基于Web服务的流感病毒基因组自动化翻译注释系统

随着流感病毒基因组测序数据的急剧增加,深入挖掘流感病毒基因组大数据蕴含的生物学信息成为研究热点。基于中国流感病毒流行特征数据,建设一个集自动化、一体化和信息化的序列库系统,对于实现流感病毒基因组批量快速翻译、注释、存储、查询、分析具有重要的应用价值。本课题组通过集成一系列软件和工具包,并结合自主研发的其他功能,在底层维护的2个关键的参考数据集基础上另外追加了翻译注释信息最佳匹配的精细化筛选规则,构建具有流感病毒基因组信息存储、自动化翻译、蛋白序列精准注释、同源序列比对和进化树分析等功能的自动化系统。结果显示,通过Web端输入fasta格式的流感病毒基因序列,本系统可针对参考序列片段数据集(blastdb.fasta)进行Blast同源性检索,可以鉴定流感病毒的型别(A、B或C)、亚型和基因片段(1~8片段);在此基础上,通过查询数据库底层用于翻译、注释的基因片段参考数据集,可以获得一组肽段数据集,然后通过循环调用ProSplign软件对其进行预测。结合精细化的筛选准入规则,选出与输入序列匹配最好的翻译后产物,作为该输入序列的预测蛋白,输出为gbk,asn和fasta等通用格式的文件,给出序列长度、是否全长、病毒型别、亚型、片段等信息。基于以上工作,另外自主研发了系统其他的附加功能如进化树分析展示、基因组数据存储等功能,构建成基于Web服务的流感病毒基因组自动化翻译注释系统。本研究提示,系统高度集成系列软件以及自有的注释翻译数据库文件,实现从序列存储、翻译、注释到序列分析和展示的功能,可全面满足我国高通量基因检测数据共享化、本土化、一体化、自动化的需求。     

芽胞杆菌中重组蛋白分泌表达的优化策略及研究进展

芽胞杆菌属具有良好的蛋白表达和分泌能力,在工业酶的生产中被广泛应用,是理想的工业宿主菌,但实现蛋白分泌表达的普遍高效性还存在许多瓶颈。本文综述了芽胞杆菌的蛋白分泌表达策略,从启动子、信号肽、分泌途径、宿主和培养条件这5个方面总结了提高芽胞杆菌中分泌表达重组蛋白的方法,对芽胞杆菌高效生产工业酶有一定的参考价值,最后展望了优化芽胞杆菌分泌表达的研究方向,各种新型生物技术的发展必将推进芽胞杆菌在分泌表达领域有更深入的应用。     

有机磷水解酶纳米胶囊的调控及其对酶活性和稳定性的影响

纳米胶囊化是提高有机磷水解酶(organic phosphorus hydrolase,OPH)稳定性,进而实现其实用化的最具前景的解决方案.纳米胶囊一方面能够有效保护有机磷水解酶免于失活,但另一方面胶囊的存在也会阻碍底物与酶活性中心的接近.因此,通过调节纳米胶囊的结构来调控有机磷水解酶纳米胶囊活性和稳定性是十分值得研...     

甘肃省大豆品种生育期组的划分及地理分布研究

甘肃省地域广大,地形复杂,气候多样,大豆品种资源丰富,但甘肃各地大豆品种生育期生态类型并不明确.本试验以25份MG 0～Ⅴ的北美大豆生育期组标准品种为对照,将从甘肃各地收集到的151个大豆品种在甘肃境内5个生态区进行生育期性状鉴定和生育期组划分.结果 表明,甘肃地区种植的大豆品种的生育期组在MG 00和MGⅥ之间.在所...     

Identification and Mapping of Two New Genes Conferring Resistance to Powdery Mildew from Aegilops tauschii （Coss,） Schmal

Two powdery mildew resistance genes were Identified from Aegilops tauschll accessions Y201 and Y212 and mapped using two different F2 populations derived from the crosses between susceptible accession Y2272 and Y201, and susceptible accession Y2263 and Y212. Genetic analysis of resistance to powdery mildew Indicated that the resistance of Y201 was controlled by a single dominant gene, whereas the resistance of Y212 was controlled by a single recessive gene. We have temporarily designated these genes as PmY201 and PmY212, respectively. By bulk segregation analysis, six mlcrosatelllte markers Including Xgwm174, cfd26, cfd57, cfdl02, Xgwm583 and Xgwm639 were found to be linked to PraY201 with genetic distances of 5.2, 7.7, 9.6, 12.5, 20.2 and 22.1 cM, respectively. Five SSR markers, including cfd57, Xgwm182, cfd7, cfd102, and cfd12, were found to be linked to PmY212 with distances of 5.6, 7.2, 11.5, 14.7, and 18.5 cM, respectively. According to the locations of the linked markers, the two resistance genes were located In the 5DL region. Based on the chromosomal locations and the resistance patterns of the two genes, we propose that PmY201 and PmY212 are two novel powdery mildew resistance genes, and are suitable for marker-assisted selection.     

