Identification and characterization of insect-specific proteins by genome data analysis

Background: Insects constitute the vast majority of known species with their importance including biodiversity, agricultural, and human health concerns. It is likely that the successful adaptation of the Insecta clade depends on specific components in its

Data analysis for pump-probe experiment with femtosecond pulses

Various analytical physical models are presented to extract the photodissociation dynamics information from the data obtained in the femtosecond pump-probe experiment. The single- and double-component models are employed to explain the single- and double-channel dissociation of parent molecules. Another single-component model for fragment dissociation or deexcitation is also presented. All cases are explanatorily demonstrated on the pump-probe experimental data.

Sequencing, annotation and comparative analysis of nine BACs of giant panda (Ailuropoda melanoleuca)

A 10-fold BAC library for giant panda was constructed and nine BACs were selected to generate finish sequences. These BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of giant panda newly generated by the Illumina GA sequencing technology. Complete sanger sequencing, assembly, annotation and comparative analysis were carried out on the selected BACs of a joint length 878 kb. Homologue search and de novo prediction methods were used to annotate genes and repeats. Twelve protein coding genes were predicted, seven of which could be functionally annotated. The seven genes have an average gene size of about 41 kb, an average coding size of about 1.2 kb and an average exon number of 6 per gene. Besides, seven tRNA genes were found. About 27 percent of the BAC sequence is composed of repeats. A phylogenetic tree was constructed using neighbor-join algorithm across five species, including giant panda, human, dog, cat and mouse, which reconfirms dog as the most related species to giant panda. Our results provide detailed sequence and structure information for new genes and repeats of giant panda, which will be helpful for further studies on the giant panda.

Characterization of complex hydrocarbons in cigarette smoke condensate by gas chromatography-mass spectrometry and comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry

Gas chromatography-mass spectrometry with electron ionization and positive-ion chemical ionization and comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC x GC-TOF-MS) were applied for the characterization of the chemical composition of complex hydrocarbons in the non-polar neutral fraction of cigarette smoke condensates. Automated data processing by TOF-MS software combined with structured chromatograms and manual review of library hits were used to assign the components from GC x GC-TOF-MS analysis. The distributions of aliphatic hydrocarbons and aromatics were also investigated. Over 100 isoprenoid hydrocarbons were detected, including carotene degradation products, phytadiene isomers and carbocyclic diterpenoids. A total of 1800 hydrocarbons were tentatively identified, including aliphatic hydrocarbons, aromatics, and isoprenoid hydrocarbons. The identified hydrocarbons by GC x GC-TOF-MS were far more than those by GC-MS. (C) 2004 Elsevier B.V. All rights reserved.

Phosphoproteome analysis of mouse liver using immobilized metal affinity purification and linear ion trap mass spectrometry

Since protein phosphorylation is a dominant mechanism of information transfer in cells, there is a great need for methods capable of accurately elucidating sites of phosphorylation. In recent years mass spectrometry has become an increasingly viable alternative to more traditional methods of phosphorylation analysis. The present study used immobilized metal affinity chromatography (IMAC coupled with a linear ion trap mass spectrometer to analyze phosphorylated proteins in mouse liver. A total of 26 peptide sequences defining 26 sites of phosphorylation were determined. Although this number of identified phosphoproteins is not large, the approach is still of interest because a series of conservative criteria were adopted in data analysis. We note that, although the binding of non-phosphorylated peptides to the IMAC column was apparent, the improvements in high-speed scanning and quality of MS/MS spectra provided by the linear ion trap contributed to the phosphoprotein identification. Further analysis demonstrated that MS/MS/MS analysis was necessary to exclude the false-positive matches resulting from the MS/MS experiments, especially for multiphosphorylated peptides. The use of the linear ion trap considerably enabled exploitation of nanoflow-HPLC/MS/MS, and in addition MS/MS/MS has great potential in phosphoproteome research of relatively complex samples. Copyright (C) 2004 John Wiley Sons, Ltd.

Application of digital image analysis to the study of banded spherulite during growing and melting process

A digital image analysis(DIA) technique can be applied directly to the image obtained by polarizing microscope. The time-resolved DIA apparatus including image collecting, showing and data analysis has been home-made. As an example, it has been used to study the banded spherulite in the blends of poly(epsilon-caprolactone) (PCL) and poly(styrene-ran-acrylonitrile) (SAN).

填土边坡水文作用机理与破坏过程研究—以深圳羊宝地填土滑坡为例

A full understanding of failure mechanism, critical hydrological condition, and process of mobilization and deposition of a landslide is essential for optimal design of stabilization measure and forecasting of landslide hazard. This requires a quantitative study of hydrological response of a slope to rainfall through field monitoring, laboratory test and numerical modelling. At 13:40 on September 18, 2002, a fill slope failed following a period of prolonged rain in Shenzhen, resulting in 5 fatalities and 31 injuries. The failed mass with a volume about 2.5×104m3 traveled about 140m on level ground. Field monitoring, laboratory test, theoretical analysis and numerical modelling were carried out to undestand the hydrological response and failure mechanism of this fill slope. This thesis mainly focuses on the following aspects: (1) The hydrological responses and failure processes of slopes under rainfall infiltration were reviewed. Firstly, the factors influencing on the hydrological responses of slopes were analysed. Secondly, the change of stress state of slope soil and modelling methods of slope failure under rainfall infiltration were reviewed. (2) The characteristics of the Yangbaodi landslide and associated rainfall triggering the failure were presented. The failure was characterized by shallow flowslide, due to an increase of ground water table caused by rainfall infiltration. (3) A fully automated instrumentation was carried out to monitor rainfall, and saturated – unsaturated hydrological response of the fill slope, using a raingauge, piezometers, tensiometers and moisture probes. A conceptual hydrogeological model was presented based on field monitoring and borehole data. Analysis of monitoring data showed that the high pore water pressure in fill slope was caused by upward flow of semiconfined groundwater in the moderately decomposed granite. (4) Laboratory and in-situ testing was performed to study the physical and mechanical properties of fills. Isotropically consolidated undrained compression tests and anisotropically consolidated constant shear stress tests were carried out to understand the failure mechanism of the fill slope. It is indicated that loosely compacted soil is of strain-softening behaviour under undrained conditions, accompanied with a rapid increase in excess pore water pressure. In anisotropically consolidated constant shear stress tests, a very small axial strain was required to induce the failure and the excess pore water pressure increased quickly at failure. This indicated that static liquefaction caused by rise in groundwater table due to rainfall infiltration occurred. (5) The hydraulic conductivity of the highly and moderately decomposed granite was estimated using monitering data of pore water pressure. A saturated – unsaturated flow was modeled to study the hydrological response of the fill slope using rainfall records. It was observed that the lagged failure was due to the geological conditions and the discrepancy of hydraulic conductivity of slope soils. The hydraulic conductivity of moderately decomposed granite is relatively higher than the other materials, resulting in a semiconfied groundwater flow in the moderately decomposed granite, and subsequent upward flow into the upper fill layer. When the ground water table in the fill layer was increased to the critical state, the fill slope failed. (6) Numerical exercises were conducted to replay the failure process of the fill slope, based on field monitoring, laboratory and in-situ testing. It was found that the fill slope was mobilized by a rapid transfer of the concentrated shear stress. The movement of failure mass was characterized by viscosity fluid with a gradual increase in velocity. The failure process, including mobilization and subsequent movement and deposition, was studied using numerical methods.