基于ITS 序列和matK 基因序列的中国药用石斛及其混伪品的分子鉴定

为了从分子水平对中国药用石斛及其混伪品进行鉴定，本文选取了核rDNA ITS 序列和叶绿体DNA 的matK 基因序列进行研究。采用改良的CTAB 法提取石斛的基因组DNA，PCR 产物直接测序法对17 种（共32 份）药用石斛的核糖体内转录间隔区ITS 全序列进行测定，克隆测序法对12 种（共22 份）药用石斛的叶绿体的matK 基因序列进行测定，运用BioEd it，MEGA4.0 等生物软件分析了石斛属植物的rDNA ITS 序列及叶绿体的matK 基因序列的特征，比较了石斛属间、种间、种内不同居群（品种）间的序列碱基差异及遗传距离，应用邻接法构建分子系统树。主要研究结果如下： （1）建立了17 种（共32 份）药用石斛rDNA ITS 区碱基全序列数据库，其中，ITS1 的长度为228~234 bp，GC 含量为45.7%~53.0%，变异位点167 个，占总位点67.34%，信息位点106 个，占总位点42.74%，ITS2 长度为241~247 bp，GC含量为44.8%~55.7%，变异位点165 个，占总位点66.27%，信息位点115 个，占总位点46.18%。 （2）建立了12 种（共22 份）药用石斛的叶绿体matK 基因全序列数据库，叶绿体matK 基因长1410 bp，变异位点51 个，信息位点11 个。除了存在碱基替换的遗传变异外，还存在碱基的插入和缺失。 （3）通过ITS 序列比较分析了各材料间的遗传距离和碱基差异，属间的遗传距离为0.295，石斛种间的平均遗传距离为0.142，碱基相差2~156 个，种内各居群间的平均遗传距离为0.002，碱基相差1~2 个。属间的遗传距离大于种间的遗传距离，种间的遗传距离大于种内不同居群（品种）间的遗传距离。 （4）根据分析石斛叶绿体的matK 基因序列得到，外类群（密花石豆兰）与石斛属间最小遗传距离为0.027，石斛种间的平均遗传距离为0.008，种间最大的遗传距离0.014， 最小的遗传距离为0.003，碱基相差8~20 个。种内不同居群（品种）遗传距离为0.001，相差1~5 个碱基。 （5）利用17 种石斛的全序列数据库及遗传分析软件，通过对待检种rDNA I TS区进行序列测定，成功地对10 个待检种进行了鉴定，并且在原植物开花后得到了验证。 （6）运用12 种石斛的matK 基因全序列数据库及遗传分析软件，成功地对4个待检种进行了鉴定，同样在原植物开花后得到了验证。 （7）本文利用石斛的核糖体内转录间隔区ITS 序列和叶绿体的matK 基因序列数据库分别构建了NJ 树，外类群与石斛属间石斛种间以及种内不同居群（品种）间均能在NJ 树中明显分化开来，二者构建的分子系统树一致，为石斛的分子鉴定提供了依据。 In order to identify Chinese Herba Dendrobii and its adulterant species on molecular level, we studied the sequences of rDNA ITS and chloroplast matK gene. Genomic DNA of Dendrobium was extracted using the modified cetyltrimethyl ammonium bromide (CTAB) method. The PCR products of the rDNA ITS sequences of Dendrobium (32 materia ls) were purified and then sequenced. The PCR products of chloroplast matK gene of Dendrobium (22 materia ls) were purified, cloned and then sequenced. The characteristic of the sequences and the genetic dista nce were compared between Bulbophyllum odoratissimum and Dendrobium, Dendrobium interspecies, and different populations. Phylogenetic trees were constructed using the NJ method by the biology softwares including BioEd it, MEGA4.0 etc. The ma in results as follows: (1) It was built up that the database of rDNA ITS sequences of 17 species of Herba Dendrobii (32 materia ls). The ITS1 was 228~234 bp, the GC content accounting for 45.7%~53.0%. Its variable sites were 167, accounting for 67.34%. The Parsim-Informative positions were 106, accounting for 42.74%. The ITS2 was 241~247 bp, the GC accounting for 44.8%~55.7%. The variable sites were 165, accounting for 66.27%. The Parsim-Informative positions were 115, accounting for 46.18%. (2) The database of the chloroplast matK gene sequences was built up, which contained 12 species of Herba Dendrobii (22 materia ls). The matK gene sequences were about 1410bp in length. There were 51 variable sites and 11 Parsim-Informative sites. And there were nucleotides insertions and deletions in some species , in addition to the nucleotides substitutions. (3) The rDNA ITS sequences were compared and analyzed by the biology softwares. The genetic dista nce between Bulbophyllum odoratissimum and Dendrobium was 0.295. The avera ge genetic dista nce was 0.142 between Dendrobium species, and there were 2~156 variable nucleotides. The avera ge genetic dista nce between different populations was 0.002, and there were 2~156 variable nucleotides. The genetic dista nce between Bulbophyllum odoratissimum and Dendrobium was greater tha n that of Denrobium interspecies. Meanwhile, the genetic dista nce between Denrobium species was also greater tha n that of different populations (variaties). (4) The characteristics of the chloroplast matK gene sequences were obtained after analyzing by the biology softwares. The minima l genetic dista nce was 0.027 between Bulbophyllum odoratissimum and Dendrobium . The ma xima l genetic dista nce was 0.014 between Dendrobium species, and there were 20 variable nucleotides. The minima l genetic dista nce between populations was 0.003, and there were 8 variable nucleotides.The genetic dista nce between populations was 0.001, and there were 1~5 variable nucleotides. (5) The molecular Phylogeny tree was constructed on the database of rDNA ITS the sequences of 17 species of Herba Dendrobii using the biology softwares. Then we authenticated 10 materia ls on molecular level. What’s more, they had been proved when these pla nts flowered. (6) The molecular Phylogeny tree was built up on the database of chloroplast matK gene sequences of 12 species of Herba Dendrobii with the biology softwares.Then 4 materia ls were authenticated on molecular level. Moreover, they had also been proved when these pla nts were in flower. (7) The Phylogenetic trees were separately constructed on the sequences of rDNA ITS and chloroplast matK gene B. odoratissimum and Dendrobium all could be distinguished on the Phylogenetic trees. Meanwhile, the Phylogenetic trees based on two groups of sequences were coincident. rDNA ITS and matK gene sequence could be used as molecular markers for authentication of Herba Dendrobii.