Genetic regulation by non-coding RNAs

Large scale cDNA sequencing and genome tiling array studies have shown that around 50% of genomic DNA in humans is transcribed, of which 2% is translated into proteins and the remaining 98% is non-coding RNAs (ncRNAs). There is mounting evidence that these ncRNAs play critical roles in regulating DNA structure, RNA expression, protein translation and protein functions through multiple genetic mechanisms, and thus affect normal development of organisms at all levels. Today, we know very little about the regulatory mechanisms and functions of these ncRNAs, which is clearly essential knowledge for understanding the secret of life. To promote this emerging research subject of critical importance, in this paper we review (1) ncRNAs' past and present, (2) regulatory mechanisms and their functions, (3) experimental strategies for identifying novel ncRNAs, (4) experimental strategies for investigating their functions, and (5) methodologies and examples of the application of ncRNAs.     

Habitat use of urban Tree Sparrows in the process of urbanization: Beijing as a case study

The Tree Sparrow (Passer montanus) is a dominant species in urban bird communities. With the development of urbanization, the habitats and sources of food for Tree Sparrows are decreasing. Can the urban Tree Sparrow adapt to changes in the urban environment? To answer this question, we studied the habitat use of Tree Sparrows in eight types of urban areas in Beijing. The results show that the number of both breeding and wintering Tree Sparrows decreased with increasing urbanization. The habitat use of Tree Sparrows, analyzed using stepwise discriminant analysis, was positively correlated with the number of brick bungalows, coniferous and broad-leaved trees and air conditioners. It was negatively correlated with the area of high buildings and hardened roads, pedestrian and automobile flux. This indicates that the Tree Sparrow had not adapted to rapid urbanization even though it is a generally adaptable species. Urban planning should take birds such as the Tree Sparrow into consideration. __________ Translated from Biodiversity Science, 2006, 14(5): 372–381 [译自:生物多样性]     

Development of an STS marker tightly linked to <Emphasis Type="Italic">Yr26</Emphasis> against wheat stripe rust using the resistance gene-analog polymorphism (RGAP) technique

The gene Yr26 confers resistance to all races of Puccinia striiformis f. sp. tritici (PST), the casual pathogen of wheat stripe rust in China. Here, we report development of a molecular marker closely linked to Yr26 using a resistance gene-analog polymorphism (RGAP) technique. A total of 787 F₂ plants and 165 F₃ lines derived from the cross Chuanmai 42/Taichung 29 were used for linkage analysis. Eighteen near-isogenic lines (NILs) and 18 Chinese wheat cultivars and advanced lines with different genes for stripe rust resistance were employed for the validation of STS markers. A total of 1,711 RGAP primer combinations were used to test the parents and resistant and susceptible bulks. Five polymorphic RGAP markers were used for genotyping all F₂ plants. Linkage analysis showed that the five RGAP markers were closely linked to Yr26 with genetic distances ranging from 0.5 to 2.9 cM. These markers were then converted into STS markers, one, CYS-5, of which was located 0.5 cM to Yr26 and was closely associated with the resistance gene when validated over 18 NILs and 18 Chinese wheat cultivars and lines. The results indicated that CYS-5 can be used in marker-assisted selection targeted at pyramiding Yr26 and other genes for stripe rust resistance.     

Effects of degU32(Hy), degQa and degR Pleiotropic Regulatory Genes on the Growth and Protease Fermentation of Bacillus Subtilis Ki-2-132

Effects of degU32 (Hy), degR genes from Bacillus subtilis 168 and deg Qa gene from Bacillus amyloliquefaciens on Bacillus subtilis Ki-2-132 cell growth, sporulation and protease fermentation were investigated by introducing these genes into B. subtilis Ki-2-132 chromosome and/or cytoplasm. Although the genes come from different species and strains, they showed pleiotropic effects in B. subtilis Ki-2-132. B. subtilis Ki-2-132degU32 (Hy) showed increased protease production, and when cooperating with deg Qa either in plasmid or in chromosome, further altered cell growth, increased protease production and affected the spore formation in a glucose and dosage dependent manner. By contrast, degR did not significantly affect the protease productivity in degU32 (Hy) mutant, consisting with that DegR was used to stabilise DegU-phosphate, which in degU32 (Hy) strain no longer further amplify the DegU-phosphate effect.     

气候变化对我国华北地区冬小麦发育和产量的影响

验证作物模型在我国华北冬小麦主产区是否适应的基础上,采用作物模型与气候模式相结合的研究方法,定量化地模拟预测了未来100年气候变化对华北冬小麦生产的影响.结果表明,从2000～2004年,华北地区冬小麦产量的模拟值与实测值的变化趋势基本一致,且生育期和产量变化不大.未来100年内华北地区冬小麦的生长期可能会有所缩短,平均缩短8.4 d;产量也会有不同程度的下降,平均减产10.1％.适当采取应对措施可以有效降低冬小麦的减产趋势.