Is there a close relationship between synonymous codon bias and codon-anticodon binding strength in human genes?

Synonymous codon bias has been examined in 78 human genes (19967 codons) and measured by relative synonymous codon usage (RSCU). Relative frequencies of all kinds of dinucleotides in 2,3 or 3,4 codon positions have been calculated, and codon-anticodon bin

The features of synonymous codon bias and GC-content relationship in human genes

728 human genes were divided to four groups according to the GC contents of their coding sequences (from GC<0.43 to GC>0.58). Examination of synonymous-codon bias in the 4 groups show that NTG (N represents any base of T, A, C, G) is most favored and NCG

Secondary structural analysis of the mRNA regions encoding the hemagglutinin cleavage site basic amino acids of the avian influenza virus H5N1 subtype samples

Here we report the codon bias and the mRNA secondary structural features of the hemagglutinin (HA) cleavage site basic amino acid regions of avian influenza virus H5N1 subtypes. We have developed a dynamic extended folding strategy to predict RNA secondar

The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii : Cyprinifonnes) and an altemative pattem of mitogenomic evolution in vertebrate

The complete mitochondrial genome sequence of the Chinese hook snout carp, Opsariichthys bidens, was newly determined using the long and accurate polymerase chain reaction method. The 16,611-nucleotide mitogenome contains 13 protein-coding genes, two rRNA genes (12S, 16S) 22 tRNA genes, and a noncoding control region. We use these data and homologous sequence data from multiple other ostariophysan fishes in a phylogenetic evaluation to test hypothesis pertaining to codon usage pattern of O. bidens mitochondrial protein genes as well as to re-examine the ostariophysan phylogeny. The mitochondrial genome of O. bidens reveals an alternative pattern of vertebrate mitochondrial evolution. For the mitochondrial protein genes of O. bidens, the most frequently used codon generally ends with either A or C, with C preferred over A for most fourfold degenerate codon families; the relative synonymous codon usage of G-ending codons is greatly elevated in all categories. The codon usage pattern of O. bidens mitochondrial protein genes is remarkably different from the general pattern found previously in the relatively closely 9 related zebrafish and most other vertebrate mitochondria. Nucleotide bias at third codon positions is the main cause of codon bias in the mitochondrial protein genes of O. bidens, as it is biased particularly in favor of C over A. Bayesian analysis of 12 concatenated mitochondrial protein sequences for O. bidens and 46 other teleostean taxa supports the monophyly of Cypriniformes and Otophysi and results in a robust estimate of the otophysan phylogeny. (C) 2007 Published by Elsevier B.V.

Effects of superimposed pulse bias on TiN coating in cathodic arc deposition

Orthogonal designs are used to investigate the main factors when doing experiments in which pulse bias is superimposed on d.c. bias during cathodic are deposition of TiN. Pulse peak, duty cycle, frequency, direct voltage, are current and pressure all are investigated when coating TiN on HSS substrates. Roughness, surface micrograph, microhardness and thickness are tested. By analysis of variance, it is shown that pressure and frequency are the main factors. R-a and droplet density of the film with (d.c. + pulse) bias decrease. A simple explanation for the result is suggested.

Guiding neutral atoms with two current-carrying wires and a vertical bias field on the atom chip

We demonstrate the guiding of neutral atoms with two parallel microfabricated current-carrying wires on the atom chip and a vertical magnetic bias field. The atoms are guided along a magnetic field minimum parallel to the current-carrying wires and confined in the other two directions. We describe in detail how the precooled atoms are efficiently loaded into the two-wire guide. We present a detailed experimental study of the motional properties of the atoms in the guide and the relationship between the location of the guide and the vertical bias field. This two-wire guide with vertical bias field can be used to realize large area atom interferometer.

Phylogeographic analysis of mitochondrial DNA haplogroup F2 in China reveals T12338C in the initiation codon of the NDS gene not to be pathogenic

In this report, we studied on a homoplasmic T12338C change in mitochondrial DNA (mtDNA), which substituted methionine in the translational initiation codon of the NADH dehydrogenase subunit 5 gene (ND5) with threonine. This nucleotide change was originall

Evidence of gene conversion in the evolutionary process of the codon 41/42 (-CTTT) mutation causing beta-thalassemia in southern China

The 4-bp deletion (-CTTT) at codon 41/42 (CD41/42) of the human beta-globin gene represents one of the most common beta-thalassemia mutations in East Asia and Southeast Asia, which is historically afflicted with endemic malaria, thus hypothetically evolvi