基于OSGi的Web容器重构

The OSGi component architecture for software development can better meet the requirements of current Internet environment in scalability, readability and reusability. This paper presents an approach to refactor legacy softwares towards service-oriented systems using the OSGi as the foundation framework. A case study on reconstructing our Web container system is also involved to validate the approach.

Structural analysis of SNARE motifs from sea perch, Lateolabrax japonicus by computerized approaches

Three cDNA sequences encoding four SNARE (N-ethylmaleimide-sensitive fusion protein attachment protein receptors) motifs were cloned from sea perch, and the deduced peptide sequences were analyzed for structural prediction by using 14 different web servers and softwares. The "ionic layer" structure, the three dimensional extension and conformational characters of the SNARE 7S core complex by using bioinformatics approaches were compared respectively with those from mammalian X-ray crystallographic investigations. The result suggested that the formation and stabilization of fish SNARE core complex might be driven by hydrophobic association, hydrogen bond among R group of core amino acids and electrostatic attraction at molecular level. This revealed that the SNARE proteins interaction of the fish may share the same molecular mechanism with that of mammal, indicating the universality and solidity of SNARE core complex theory. This work is also an attempt to get the protein 3D structural information which appears to be similar to that obtained through X-ray crystallography, only by using computerized approaches. (C) 2007 Elsevier Ltd. All rights reserved.

CFX与USAERO的水下机器人操纵性仿真计算研究

研究了借助计算流体力学软件CFX与USAERO对水下机器人的操纵性进行仿真计算的方法,并将仿真计算结果与模型试验结果对比,验证仿真计算的可行性,指出仿真计算的适用范围.该方法可以对某些现实中难以进行的操纵性试验进行仿真计算,对于研究水下机器人的操纵性尤其是在方案设计阶段的操纵性设计和降低试验成本有一定的现实意义.

