Mutations stabilize small subunit ribosomal RNA in desiccation-tolerant cyanobacteria Nostoc

The ribosomal RNA molecule is an ideal model for evaluating the stability of a gene product under desiccation stress. We isolated 8 Nostoc strains that had the capacity to withstand desiccation in habitats and sequenced their 16S rRNA genes. The stabilities of 16S rRNAs secondary structures, indicated by free energy change of folding, were compared among Nostoc and other related species. The results suggested that 163 rRNA secondary structures of the desiccation-tolerant Nostoc strains were more stable than that of planktonic Nostocaceae species. The stabilizing mutations were divided into two categories: (1) those causing GC to replace other types of base pairs in stems and (2) those causing extension of stems. By mapping stabilizing mutations onto the Nostoc phylogenetic tree based on 16S rRNA gene, it was shown that most of stabilizing mutations had evolved during adaptive radiation among Nostoc spp. The evolution of 16S rRNA along the Nostoc lineage is suggested to be selectively advantageous under desiccation stress.

Molecular phylogeny of Stentor (Ciliophora : Heterotrichea) based on small subunit ribosomal RNA sequences

To determine the phylogenetic position of Stentor within the Class Heterotrichea, the complete small subunit rRNA genes of three Stentor species, namely Stentor polymorphus, Stentor coeruleus, and Stentor roeseli, were sequenced and used to construct phylogenetic trees using the maximum parsimony, neighbor joining, and Bayesian analysis. With all phylogenetic methods, the genus Stentor was monophyletic, with S. roeseli branching basally.

Triploid origin of the gibel carp as revealed by 5S rDNA localization and chromosome painting

5S ribosomal DNA (rDNA) was isolated and sequenced from the gibel carp Carassius auratus gibelio with 162 chromosomes and crucian carp Carassius auratus with 100 chromosomes, and fluorescent probes for chromosome localization were prepared to ascertain the ploidy origin and evolutionary relationship between the two species. Using fluorescence in-situ hybridization (FISH), major 5S rDNA signals were localized to the short arms of three subtelocentric chromosomes in the gibel carp and to the short arms of two subtelocentrics in the crucian carp. In addition, some minor signals were detected on other chromosomes of both species. Simultaneously, six chromosomes were microdissected from the gibel carp metaphase spreads using glass needles, and the isolated chromosomes were amplified in vitro by degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR). Significantly, when the DOP-PCR-generated probes prepared from each single chromosome were hybridized, three same-sized chromosomes were painted in each gibel carp metaphase, whereas only two painted chromosomes were observed in each crucian carp metaphase spread. The data indicate that gibel carp is of triploid origin in comparison with diploid crucian carp.

De novo RNA synthesis and homology modeling of the classical swine fever virus RNA polymerase

Classical swine fever virus (CSFV) non-structural protein 5B (NS5B) encodes an RNA-dependent RNA polymerase (RdRp), a key enzyme which initiates RNA replication by a de novo mechanism without a primer and is a potential target for anti-virus therapy. We expressed the NS5B protein in Escherichia coli. The rGTP can stimulate de novo initiation of RNA synthesis and mutation of the GDD motif to Gly-Asp-Asp (GAA) abolishes the RNA synthesis. To better understand the mechanism of viral RNA synthesis in CSFV, a three-dimensional model was built by homology modeling based on the alignment with several virus RdRps. The model contains 605 residues folded in the characteristic fingers, palm and thumb domains. The fingers domain contains an N-terminal region that plays an important role in conformational change. We propose that the experimentally observed promotion of polymerase efficiency by rGTP is probably due to the conformational changes of the polymerase caused by binding the rGTP. Mutation of the GDD to GAA interferes with the interaction between the residues at the polymerase active site and metal ions, and thus renders the polymerase inactive. (c) 2005 Elsevier B.V. All rights reserved.

