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.

Statistical correlation between protein secondary structure and messenger RNA stem-loop structure

Anew integrated sequence-structure database, called IADE (Integrated ASTRAL-DSSP-EMBL), incorporating matching mRNA sequence, amino acid sequence, and protein secondary structural data, is constructed. It includes 648 protein domains. Based on the IADE database, we studied the relation between RNA stem-loop frequencies and protein secondary structure. It was found that the alpha-helices and beta-strands on proteins tend to be preferably "coded" by mRNA stem region, while the coils on proteins tend to be preferably "coded" by mRNA loop region. These tendencies are more obvious if we observe the structural words (SWs). An SW is defined by a four-amino-acid-fragment that shows the pronounced secondary structural (alpha-helix or beta-strand) propensity. It is demonstrated that the deduced correlation between protein and mRNA structure can hardly be explained as the stochastic fluctuation effect. (C) 2003 Wiley Periodicals, Inc.

Population dynamics and maturation cycle of Camallanus cotti (Nematoda : Camallanidae) in the Chinese hooksnout carp Opsariichthys bidens (Osteichthyes : Cyprinidae) from a reservoir in China

The seasonal population dynamics and maturation cycle of the nematode Camallanus cotti in the posterior intestine of Chinese hooksnout carp Opsariichthys bidens have been studied in the Danjiangkou Reservoir of the Hubei Province in central China from September 2004 to November, 2005. The overall prevalence, mean abundance and intensity of C cotti among fish sampled (n = 700 fish) were 47%, 2.29 +/- 12.38 ( +/- S.D.) and 1-307 (average 4.89 +/- 17.74), respectively. The overall sexual ratio of female to male nematodes (excluding L3 and L4 juveniles) was 1.17:1. Statistical results showed weakly positive correlations betweerl fish length and the number of nematodes per host. The dynamics of infection of the nematode exhibited significant seasonal pattern in changes in mean abundance. A similar pattern was found for changes in nematode prevalence, although this was not statistically significant. Higher levels of infection were observed among fish sampled in summer months and the lower in the winter. Neither the prevalence nor the abundance of the parasite was significantly different between male and female hosts. The pattern of frequency distribution of the parasite in the host was found to be over-dispersed throughout the sampling period. In addition, studies on the development and maturation of the parasite in O. bidens revealed that development (maturation), recruitment of the next generation, and reproduction may be continuous year-round, although reproduction may peak during the winter. (c) 2007 Elsevier B.V. All rights reserved.

Peak identification for PCDD/Fs in environmental samples at different temperature programs

A method has been developed for peak recognition of 136 polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) at different temperature programs. Their retention behaviours are predicted on the basis of an identification database of retention values (A, B) of gas chromatography. By the retention times of C-13 labelled 2,3,7,8-substituted PCDD/F internal standards, the retentions of all PCDDs and PCDFs can be calculated. After comparison with the retentions of practical environmental samples, the predicted values have been proved to be very accurate. (C) 2000 Elsevier Science Ltd. All rights reserved.

Computer assisted peak recognition for polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF) in environmental samples

A software has been developed for the peak recognition of 136 polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF) after high resolution gas chromatography coupled with mass spectrometry (HRGC/HRMS). Based on the retention times of C-13 labelled 2,3,7,8-substituted PCDD/F internal standards, the retention times of all PCDD and PCDF can be calibrated automatically and accurately. Therefore, it is very convenient to identify the peaks by comparing the retention of samples and the calibrated retention times of their chromatograms. Hence, this approach is very significant because it is impossible to obtain always a standard chromatogram and PCDD/F analysis are very expensive and time consuming. The calibration results can be transferred to Excel for calculation. The approach is a first step to store costly and environmentally relevant data for future application.

IMPROVED PEAK POWER METHOD FOR MEASURING FREQUENCY RESPONSES OF PHOTODETECTORS IN A SELF-HETERODYNE SYSTEM

An improved peak power method for measuring frequency responses of photodetectors in a self-heterodyne system consisting of a distributed Bragg reflector laser is proposed. The time-resolved spectrum technique is used to measure the peak power of the beat signal and the intrinsic linewidth of heat signal for calibration. The experimental results show that the impact of the thermal-induced frequency drift, which is the main reason for producing an error in measurement by conventional peak power method and spectrum power method, can be removed.

ac gate-induced Fano resonance and peak splitting of conductance in a quantum dot

We have investigated the conductance of a quantum dot system suffering an anti-symmetric ac gate voltage which induces the transition between dot levels in the linear regime at zero temperature in the rotating wave approximation. Interesting Fano resonances appear on one side of the displaced resonant tunnelling peaks for the nonresonant case or the peak splitting for the resonant case. The line shape of conductance (vs Fermi energy) near each level of the quantum dot can be decomposed into two profiles: a Breit-Wigner peak and a Fano profile, or a Breit-Wigner peak and a dip in both cases.