油气运聚动力学的模拟分析——以准噶尔盆地为例

The petroleum migration, happening in the geologic past, is the very important and complex dynamic processes in the petroleum systems. It plays a linking role among all static factors in a system. The accumulation is in fact the result of the petroleum migration. For the petroleum geology, the dynamics research of the petroleum migration refers to the mechanism and process research, as well as the use of the quantitative methods. In this thesis, combining with the qualitative analysis and quantitative modeling, the author manages to discuss theoretically some key problems dealing with migration processes, which have not been solved yet, and to apply the studied results in petroleum system analysis in actual basins. The basin analysis offers the base of the numerical modeling for geological phenomena occurring in sedimentary basins, that consists of the sedimentary facies analysis, the section reconstructing technique, eroded thickness estimating, etc. The methods to construct the geologic model, which is needed in the research of oil and gas migration and accumulation, are discussed. The basin analysis offers also the possibility for the latter modeling works to get and select the parameters, such as stratum's thickness, age, stratigraphy etc. Modeling works were done by using two basin modeling softwares: Basin_Mod and TPC_Mod. The role of compaction during the secondary migration and the heterogeneity of migrating paths within the clastic carrier are modeled. And the conclusions were applied in the migration studies in the Jungaer Basin, lying on the Northwest part of the China. To construct a reliable migration model, the author studied the characteristics of the sedimentation, the pore fluid pressure evolution, as well as the distribution and the evolution of fluid potential, following the tectonic evolution of the Jungaer Basin. The geochemical prospecting results were used to evidence and to calibrate the migration processes: the oil-source correlation, the distribution of the properties of oil, gas and water. Finally, two important petroleum systems, Permian one and Jurassic one were studied and identified, according, principally, to the studies on the petroleum migration within the Jungaer Basin. Since the oil, as well as the gas, moves mainly in separate phase during the secondary migration, their migrating behaviors would be determined by the dynamics conditions of migration, including the driving forces and pathways. Based on such a consideration, the further understandings may be acquired: the roles played by permeable carriers and low-permeable source rock would be very different in compaction, overpressure generation, petroleum migration, and so on. With the numerical method, the effect of the compaction on the secondary migration was analyzed and the results show that the pressure gradient and the flux resulted from compaction are so small that could be neglected by comparing to the buoyancy of oil. The main secondary migration driving forces are therefore buoyancy and capillary within a hydrostatic system. Modeling with the commercial software-Basin_Mod, the migration pathways of petroleum in clastic carriers seem to be inhomogeneous, controlled by heterogeneity of the driving force, which in turn resulted from the topography of seals, the fabrics and the capillary pressure of the clastic carriers. Furthermore, the direct and indirect methods to study fault-sealing properties in the course of migration were systemically summarized. They may be characterized directly by lithological juxtaposition, clay smear and diagenesis, and indirectly the comparing the pressures and fluid properties in the walls at two apartments of a fault. In Jungaer Basin, the abnormal pressures are found in the formations beneath Badaowan or Baijantan Formation. The occurrence of the overpressure seems controlled by the stratigraphy. The rapid sedimentation, tectonic pressuring, clay sealing, chemical diagensis were considered as the principal pressuring mechanisms. The evolution of fluid pressure is influenced differently at different parts of the basin by the tectonic stresses. So the basin appears different pressure evolution cycles from each part to another during the geological history. By coupling the results of thermal evolution, pressure evolution and organic matter maturation, the area and the period of primary migration were acquired and used to determine the secondary migration time and range. The primary migration in Fengcheng Formation happened from latter Triassic to early Jurassic in the main depressions. The main period of lower-Wuerhe Formation was at latter Jurassic in Changji, Shawan and Pen-1-jing-xi Depression, and at the end of early Cretaceous in Mahu Depression. The primary migration in Badaowan and Sangonghe Formation is at the end of early-Cretaceous in Changji Depression. After then, the fluid potential of oil is calculated at the key time determined from area and time of the primary migration. Generally, fluid potential of oil is high in the depressions and low at the uplifts. Synthetically, it is recognized that the petroleum migration in the Jungaer Basin is very complex, that leads us to classify the evolution of petroleum systems in Northwestern China as a primary stage and a reformed one. The remigration of accumulated petroleum, caused by the reformation of the basin, results in the generation of multiple petroleum systems. The faults and unconformities are usually the linkers among the original petroleum systems. The Permian petroleum system in Jungaer Basin is such a multiple petroleum system. However, the Jurassic petroleum system stays still in its primary stage, thought the strong influences of the new tectonic activities.

