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Development Of IMIRS Software Package And Preliminary 3D Reconstruction Of Cytoplasmic Polyhedrosis Virus By Using IMIRS

Posted on:2003-11-13Degree:DoctorType:Dissertation
Country:ChinaCandidate:Y Y LiangFull Text:PDF
GTID:1100360155961901Subject:Biophysics
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Recently, the technology of high-resolution 3D reconstruction by using cryo-electron microscopy instrumentation gets more and more advanced achievements. Firstly, it is because of the implement of high voltage cryoEM with field emission source. Nowadays, in the low electron dose condition, the information about 3-4? can be recorded on the cryoEM micrograph, and the high-resolution reconstruction using the cryoEM has reached 6.5-8? levels. The reconstruction can reveal the protein αhelical and recognise βfold secondary structure. Secondly, it is due to the development in 3D reconstruction method, which can be more efficient to determine the orientation and center parameters. The last but not least, it is also owning to the rapid development in computer science and information technology. Such as, some computational task, which previously must be executed by using super-computer, now can be carried out by personal computer, and at the same time, the network speed and band width of data bus and input/output equipment have increased several times. In addition, the improvement of the high quality graphic displaying is available. All these provide strong support for cryoEM high-resolution reconstruction study. At present, the 3D reconstruction packages used in the most laboraries were transplanted from early VAX platform to other UNIX platform, such as Solaris, Irix etc. However, with the popularity of using personal computer and their great performance improvement, more laboraries expect that the 3D reconstruction task could be taken on PC platform. On the other hand, for the sake of undertaking the high-resolution reconstruction, the amount of image data grows exponentially as the resolution improving. As a result, it is harder and harder to manage the data based on file format, and gernerated by command-line data processing application. It needs the high-resolution reconstruction package with more efficienct database management to achieve the tough task. According to the characteristics of the study in high-resolution reconstruction by using cryoEM, we achieve some progress as following: firstly we successfully transplanted the reconstruction software package from SGI platform to PC platform Windows operating system. And it leads to that the command-line application included in old platform can be carried out in PC platform. Secondly, a graphic user interface was designed to provide more easy way to use and to learn the icosahedral virus reconstruction, and it made the more interactivity for the user. Also we provided some tool modules for user and implemented the database, which is a genuine relational database employed in the data process modules and undertakes the data management and organization in data processing. Furthermore, we organized all these modules as Image Management and Icosahedral Reconstruction System (IMIRS). By applying the IMIRS, Boxbyx mori cytoplasmic polyhedrosis virus (BmCPV) as the material was studied in this research. Cytoplasmic polyhedrosis virus (CPV) is an insect virus belonging to Reoviridae family, which is a group of segmented, double-stranded RNA(dsRNA) icosahedral viruses. CPV is a widespread insect pathogen and can infect more than 200 species of insects, so it is a key biological insecticide of forest pests. However, BmCPV is one of the CPV members, and it is the most fearful pathogen of the important economical insect—silkworm. Because of CPV's structurally stability and simplicity in Reoviridae family, as well as its self-competent transcription, possessing within the intact virus all the enzyme activities necessary for mRNA synthesis and processing, and at the same time because of its ease to be planted and purified, the virus is a ideal material for the cryoEM high resolution study. In our study, the cryoEM micrographs of CPV were taken by 300kV FEG cryoEM instrumentations equipped with liquid helium specimen stage and were digitized with the step of 7 μm. By using the incoherent averaged Fourier transform of focal pairs of these micrographs, it indicates the micrographs of in-focus including 5-6? information. The whole data processing was carried out by using IMIRS software package on PC platform. By using the focal pair method, a structure with the 14 ? resolution was obtained from close-to-focus micrograph, and it reveals that the T=1 capsid shell has a radius of 285 ? and is decorated on its icosahedral vertices with twelve pentameric spikes extending to a radius of 360 ?. From the CPV 3D reconstruction result, the data processing correction and database management reliability of using IMIRS software package are both proved. And it is also a stable foundation to proceed with high-resolution reconstruction of the icosahedral virus, and to reach the 5-6 ? resolutions.
Keywords/Search Tags:cryo-electron microscopy, icosahedral, high-resolution, three dimension reconstruction, database management
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