Efficient RNA interference in zebrafish embryos using siRNA synthesized with SP6 RNA polymerase

Double-stranded RNA (dsRNA) has been shown to be a useful tool for silencing genes in zebrafish (Danio rerio), while the blocking specificity of dsRNA is still of major concern for application. It was reported that siRNA (small interfering RNA) prepared by endoribonuclease digestion (esiRNA) could efficiently silence endogenous gene expression in mammalian embryos. To test whether esiRNA could work in zebrafish, we utilized Escherichia coli RNaseIII to digest dsRNA of zebrafish no tail (ntl), a mesoderm determinant in zebrafish and found that esi-ntl could lead to developmental defects, however, the effective dose was so close to the toxic dose that esi-ntl often led to non-specific developmental defects. Consequently, we utilized SP6 RNA polymerase to produce si-ntl, siRNA designed against ntl, by in vitro transcription. By injecting in vitro synthesized si-ntl into zebrafish zygotes, we obtained specific phenocopies of reported mutants of ntl. We achieved up to a 59%no tail phenotype when the injection concentration was as high as 4 mu g/mu L. Quantitative reverse transcription-polymerase chain reaction (RT-PCR) and whole-mount in situ hybridization analysis showed that si-ntl could largely and specifically reduce mRNA levels of the ntl gene. As a result, our data indicate that esiRNA is unable to cause specific developmental defects in zebrafish, while siRNA should be an alternative for downregulation of specific gene expression in zebrafish in cases where RNAi techniques are applied to zebrafish reverse genetics.

The molecular characterization of RNA segment S9 of grass carp hemorrhage virus (GCHV), an aquareovirus

Although reovirus infection is one of the major virus diseases of grass carp in China, the available knowledge on the structure and function of genes and proteins of the virus is limited. The complete sequence of the S9 genome segment of grass carp hemorrhage virus (GCHV) was determined. The segment consists of 1130 nucleotides and has a large open reading frame (ORF) encoding a protein of 352 amino acids with predicted molecular mass of 37.7 kDa. Amino acid sequence comparison revealed that the deduced protein encoded by GCHV S9 is closely related to the sigma NS proteins of mammalian reovirus (MRV) and avian reovirus (ARV). Secondary structure analysis displayed that the form of alpha -helices (40.1%) and beta -sheets (49.4%) are the richest two contents in the protein encoded by S9, and this protein is predicted to be a nonstructural protein. (C) 2001 Elsevier Science B.V. All rights reserved.

A SERINE KINASE REGULATES INTRACELLULAR-LOCALIZATION OF SPLICING FACTORS IN THE CELL CYCLE

Small nuclear ribonucleoprotein particles (snRNPs) and non-snRNP splicing factors containing a serine/arginine-rich domain (SR proteins) concentrate in 'speckles' in the nucleus of interphase cells(1). It is believed that nuclear speckles act as storage sites for splicing factors while splicing occurs on nascent transcripts(2). Splicing factors redistribute in response to transcription inhibition(3,4) or viral infection(5), and nuclear speckles break down and reform as cells progress through mitosis(6). We have now identified and cloned a kinase, SRPK1, which is regulated by the cell cycle and is specific for SR proteins; this kinase is related to a Caenorhabditis elegans kinase and to the fission yeast kinase Dsk1 (ref. 7). SRPK1 specifically induces the disassembly of nuclear speckles, and a high level of SRPK1 inhibits splicing in vitro. Our results indicate that SRPK1 mag have a central role in the regulatory network for splicing, controlling the intranuclear distribution of splicing factors in interphase cells, and the reorganization of nuclear speckles during mitosis.

Simulation of light coupling enhancement and localization of transmission field via subwavelength metallic gratings

Surface plasmons(SPs) generated in nano metallic gratings on medium layer can greatly enhance the transmission field through the metallic gratings. The enhancement effect is achieved from lambda = 500 nm to near-infrared domain. The enhancement rate is about 110 % at the wavelength of about 6 10 nm and about 180 % at lambda = 700 nm and 740 nm where most kinds of thin film solar cells have a high spectral response. These structures should provide a promising way to increase the coupling efficiency of thin film solar cells and optical detectors of different wavelength response.

