粗糙集算法在预测RNA保守功能二级结构中的应用

提出了一种预测RNA保守功能二级结构的粗糙集算法.使用粗糙集工具Rosetta软件,在保守结构预测过程的数据挖掘模块中,应用经过整理和离散化的RNA备择碱基对数据生成规则确定出将要出现在同源RNA序列的保守二级结构中的碱基对.将此算法应用在对爱滋病病原体HIV病毒RNA中REV应答元件单元的保守二级结构预测的结果表明,与传统的非数据挖掘算法相比,使用了这种机器学习算法的粗糙集预测方法,使得保守功能结构与野生型结构更加相似,重要的功能结构分支更加清晰明确.     

栖热菌噬菌体TSP4密码子偏嗜性及其对基因异源表达的影响

 为了探索噬菌体TSP4、栖热菌模式菌株Thermus thermophilus HB27中6种蛋白编码序列和Escherichia coli基因组遗传密码子使用偏嗜性,探索TSP4基因密码子偏嗜性对其基因异源表达的影响本研究利用生物学软件Editseq和RSCU算法统计噬菌体TSP4密码子使用频率并分析其偏嗜性,与栖热菌HB27的同源基因以及常温菌E.coli基因组的密码子使用偏嗜性进行对比分析.结果显示,噬菌体TSP4与栖热菌HB27优势密码子相似度高达85%,而与E.coli的相似性仅有65%.为了验证分析结果,选取TSP4基因组中一个潜在分子伴侣基因序列在E.coli BL21和E.coli Rosetta(补充了BL21菌株中缺失的6个稀有密码子)中进行异源表达.噬菌体TSP4与其宿主菌HB27之间密码子高相似性说明在长期的进化过程中TSP4在基因水平上形成对宿主的一种适应性机制.异源表达结果显示,分子伴侣基因在E.coli BL21中未见明显表达,但在Rosetta中高效表达,说明Rosetta中补充的 6个稀有密码子明显有助于分子伴侣基因的表达,该结果也进一步证明密码子偏嗜性是否一致在很大程度上影响基因的表达.     

Ion trap mass spectrometry on a comet nucleus: the Ptolemy instrument and the Rosetta space mission

In May 2014, the Rosetta spacecraft is scheduled to rendezvous with the comet Churyumov-Gerasimenko ('67P'). One of the instruments on board the 'Lander' which will descend on to the surface of the comet is a miniaturised GC/MS system that incorporates an ion trap mass spectrometer, specially developed for isotope ratio analysis. This article describes the development and optimisation of the ion trap for this unique application, and presents a summary of the range of pre-programmed experiments that will contribute to the characterisation of the solid and volatile cometary materials.     

Optimization of mass spectrometers using the adaptive particle swarm algorithm

Optimization of mass spectrometers using the adaptive particle swarm algorithm (APSA) is described along with implementations for ion optical simulations and various time-of-flight (TOF) instruments. The need for in situ self optimization is addressed through discussion of the reflectron TOF mass spectrometer (RTOF) on the European Space Agency mission Rosetta. In addition, a tool for optimization of laboratory mass spectrometers is presented and tested on two different instruments. After the application of APSA optimization, a substantial increase in performance for mass spectrometers that have manually been tuned for several weeks or months is demonstrated.     

Molecular Chirality in Meteorites and Interstellar Ices,and the Chirality Experiment on Board the ESA Cometary Rosetta Mission

Life, as it is known to us, uses exclusively L ‐amino acid and D ‐sugar enantiomers for the molecular architecture of proteins and nucleic acids. This Minireview explores current models of the original symmetry‐breaking influence that led to the exogenic delivery to Earth of prebiotic molecules with a slight enantiomeric excess. We provide a short overview of enantiomeric enhancements detected in bodies of extraterrestrial origin, such as meteorites, and interstellar ices simulated in the laboratory. Data are interpreted from different points of view, namely, photochirogenesis, parity violation in the weak nuclear interaction, and enantioenrichment through phase transitions. Photochemically induced enantiomeric imbalances are discussed more specifically in the topical context of the “chirality module” on board the cometary Rosetta spacecraft of the ESA. This device will perform the first enantioselective in situ analyses of samples taken from a cometary nucleus.     

Residue‐centric modeling and design of saccharide and glycoconjugate structures

The RosettaCarbohydrate framework is a new tool for modeling a wide variety of saccharide and glycoconjugate structures. This report describes the development of the framework and highlights its applications. The framework integrates with established protocols within the Rosetta modeling and design suite, and it handles the vast complexity and variety of carbohydrate molecules, including branching and sugar modifications. To address challenges of sampling and scoring, RosettaCarbohydrate can sample glycosidic bonds, side‐chain conformations, and ring forms, and it utilizes a glycan‐specific term within its scoring function. Rosetta can work with standard PDB, GLYCAM, and GlycoWorkbench (.gws ) file formats. Saccharide residue‐specific chemical information is stored internally, permitting glycoengineering and design. Carbohydrate‐specific applications described herein include virtual glycosylation, loop‐modeling of carbohydrates, and docking of glyco‐ligands to antibodies. Benchmarking data are presented and compared to other studies, demonstrating Rosetta's ability to predict glyco‐ligand binding. The framework expands the tools available to glycoscientists and engineers. © 2016 Wiley Periodicals, Inc.     

云端装配知识发现系统的设计与实现

主要介绍了云端装配知识发现系统的总体设计思路、总体设计结构、粗糙集处理引擎设计、软件架构设计和详细实现,用户在浏览器就可以完成对上传的数据进行参数设置、完整性处理、离散化处理、属性约简、知识生成和知识过滤等一系列操作。