大港千米桥地区综合地质地球物理研究

Qianmiqiao buried hill, which is a high-yield burial hill pool, was discovered at Dagang oilfield in 1998. To employ the integrated geological and geophysical research at Qianmiqiao area, it is very valuable and meaningful for the petroleum exploration of Bohai Bay Basin and even the whole country. Based on the previous results, this paper is carried out from the research on Huanghua depression, following the law, i.e. the deep part constrains the shallow, the regional constrains the local, takes the geophysical research in Qianmiqiao oilfield, discusses the formation history of burial hills, burial history, thermal history, the generated and expelling history of hydrocarbon, and migration characteristics, probes into the formation of burial hill pool. This paper uses the gravity and magnetic methods which are based on potential field, with natural sources, configures the inner structure of the earth according to the difference in the density and magnetism of the rock. The geophysical characteristics of Dagang oil field is that it is an area with positive Buge gravity anomal. The upheaval of Moho boundary is in mirror symmetry with the depression of the basin's basement. The positive and negative anomaly distributein axis symmetry, and the orientation is NNE. The thickness of the crust gradually reduces from west to east, from land to sea. The depth gradient strip of Curie surface is similar to Moho boundary, whereas their local buried depth is different. Local fractures imply that the orientation of base rock fractures is NNE-NE, and the base rock is intersected by the fractures of the same/ later term, whose orientation is NW, so the base rock likes rhombic mosaic. The results of tomography show that there exists significant asymmetry in vertical and horizontal direction in the velocity configuration of Huanghua depression. From Dezhou to Tianjin, there exits high-speed block, which extends from south to north. The bottom of this high-speed block is in good agreement with the depth of Moho boundary. Hence we can conclude that the high-speed block is actually the crystal basement. According to seismic data, well data and outcrop data, Huanghua depression can be divided into four structure layers, i.e. Pi,2-T, Ji,2-K, E, N-Q. Qianmiqiao burial hills undergo many tectonic movement, where reverse faults in developed in inner burial hill from Indosinian stage to Yanshanian stage, the normal faults extended in Himalayan stage. Under the influence of tectonic movements, the burial hills show three layers, i.e. the reverse rushing faults in buried hills, paleo-residual hill, and extended horst block. The evolution of burial hills can be divided into four stages: steady raising period from Calenonian to early Hercynian, rushing brake drape period from Indosinian to middle Yanshanian, block tilting period in early Tertiary, and heating depression period from late Tertiary to Quaternary. The basin modeling softwares BasinMod 1-D and Basin 2-D, which are made by PRA corporation, are used in this paper, according to the requirement, corresponding geological model is designed. And we model the burial history, thermal history, hydrocarbon generation and hydrocarbon expelling history of Qianmiqiao area. The results show that present bury depth is the deepest in the geological history, the sedimentary rate of Tertiary is highest and its rising rate of temperature rate is higher. During sedimentary history, there is no large erosion, and in the Tertiary, the deeper sediment was deposited in large space, therefore it is in favor of the conservation and transformation of oil and gas. The thermal research shows that the heat primarily comes from basement of the basin, present geotherm is the highest temperature in the geological history. Major source rock is the strata of ES3, whose organic is abundant, good-typed, maturative and of high-expulsive efficiency. The organic evolution of source rock of O has come to the overmature stage, the evolving time is long and the source rock can be easily destroyed. Therefore it is more difficult for the O formation source rock to form the huge accumulation of oil and gas than Es3 formation. In the research of oil assembling, we first calculated the characteristics of the fluid pressure of single well, then analyzed the distribution of the surplus fluid pressure of each formation and profile, and probe the first hydrocarbon migration situation and the distribution of pressure system of buried hill pool. In every formation, the pressure system of each burial hill has its own characteristics, e.g. high pressure or low pressure. In the research of secondary migration, the fluid potential is calculated while the relative low potential area is figured out. In Qianmiqiao area, the west margin faults have the low potential, and hence is the favorable reconnoiter belt.

油藏数值模拟中的网格粗化和细化技术研究

The grid is a foundation of reservoir description and reservoir simulation. The scale of grid size is vital influence for the precision of reservoir simulation the gridding of reservoir parameters require reasonable interpolation method with computing quickly and accurately. The improved distant weighted interpolation method has many properties, such as logical data points selection, exact interpolation, less calculation and simply programming, and its application can improve the precision of reservoir description and reservoir simulation. The Fractal geologic statistics describes scientifically the distribution law of various geological properties in reservoir. The Fractal interpolation method is applied in grid interpolation of reservoir parameters, and the result more accorded with the geological property and configuration of reservoir, and improved the rationality and quality of interpolation calculation. Incorporating the improved distant weighted interpolation method with Fractal interpolation method during mathematical model of grid-upscaling and grid-downscaling, the softwares of GROUGH(grid-upscaling) and GFINE (grid-downscaling) were developed aiming at the questions of grid-upscaling and grid-downscaling in reservoir description and reservoir simulation. The softwares of GROUGH and GFINE initial applied in the research of fined and large-scale reservoir simulation. It obtained fined distribution of remaining oil applying grid-upscaling and grid-downscaling technique in fined reservoir simulation of Es21-2 Shengtuo oilfield, and provided strongly and scientific basis for integral and comprehensive adjustment. It's a giant tertiary oil recovery pilot area in the alkaline/surfactant/polymer flooding pilot area of west district of Gudao oilfield, and first realized fined reservoir simulation of chemical flooding using grid-upscaling and grid-downscaling technique. It has wide applied foreground and significant research value aiming at the technique of grid-upscaling and grid-downscaling in reservoir description and reservoir simulation.