Transcription rates of yeast genes are influenced by the distribution of introns

A comparative analysis on the intron sequence oligonucleotide usages in two sets of yeast genes with higher and lower transcription frequencies, respectively, has shown that the intron sequence structures of the two sets of genes are different. There are more potential binding sites for transcription factors in the introns of the genes with high transcription frequencies. So it is speculated that introns regulate the transcription of genes. But more evidences are needed to favor this speculation. The detailed comparative analyses on the distribution ( length and position) of introns and exons in the two sets of gene sequences also show that there is an obvious boundary between the lengths of the two sets of introns. There is no boundary between the lengths of the two sets of exons, although the means of their lengths are of discrepancy. The situation of the gene lengths ( length of intron and exon) is similar to exon lengths. As far as the relative position, the introns in two sets of genes all have a bias toward the 5' ends of genes. But as the actual position is considered, more introns in high transcription genes have a tendency to be located toward the 5' ends of genes, some even located at 5'-UTR. These results suggest that the gene transcription rates are related to the length of intron, but not to the lengths of exons and genes sequences. The positions of introns may also influence the transcription rates. The transcriptional regulation of introns may be correlative with the transcriptional regulation of the upstream of genes, or be its continuous action.

Statistical analysis of sequence features of introns with positive transcriptional regulation in yeast genes

A great deal of experimental studies have shown that many introns of eukaryotic genes function as regulators of transcription. However, comprehensive studies of this problem have not yet been conducted. After checking the transcription frequencies of some Saccharomyces cerevisiae (yeast), genes and their introns, a remarkable phenomenon was discovered that generally the introns of the genes with higher transcription frequencies are longer, and the introns of the genes with lower transcription frequencies are shorter. This suggests that the longer introns of genes with higher transcription frequencies may contain some characteristic sequence structures, which could enhance the transcription of genes. Therefore, two sets of introns of yeast genes were chosen for further study. The transcription frequencies of the first set of genes are higher (>30), and those of the second set of genes are lower (less than or equal to10). Some oligonucleotides are detected by statistically comparative analyses of the occurrence frequencies of oligonucleotides (mainly tetranucleotides and pentanucleotides), whose occurrence frequencies in the first set of introns; are significantly higher than those in the second set of introns, and are also significantly higher than those in the exons flanking the introns of the first set. Some of these extracted oligonucleotides are the same as the regulatory elements of transcription revealed by experimental analyses. Besides, the distributions of these extracted oligonucleotides in the two sets of introns and the exons show that the sequence structures of the first set of introns are favorable for transcription of genes.

Detection of potential positive regulatory motifs of transcription in yeast introns by comparative analysis of oligonucleotide frequencies

We conducted a comparative statistical analysis of tetra- through hexanucleotide frequencies in two sets of introns of yeast genes. The first set consisted of introns of genes that have transcription rates higher than 30 mRNAs/h while the second set contained introns of genes whose transcription rates were lower than or equal to 10 mRNAs/h. Some oligonucleotides whose occurrence frequencies in the first set of introns are significantly higher than those in the second set of introns were detected. The frequencies of occurrence of most of these detected oligonucleotides are also significantly higher than those in the exons flanking the introns of the first set. Interestingly some of these detected oligonucleotides are the same as well known "signature" sequences of transcriptional regulatory elements. This could imply the existence of potential positive regulatory motifs of transcription in yeast introns. (C) 2003 Elsevier Ltd. All rights reserved.

Body loadings and health risk assessment of polychlorinated dibenzo-p-dioxins and dibenzofurans at an intensive electronic waste recycling site in China