Gain measurement and anomalous decrease of peak gain at long wavelength for InAs/GaAs quantum-dot lasers

Mode gain spectrum is measured by the Fourier series expansion method for InAs/GaAs quantum-dot (QD) lasers with seven stacks of QDs at different injection currents. Gain spectra with distinctive peaks are observed at the short and long wavelengths of about 1210 nm and 1300 nm. For a QD laser with the cavity length of 1060 mu m, the peak gain of the long wavelength first increases slowly or even decreases with the injection current as the peak gain of the short wavelength increases quickly, and finally increases quickly before approaching the saturated values as the injection current further increases.

Nanoelectronic devices-resonant tunnelling diodes grown on InP substrates by molecular beam epitaxy with peak to valley current ratio of 17 at room temperature

This paper reports that lnAs/In0.53Ga0.47As/AlAs resonant tunnelling diodes have been grown on InP substrates by molecular beam epitaxy. Peak to valley current ratio of these devices is 17 at 300K. A peak current density of 3kA/cm(2) has been obtained for diodes with AlAs barriers of ten monolayers, and an In0.53Ga0.47As well of eight monolayers with four monolayers of InAs insert layer. The effects of growth interruption for smoothing potential barrier interfaces have been investigated by high resolution transmission electron microscope.

A differential recursive scheme for suppression of Peak to average power ratio for OFDM

A differential recursive scheme for suppression of Peak to average power ratio (PAPR) for Orthogonal frequency division multiplexing (OFDM) signal is proposed in this thesis. The pseudo-randomized modulating vector for the subcarrier series is differentially phase-encoded between successive components in frequency domain first, and recursion manipulates several samples of Inverse fast Fourier transformation (IFFT) output in time domain. Theoretical analysis and experimental result exhibit advantage of differential recursive scheme over direct output scheme in PAPR suppression. And the overall block diagram of the scheme is also given.

Anomalous temperature dependence of photoluminescence peak energy in InAs/InAlAs/InP quantum dots

We have observed an unusual temperature sensitivity of the photoluminescence (PL) peak energy for InAs quantum dots grown on InAs quantum wires (QDOWs) on InP substrate. The net temperature shift of PL wavelength of the QDOWs ranges from 0.8 to -4. angstrom/degrees C depending upon the Si doping concentration in the samples. This unusual temperature behavior can be mainly ascribed to the stress amplification in the QDOWs when the thermal strain is transferred from the surrounding InAs wires. This offers an opportunity for realizing quantum dot laser devices with a temperature insensitive lasing wavelength. (c) 2006 Elsevier Ltd. All rights reserved.

High-resolution X-ray diffraction analysis of the Bragg peak integrated intensity in highly mismatched III-N epilayers

A new method of measuring the thickness of GaN epilayers on sapphire (0 0 0 1) substrates by using double crystal X-ray diffraction was proposed. The ratio of the integrated intensity between the GaN epilayer and the sapphire substrate showed a linear relationship with the GaN epilayer thickness up to 2.12 mum. It is practical and convenient to measure the GaN epilayer thickness using this ratio, and can mostly eliminate the effect of the reabsorption, the extinction and other scattering factors of the GaN epilayers. (C) 2003 Elsevier Science B.V. All rights reserved.

Statistical investigation on morphology development of gallium nitride in initial growth stage

Morphology of Gallium Nitride (GaN) in initial growth stage was observed with atomic force microscopy (AFM) and scanning electron microscopy (SEM), It was found that the epilayer developed from islands to coalesced film. Statistics based on AFM observation was carried out to investigate the morphology characteristics. It was found that the evolution of height distribution could be used to describe morphology development. Statistics also clearly revealed variation of top-face growth rate among islands. Indium-doping effect on morphology development was also statistically studied. The roughening and smoothing behavior in morphology development was explained. (C) 2002 Elsevier Science B.V. All rights reserved.