Optical properties and exciton localization in GaNas/GaAs

GaNAs/GaAs single quantum wells (SQWs) and dilute GaNAs bulk grown by molecular beam epitaxy(MBE) were studied by photoluminescence (PL), selectively-excited PL, and time-resolved PL. Exciton localization and delocalization were investigated in detail. Under short pulse laser excitation, the delocalization exciton emission was revealed in GaNAs/GaAs SQWs. It exhibits quite different optical properties from N-related localized states. In dilute GaNAs bulk, a transition of alloy band related recombination was observed by measuring the PL dependence on temperature and excitation intensity and time-resolved PL, as well. This alloy-related transition presents intrinsic optical properties. These results are very important for realizing the abnomal features of III-V-N semiconductors.

Sulfur-induced exciton localization in Te-rich ZnSTe alloy

Exciton localization in Te-rich ZnSTe epilayers has been studied by photoluminescence (PL) and time-resolved PL. The sulfur-related exciton emission is found to dominate the radiative recombination at low temperature and is shifted to the low energy with the increase of S concentration. By measuring the PL dependence on temperature and by analyzing the PL decay process, we have clarified the localization nature of the sulfur-related exciton emission. Furthermore, the difference of the localization effect in Te- and S-rich ZnSTe is also compared and discussed. © 2005 American Institute of Physics.

Effects of the wave function localization in AlInGaN quaternary alloys

Using the first-principles band-structure method and the special quasirandom structures approach, the authors have investigated the band structure of random AlxInyGa1-x-yN quaternary alloys. They show that the wave functions of the band edge states are more localized on the InN sites. Consequently, the photoluminescence transition intensity in the alloy is higher than that in GaN. The valence band maximum state of the quaternary alloy is also higher than GaN with the same band gap, indicating that the alloy can be doped more easily as p-type. (c) 2007 American Institute of Physics.

Weak anti-localization in InAlAs/InGaAs/InAlAs high mobility two-dimensional electron gas systems

Magneto-transport measurements have been carried out on three heavily Si delta-doped In-0.52 Al-0.48 As/In-0.53 Ga-0.47 As/In-0.52 A(10.48) As single quantum well samples in which two subbands were occupied by electrons. The weak anti-localization (WAL) has been found in such high electron mobility systems. The strong Rashba spin-orbit (SO) coupling is due to the high structure inversion asymmetry (SIA) of the quantum wells. Since the WAL theory model is so complicated in fitting our experimental results, we obtained the Rashba SO coupling constant alpha and the zero-field spin splitting Delta(0) by an approximate approach. The results are consistent with that obtained by the Shubnikov-de Haas (SdH) oscillation analysis. The WAL effect in high electron mobility system suggests that finding a useful approach for deducing alpha and Delta(0) is important in designing future spintronics devices that utilize the Rashba SO coupling.

Photon localization in amorphous photonic crystal

The photon localization in disordered two-dimensional photonic crystal is studied theoretically. It is found that the mean transmission coefficient in the photonic band decreases exponentially as the disorder degree increases, reflecting the occurrence of Anderson localization. The strength of photon localization can be controlled by tuning the disorder degree in the photonic crystal. We think the variation regular of the transmission coefficient in our disordered system is equivalent to that of the scaling theory of localization.

Photon localization in amorphous photonic crystal

The photon localization in disordered two-dimensional photonic crystal is studied by use of multiple- scattering method. The disorder degree can be controlled by adjusting the random rotating angle of the square cell. It is found that the transmission in the band decreases and that in the gap increases as the disorder degree increases, and localization induced by disorder will spread from the band gap edge to the band center and the gap center. Moreover, the mean transmission of the band will decrease exponentiatly with disorder increasing.

Non-exponential photoluminescence decay dynamics of localized carriers in disordered InGaN/GaN quantum wells: the role of localization length

In this article, we report a combined experimental and theoretical study on the luminescence dynamics of localized carriers in disordered InGaN/GaN quantum wells. The luminescence intensity of localized carriers is found to exhibit an unusual non-exponential decay. Adopting a new model taking the radiative recombination and phonon-assisted hopping transition between different localized states into account, which was recently developed by Rubel et al., the non-exponential decay behavior of the carriers can be quantitatively interpreted. Combining with precise structure characterization, the theoretical simulations show that the localization length of localized carriers is a key parameter governing their luminescence decay dynamics. (c) 2006 Optical Society of America.