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.

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).

金川镍矿岩体移动与开采稳定性研究

The two major issues in mining industry are work safety and protection of ground environment when carrying on underground mining activities. Cut-and-fill mining method is increasingly applied in China owing to its advantages of controlling ground pressure and protecting the ground environment effectively. However, some cut-and-fill mines such as Jinchuan nickel mine which has big ore body, broken rock mass and high geostress have unique characteristics on the law of ground pressure and rock mass movement that distinguish from other mining methods. There are still many problems unknown and it is necessary for the further analysis. In this dissertation, vast field survey, geology trenching and relative data analysis are carried out. The distribution of ground fissures and the correlation of the fissures with the location of underground ore body is presented. Using of monitoring data by three-dimension fissure meter and GPS in Jinchuan Deposit Ⅱ, the rule of the surface deformation and the reason of ground fissures generation are analyzed. It is shown that the stress redistribution in surrounding rocks resulting from mining, the existence of the void space underground and the influence of on-going mining activities are three main reasons for the occurrence of ground fissures. Based on actual section planes of No.1 ore body, a large-scale 3D model is established. By this model, the complete process of excavation and filling is simulated and the law of rock mass movement and stability caused by Cut-and-fill Mining is studied. According to simulation results, it is concluded that the deformation of ground surface is still going on developing; the region of subsidence on the ground surface is similar with a circle; the area on the hanging wall side is larger than one on the lower wall side; the contour plots show the centre of subsidence lay on the hanging wall side and the position is near the ore body boundary of 1150m and 1250m where ore body is the thickest. Along strike-line of Jinchuan Deposit Ⅱ, the deformation at the middle of filling body is larger than that in the two sides. Because of the irregular ore body, stress concentrates at the boundary of ore body. With the process of excavation and filling, the high stress release and the stress focus disappear on the hanging wall side. The cut-and-fill mechanism is studied based on monitoring data and numerical simulation. The functions of filling body are discussed. In this dissertation, it is concluded that the stress of filling body is just 2MPa, but the stress of surrounding rock mass is 20MPa. We study the surface movement influenced by the elastic modulus of backfill. The minimal value of the elastic modulus of backfill which can guarantee the safety production of cut-and-fill mine is obtained. Finally, based on the real survey results of the horizontal ore layer and numerical simulation, it is indicated that the horizontal ore layer has destroyed. Key words: cut-and-filling mining, 3D numerical simulation, field monitoring, rock mass movement, cut-and-filling mechanism, the elastic modulus of backfill, the horizontal ore layer

金川矿山岩体移动规律及竖井变形、破坏机理研究

The Jinchuan Nickel Mine is the largest underground mine with cut-and-fill mining in China. It is very difficult to be exploited for very low safety stability of rock mass caused by complex geological conditions, developed faults, cracked rock mass and high stress. In this paper, the laws of rock mass movement、mechanics of shaft deformation and destroy were analyzed based on the collection of date, the detailed field engineering investigations, ground movement monitoring by GPS, theoretical analysis and numerical simulation. According to the GPS monitoring result of ground surface movement, there are different ground movement characteristics among the three Mine area of Jinchuan Nickel Mine. In No. 2 Mine area, the ground movement funnel with apparent asymmetry is developing, the influence scope is larger in the up faulted block than in the down faulted block, and the centre of ground movement is moving along the up faulted block direction with increasing depth of mining. Moreover, the tunnels in the corresponding area with the centre of ground movement are damaged seriously. In Longshou Mine area, the ground movement funnel is also developing, but the moving path and the nonlinear characters are more sophisticated because of the long-term effects of open excavating and the effects of underground mining together. In No. 3 Mine area, the underground mining impact on surface is not serious for the time of mining activity is not for long, but the ground movement funnel is also forming now. The underground mining has caused widespread land subsidence in Jinchuan Nickel Mine area, but the phenomena of surface raise appeared in some partial areas of Longshou Mine area and No. 3 Mine area. Analysis proved that the reason for the open pit bottom raise is the slope deformation activation caused by the excavation from open pit into underground mine; and that the raise of surface in No.3 Mine area is caused by the effect of elastic foundation due to underground mining. Although the GPS Monitoring results show the amount of subsidence is increasing constantly, the subsidence rate has a descending tendency with fluctuation in Jinchuan No. 2 Mine area. The subsidence rate curve is a time function and exists an extreme point, the rate increasing before extreme point and decreasing after the extreme point ,but the scale of decreasing rate will be very small after the rate decreasing up to a certain degree, moreover, the characteristics is different among different areas, which have some relation with the distance to the mining section and the dip of the ore body. ArcView is GIS software, which we adopted as a development platform, and made secondary development by its development language “avenue”, through which we developed a ground movement analysis and forecast System for Jinchuan Nickel Mine, which contain three modules : management of ground movement information; analysis and evaluation of ground movement; and ground movement forecast. In the module of evaluation, using the technique of MATLAB6.5 program with VB6.0, the system can achieve the ANN prediction model for GPS monitoring data, data preparation results analysis and model integrated was realized by Avenue programming. Finally, the author analyzed the mechanical of deformation and destroy of the No. 14 shaft, and its repair and artificial-support effectiveness also given detailed demonstration in various aspect. The result showed that the reason for the destroy of No. 14 shaft is underground mining, and being the case, the destroy of the shaft also has its special features, which mainly contains forked stress contour for mining steep ore and fault effect caused by mining activities. The repair and artificial-support played some restrictions on the rock mass movement and deformation, but did not show a strong or marked effect. With the increasing of mining depth and large-scale, the closure rock of the shaft will still deformed, even be destroyed.