This study is one of the very few investigating the dioxin body burden of a group of child-bearing-aged women at an electronic waste (e-waste) recycling site (Taizhou, Zhejiang Province) (24 +/- 2.83 years of age, 40% were primiparae) and a reference site (Lin'an city, Zhejiang Province, about 245 km away from Taizhou) (24 +/- 2.35 years of age, 100% were primiparae) in China. Five sets of samples (each set consisted of human milk, placenta, and hair) were collected from each site. Body burdens of people from the e-waste processing site (human milk, 21.02 +/- 13.81 pg WHO-TEQ(1998/g) fat (World Health Organization toxic equivalency 1998); placenta, 31.15 +/- 15.67 pg WHO-TEQ(1998/g) fat; hair, 33.82 +/- 17.74 pg WHO-TEQ(1998/g) dry wt) showed significantly higher levels of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurnas (PCDD/Fs) than those from the reference site (human milk, 9.35 +/- 7.39 pg WHO-TEQ(1998/g) fat, placenta, 11.91 +/- 7.05 pg WHO-TEQ(1998/g) fat; hair, 5.59 +/- 4.36 pg WHO-TEQ(1998/g) dry wt) and were comparatively higher than other studies. The difference between the two sites was due to e-waste recycling operations, for example, open burning, which led to high background levels. Moreover, mothers from the e-waste recycling site consumed more foods of animal origin. The estimated daily intake of PCDD/Fs within 6 months by breast-fed infants from the e-waste processing site was 2 times higher than that from the reference site. Both values exceeded the WHO tolerable daily intake for adults by at least 25 and 11 times, respectively. Our results implicated that e-waste recycling operations cause prominent PCDD/F levels in the environment and in humans. The elevated body burden may have health implications for the next generation.

Identification of genome organization in the unusual allotetraploid form of Carassius auratus gibelio

The unusual allotetraploid form with unequal contribution of chromosome sets was discovered from the gynogenetic offspring of Carassius auratus gibelio stimulated by red common carp sperm. In this study, genomic in situ hybridization (GISH) and fluorescent in situ hybridization (FISH) with 45S rDNA probe are used. The GISH results lead to the identification of species-specific chromosomes, which permits to demonstrate the origin and genome organization in the allotetraploid form. Moreover, chromosome localization of 45S rDNA and co-localizations of 45S rDNA and Cyprinus carpio genomic DNA further confirm that one extra 45S rDNA positive chromosome in the allotetraploid form originates from the paternal haploid genome of C carpio, and other 5 45S rDNA-containing chromosomes are from the maternal genome of Carassius auratus gibelio. And, the correlation between 45 rDNA and the nucleolar organizer regions (NORs) is confirmed by silver nitrate staining. The data provide direct experiment evidence that the allotetraploid actually contains three chromosome sets of Carassius auratus gibelio and one chromosome set of C carpio, and will be a useful genetic material for both basic research and breeding practice. (c) 2006 Elsevier B.V. All rights reserved.

Removal of dibutyl phthalate by a staged, vertical-flow constructed wetland

Two sets of small scale systems of staged, vertical-flow constructed wetlands (VFCW) were operated in a greenhouse to study the purification of dibutyl phthalate (DBP) in admeasured water. Each system consisted of two chambers in which water flowed downward in chamber I and then upward in chamber 2. The systems were intermittently fed with wastewater under a hydraulic load of 420 mm(.)d(-1). The measured influent concentrations of DBP in the experimental system were 9.84 mg(.)l(-1), while the other system was used as a control and received no DBP. Effluent concentrations of the treated system averaged 5.82 mug(.)l(-1) and were far below the Chinese DBP discharge standard of less than or equal to0.2 mg(.)l(-1). These results indicate the potential purification capacity of this new kind of constructed wetland in removing DBP from a polluted water body.

Low threshold lasing of GaN-based vertical cavity surface emitting lasers with an asymmetric coupled quantum well active region

We have fabricated and characterized GaN-based vertical cavity surface emitting lasers (VCSELs) with a unique active region structure, in which three sets of InGaN asymmetric coupled quantum wells are placed in a half-wavelength (0.5 lambda) length. Lasing action was achieved under optical pumping at room temperature with a threshold pumping energy density of about 6.5 mJ/cm(2). The laser emitted a blue light at 449.5 nm with a narrow linewidth below 0.1 nm and had a high spontaneous emission factor of about 3.0x10(-2). The results indicate that this active region structure is useful in reducing the process difficulties and improving the threshold characteristics of GaN-based VCSELs.

