomogeneous pion-condensation phase advocated by Migdal and others.     

The diffusion flame structure of an ammonium perchlorate based composite propellant at elevated pressures

Examination of the surface behavior and flame structure of a bimodal ammonium perchlorate (AP) composite propellant at elevated pressure was performed using high speed (5 kHz) planar laser-induced fluorescence (PLIF) from 1 to 12 atm and visible surface imaging spanning 1–20 atm. The dynamics of the combustion of single, coarse AP crystals were resolved using these techniques. It was found that the ignition delay time for individual AP crystals contributed significant to the particle lifetime only at pressures below about 6 atm. In situ AP crystal burning rates were found to be higher than rates reported for pure AP deflagration studies. The flame structure was studied by exciting OH molecules in the gas phase. Two types of diffusion flames were observed above the composite propellant: jet-like flames and v-shaped, inverted, overventilated, flames (IOF) lifted off the surface. While jet-like diffusion flames have been imaged at low pressures and simulated by models, the lifted IOFs have not been previously reported or predicted. The causes for the observed flame structures are explained by drawing on an understanding of the surface topography and disparities in the burning rates of the fuel and oxidizer.     

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.