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.

沾化凹陷泥质岩油气藏成藏特征研究

Mudstone reservoir is a subtle reservoir with extremely inhomogeneous, whose formation is greatly related to the existence of fracture. For this kind of reservoir, mudstone is oil source rock, cover rock and reservoir strata, reservoir type is various, attitude of oil layer changes greatly, and the distribution of oil and gas is different from igneous or clastic rock reservoir as well as from carbonate reservoir of self-producing and self-containing of oil and gas. No mature experience has been obtained in the description, exploration and development of the reservoir by far. Taking Zhanhua depression as an example, we studied in this thesis the tectonic evolution, deposit characteristics, diagenesis, hydrocarbon formation, abnormal formation pressure, forming of fissure in mudstone reservoir, etc. on the basis of core analysis, physical simulation, numerical simulation, integrated study of well logging and geophysical data, and systematically analyzed the developing and distributing of mudstone fissure reservoir and set up a geological model for the formation of mudstone fissure reservoir, and predicted possible fractural zone in studied area. Mudstone reservoir mainly distributed on the thrown side of sedimentary fault along the sloping area of the petroleum generatiion depression in Zhanhua depression. Growing fault controlled subsidence and sedimentation. Both the rate of subsidence and thickness of mudstone are great on the thrown side of growing fault, which result in the formation of surpressure in the area. The unlocking of fault which leads to the pressure discharges and the upward conduct of below stratum, also makes for the surpressure in mudstone. In Zhanhua depression, mudstone reservior mainly developed in sub-compacted stratum in the third segment of Shahejie formation, which is the best oil source rock because of its wide spread in distribution, great in thickness, and rich in organic matter, and rock types of which are oil source mudstone and shale of deep water or semi-deep water sediment in lacustrine facies. It revealed from core analysis that the stratum is rich in limestone, and consists of lamina of dark mudstone and that of light grey limestone alternately, such rock assemblage is in favor of high pressure and fracture in the process of hydrocarbon generation. Fracture of mudstone in the third segment of Shahejie formation was divided into structure fracture, hydrocarbon generation fracture and compound fracture and six secondary types of fracture for the fist time according to the cause of their formation in the thesis. Structural fracture is formed by tectonic movement such as fold or fault, which develops mainly near the faults, especially in the protrude area and the edge of faults, such fracture has obvious directivity, and tend to have more width and extension in length and obvious direction, and was developed periodically, discontinuously in time and successively as the result of multi-tectonic movement in studied area. Hydrocarbon generation fracture was formed in the process of hydrocarbon generation, the fracture is numerous in number and extensively in distribution, but the scale of it is always small and belongs to microfracture. The compound fracture is the result of both tectonic movement and hydrocarbon forming process. The combination of above fractures in time and space forms the three dimension reservoir space network of mudstone, which satellites with abnormal pressure zone in plane distribution and relates to sedimentary faces, rock combination, organic content, structural evolution, and high pressure, etc.. In Zhanhua depression, the mudstone of third segment in shahejie formation corresponds with a set of seismic reflection with better continuous. When mudstone containing oil and gas of abnormal high pressure, the seismic waveform would change as a result of absorb of oil and gas to the high-frequency composition of seismic reflection, and decrease of seismic reflection frequency resulted from the breakage of mudstone structure. The author solved the problem of mudstone reservoir predicting to some degree through the use of coherent data analysis in Zhanhua depression. Numerical modeling of basin has been used to simulate the ancient liquid pressure field in Zhanhua depression, to quantitative analysis the main controlling factor (such as uncompaction, tectonic movement, hydrocarbon generation) to surpressure in mudstone. Combined with factual geologic information and references, we analyzed the characteristic of basin evolution and factors influence the pressure field, and employed numerical modeling of liquid pressure evolution in 1-D and 2-D section, modeled and analyzed the forming and evolution of pressure in plane for main position in different periods, and made a conclusion that the main factors for surpressure in studied area are tectonic movement, uncompaction and hydrocarbon generation process. In Zhanhua depression, the valid fracture zone in mudstone was mainly formed in the last stage of Dongying movement, the mudstone in the third segment of Shahejie formation turn into fastigium for oil generation and migration in Guantao stage, and oil and gas were preserved since the end of the stage. Tectonic movement was weak after oil and gas to be preserved, and such made for the preserve of oil and gas. The forming of fractured mudstone reservoir can be divided into four different stages, i.e. deposition of muddy oil source rock, draining off water by compacting to producing hydrocarbon, forming of valid fracture and collecting of oil, forming of fracture reservoir. Combined with other regional geologic information, we predicted four prior mudstone fracture reservoirs, which measured 18km2 in area and 1200 X 104t in geological reserves.