A full spd tight-binding treatment for electronic bands of graphitic tubes

A tight-binding (TB) treatment with the inclusion of d orbitals is applied to the electronic structures of graphitic tubes. The results show that the high angular moment bases in TB scheme are necessary to account the severe curvature effect in ultra-thin single wall carbon nanotubes, especially for properly reproducing the band edge overlap behavior in (5, 0) tube, predicted by the existing ab initio calculations. In the large diameter limit, the participation of two synnmetry-allowed d bases provides a natural replication to the recent measured electronic dispersions of valence band of graphene when the strong anisotropy due to the two-dimensional planar hexagonal sheet structure is dealt with properly. In addition, the detailed relation between the two sets of quantum numbers of screw symmetry and that of zone folding is formulated in appendix. (C) 2008 Elsevier Ltd. All rights reserved.

One-dimensional quantum waveguide theory of Rashba electrons

The ballistic spin transport in one-dimensional waveguides with the Rashba effect is studied. Due to the Rashba effect, there are two electron states with different wave vectors for the same energy. The wave functions of two Rashba electron states are derived, and it is found that their phase depend on the direction of the circuit and the spin directions of two states are perpendicular to the circuit, with the +pi/2 and -pi/2 angles, respectively. The boundary conditions of the wave functions and their derivatives at the intersection of circuits are given, which can be used to investigate the waveguide transport properties of Rashba spin electron in circuits of any shape and structure. The eigenstates of the closed circular and square loops are studied by using the transfer matrix method. The transfer matrix M(E) of a circular arc is obtained by dividing the circular arc into N segments and multiplying the transfer matrix of each straight segment. The energies of eigenstates in the closed loop are obtained by solving the equation det[M(E)-I]=0. For the circular ring, the eigenenergies obtained with this method are in agreement with those obtained by solving the Schrodinger equation. For the square loop, the analytic formula of the eigenenergies is obtained first The transport properties of the AB ring and AB square loop and double square loop are studied using the boundary conditions and the transfer matrix method In the case of no magnetic field, the zero points of the reflection coefficients are just the energies of eigenstates in closed loops. In the case of magnetic field, the transmission and reflection coefficients all oscillate with the magnetic field; the oscillating period is Phi(m)=hc/e, independent of the shape of the loop, and Phi(m) is the magnetic flux through the loop. For the double loop the oscillating period is Phi(m)=hc/2e, in agreement with the experimental result. At last, we compared our method with Koga's experiment. (C) 2009 American Institute of Physics. [doi: 10.1063/1.3253752]

Magnetointersubband oscillations of the two-dimensional electron gas in AlxGa1-xN/GaN heterostructures

Shubmkov-de Haas (SdH) measurements are performed over a temperature range of 1.5-20K in AL(0.22)Ga(0.78)N/GaN heterostructures with two subbands occupied. In addition to an intermodulation between two sets of SdH oscillations from the first and second subbands, a beating in oscillatory magnetoresistance at 12K is observed, due to the mixing of the first subband SdH oscillations and 'magnetointersubband' (MIS) oscillations. A phase shift of pi between the SdH and MIS oscillations is also clearly identified. Our experimental results, i.e. that the SdH oscillations dominate at low temperature and MIS oscillations dominate at high temperature, fully comply with the expected behaviour of MIS oscillations.

Experimental investigation of photoluminescence dynamics of cavity polaritons under nonresonant excitation

Low-temperature time-resolved photoluminescence (PL) experiments have been performed on a semiconductor planar microcavity, which contains two sets of three In0.13Ga0.87As/GaAs quantum wells embedded in a 3 lambda /2 GaAs cavity. The spontaneous emission dynamics of both lower- and upper-branch polaritons is investigated as a function of exciton-cavity detuning under nonresonant optical excitation. It is found that the PL decay times of both branches are independent of cavity detuning while the PL rising kinetics of the lower- and upper-branch polaritons exhibits a significant difference. The rise time of the upper polarition branch shows a strong dependence on cavity detuning, while the rise time of the lower polarition branch is less sensitive to cavity detuning. Our results can be well understood in the framework of the theoretical prediction of Tassone et al.