大肠杆菌mRNA 编码区长度、形成二级结构倾向与密码子偏好性的关系

从GenBank获得大肠杆菌K-12MG1655株的全基因组序列,计算了与基因密码子偏好性相关的多个参数(Nc、CAI、GC、GC3s),对其mRNA编码区长度、形成二级结构倾向与密码子偏好性之间的关系进行了统计学分析,发现虽然翻译效率(包括翻译速度和翻译精度)是制约大肠杆菌高表达基因的密码子偏好性的主要因素,同时,mRNA编码区长度及其形成二级结构的倾向也是形成这种偏好性的不可忽略的原因,而且对偏好性有一定程度的削弱。另外对mRNA编码区形成二级结构倾向的生物学意义进行了讨论分析。

Investigation of responsivity decreasing with rising bias voltage in a GaN Schottky barrier photodetector

The unexpected decrease in measured responsivity observed in a specific GaN Schottky barrier photodetector (PD) at high reverse bias voltage was investigated and explained. Device equivalent transforms and small signal analysis were performed to analyse the test circuit. On this basis, a model was built which explained the responsivity decrease quantitatively. After being revised by this model, responsivity curves varying with bias voltage turned out to be reasonable. It is proved that the decrease is related to the dynamic parallel resistance of the photodiode. The results indicate that with a GaN Schottky PD, the choice of load resistance is restricted according to the dynamic parallel resistance of the device to avoid responsivity decay at high bias voltage.

Dielectric relaxation and giant dielectric constant of Nb-doped CaCu3Ti4O12 ceramics under dc bias voltage

CaCu3Ti(4-x)Nb(x)O(12) (x = 0, 0.01, 0.08, 0.2) ceramics were fabricated by a conventional solid-state reaction method. The ceramics showed the body-centered cubic structure without any foreign phases and the grain size decreases with Nb doping. Two Debye-type relaxations were observed for the Nb-doped samples at low frequency and high frequency, respectively. The complex electric modulus analysis revealed that the surface layer, grains and grain boundaries contributed to the dielectric constant. The low-frequency dielectric constant relative to the surface layer decreased to a minimum and then increased with the dc bias voltage at 100 Hz, which were well explained in terms of a model containing two metal oxide semiconductors in series, confirming the surface layer in the ceramics. The shift voltage V-B corresponding to the minimal capacitance increased with increase of the composition x. (C) 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interdot interaction induced zero-bias maximum of the differential conductance in parallel double quantum dots

We have studied the equilibrium and nonequilibrium electronic transports through a double quantum dot coupled to leads in a symmetrical parallel configuration in the presence of both the inter- and the intradot Coulomb interactions. The influences of the interdot interaction and the difference between dot levels on the local density of states (LDOS) and the differential conductance are paid special attention. We find an interesting zero-bias maximum of the differential conductance induced by the interdot interaction, which can be interpreted in terms of the LDOS of the two dots. Due to the presence of the interdot interaction, the LDOS peaks around the dot levels epsilon(i) are split, and as a result, the most active energy level which supports the transport is shifted near to the Fermi level of the leads in the equilibrium situation. (c) 2006 American Institute of Physics.

HYDROGEN DIFFUSION IN A-SI-H/A-SI STRUCTURE UNDER ELECTRICAL BIAS

By using the technique of elastic recoil detection (ERD), we have measured the hydrogen profiles in a-Si:H/a-Si structure samples annealed at various temperatures with and without electrical bias, and investigated the influence of electrical bias on hydrogen diffusion. The results show that hydrogen diffusion in a-Si is significantly enhanced by the action of electrical bias. The existence of the excess carriers, which are introduced by electrical injection, is considered to be responsible for the enhancement of hydrogen diffusion, and the microprocess of hydrogen transport has been exploited.

CONTROLLING OF SCHOTTKY-BARRIER HEIGHTS FOR AU/N-GAAS AND TI/N-GAAS WITH HYDROGEN INTRODUCED AFTER METAL-DEPOSITION BY BIAS ANNEALING

Up to now, in most of the research work done on the effect of hydrogen on a Schottky barrier, the hydrogen was introduced into the semiconductor before metal deposition. This letter reports that hydrogen can be effectively introduced into the Schottky barriers (SBs) of Au/n-GaAs and Ti/n-GaAs by plasma hydrogen treatment (PHT) after metal deposition on [100] oriented n-GaAs substrates. The Schottky barrier height (SBH) of a SB containing hydrogen shows the zero/reverse bias annealing (ZBA/RBA) effect. ZBA makes the SBH decrease and RBA makes it increase. The variations in the SBHs are reversible. In order to obtain obvious ZBA/RBA effects, selection of the temperature for plasma hydrogen treatment is important, and it is indicated that 100-degrees-C for Au/n-GaAs and 150-degrees-C for Ti/n-GaAs are suitable temperatures. It is concluded from the analysis of experimental results that only the hydrogen located at or near the metal-semiconductor interface, rather than the hydrogen in the bulk of either the semiconductor or the metal, is responsible for the ZBA/RBA effect on SBH.