Photoluminescence study of InAlAs quantum dots grown on differently oriented surfaces

We reported the optical properties of self-assembled In0.55Al0.45As quantum dots grown by molecular beam epitaxy on (001) and (n11)A/B(n = 3,5)GaAs substrates. Two peaks were observed in the photoluminescence (PL) spectra from quantum dots in the (001) substrate and this suggested two sets of quantum dots different in size. For quantum dots in the high-index substrates, the PL spectra were related to the atomic-terminated surface (A or B substrate). The peaks for the B substrate surfaces were in the lower energy position than that for the (001) and A type. In addition, quantum dots in the B substrate have comparatively high quantum efficiency. These results suggested that high-index B-type substrate is more suitable for the fabrication of quantum dots than (001) and A-type substrates at the same growth condition. (C) 2000 American Vacuum Society. [S0734-211X(00)04701-6].

Influence of (001) vicinal GaAs substrates on the optical properties of defects in low-temperature grown GaAs/AlGaAs multiple quantum wells

Photoluminescence (PL) spectroscopy and carrier lifetime measurement has been used to characterize optical properties of defects in the low-temperature (LT) grown GaAs/AlGaAs multiple quantum well structures. Two sets of samples were grown at 400 degrees C by molecular beam epitaxy on nominal (001) and miscut [4 degrees off (001) towards (111) A] GaAs substrates, respectively. After growth, samples were subjected to 30 s rapid thermal annealing at 600-800 degrees C. It is found that after annealing, two defect-related PL features appear in the samples grown on nominal (001) GaAs substrates, but not in those grown on miscut (001) GaAs substrates. The carrier lifetimes are about 31 and 5 ps in as-grown samples grown on nominal and miscut (001) GaAs substrates, respectively. The different PL spectra and carrier lifetimes in two sets of samples are attributed to different structures of the As-Ga-like defects formed during LT growth. (C) 1999 American Institute of Physics. [S0003-6951(99)00230-2].

Self-organization of the InGaAs GaAs quantum dots superlattice

The mechanism of self-organization of quantum dots (QDs) during the growth of InGaAs/GaAs multilayers on GaAs (1 0 0) was investigated with cross-sectional transmission electron microscopy (XTEM), and double-crystal X-ray diffraction (DCXD). We found that the QDs spacing in the first layer can affect the vertical alignment of QDs. There seems to exist one critical lateral QD spacing, below which merging of QDs with different initial size is found to be the dominant mechanism leading to perfect vertical alignment. Once the critical value of QDs spacing is reached, the InGaAs QDs of the first layer are simply reproduced in the upper layers. The X-ray rocking curve clearly shows two sets of satellite peaks, which correspond to the QDs superlattice, and multi-quantum wells (QW) formed by the wetting layers around QDs. (C) 1999 Elsevier Science B.V. All rights reserved.

Structural characterization of InGaAs/GaAs quantum dots superlattice infrared photodetector structures

InGaAs/GaAs quantum dots (QDs) superlattice grown by molecular beam epitaxy (MBE) at different substrate temperatures for fabricating 8-12 mu m infrared photodetector were characterized by transmission electron microscopy (TEM), double-crystal X-ray diffraction (DCXRD) and photoluminescence (PL). High-quality QDs superlattice can be achieved by higher growth temperature. Cross-sectional TEM shows the QDs in the successive layers are vertically aligned along growth direction. Interaction of partial vertically aligned columns leads to a perfect vertical ordering. With increasing number of bilayers, the average QDs size becomes larger in height and rapidly saturates at a certain value, while average lateral length nearly preserves initial size. This change leads to the formation of QDs homogeneous in size and of a particular shape. The observed self-organizations are attributed to the effect of strain distribution at QDs on the kinetic growth process. DCXRD measurement shows two sets of satellite peaks which corresponds to QDs superlattice and multi quantum wells formed by the wetting layers. Kinematical simulations of the wetting layers indicate that the formation of QDs is associated with a decrease of the effective indium content in the wetting layers. (C) 1999 Elsevier Science B.V. All rights reserved.