T-DNA插入水稻群体中卷叶突变体R1-A2的遗传分析

在根癌农杆菌介导的T-DNA(携带有除草剂Basta抗性基因bar和Ds因子)转化中花11水稻群体中,获得了一个叶片发生明显内卷的突变体R1-A。经过连续三代的分离鉴定,获得突变体的纯合株(R1-A2),并与中花11号进行杂交,在调查的36个F_1植株中,全部表现为卷叶,并对Basta除草剂都表现为抗性。在852个F_2单株中,卷叶为645株,正常叶207株,卷叶和正常叶的比例为3:1,其中,卷叶株均对Basta表现抗性,正常叶株均对Basta表现敏感,表明卷叶性状和Basta抗性存在着共分离关系。用扩增Ds因子的引物,对F_2中45个卷叶抗性株进行PCR鉴定,都获得预期长度的Ds因子片段,进一步表明在这些卷叶的植株中都有T-DNA的插入;而30个正常叶敏感株都不能检测到Ds的特征片段。在以卷叶突变(R1-A2)为回交亲本的F_1B_1植株中,全部植株表现卷叶;在以中花11号为回交亲本的F_1B_1植株中,卷叶和正常叶植株的分离比为1:1。上述结果表明该卷叶突变是个显性突变,受一个基因所控制,且该基因的突变与T-DNA的插入有关。     

慢性胃炎肠化生CD_(44)、CD_(44V6)及Cyclin D_1、Cyclin E的表达和意义

目的探讨慢性胃炎胃粘膜肠化生CD44、CD44V6及cyclin D1、Cyclin E表达的意义。方法利用免疫细胞化学技术对39例伴有肠化生的慢性胃炎和5例正常人胃窦粘膜的活检组织进行检查。结果正常人胃窦粘膜上皮,腺上皮对CD44、CD44V6、Cyclin D1和Cyclin E均为阴性,但在有神经内分泌样细胞的粘膜,CD44V6和cyclin D1为阳性。慢性胃炎肠化生区和不典型增生区除CD44为阴性外,CD44V6、cyclin D1和cyclin E均呈现不同的阳性反应,但未见有阳性的神经内分泌样细胞。间质细胞大都呈阳性反应。结论CD44V6、cyclin D1和cyclin E可能是胃癌前状态的早期事件,而CD44可能为胃癌晚期的标志物。     

表达流感病毒神经氨酸酶基因的重组腺病毒的构建

通过RT-PCR方法扩增流感病毒神经氨酸酶基因,将其克隆到腺病毒穿梭载体pTrackCMV,此重组质粒与腺病毒DNA共转化大肠杆菌BJ5183,通过细菌内同源重组获得重组腺病毒DNA,将其转染293细胞获得重组腺病毒.经PCR证实目的基因已整合至腺病毒基因组中,western blot检测到神经氨酸酶的表达.重组病毒经滴鼻和灌胃两种途径免疫小鼠,结果表明2次免疫后滴鼻组和灌胃组均产生明显的免疫应答反应,滴鼻组的免疫效果优于灌胃组.     

伯克霍尔德氏菌ZYB002脂肪酶lipC24基因的克隆、表达及其酶学性质

【目的】克隆伯克霍尔德菌ZYB002菌株中的新型脂肪酶lip C24基因,测定其基本酶学性质,为后续深入研究该基因在菌株中的生理功能奠定基础。【方法】根据洋葱伯克霍尔德菌JK321菌株的全基因组DNA信息,直接设计引物从伯克霍尔德菌ZYB002菌株基因组中扩增出lip C24基因,并对之进行原核表达、重组蛋白的纯化及酶学性质分析。【结果】lip C24基因全长1317 bp,编码438个氨基酸残基;多肽链中具有保守五肽-G-X1-S-X2-G-序列;重组蛋白Lip C24的分子量为45 k Da;能有效水解各种对硝基苯酯,对中链脂肪酸的对硝基苯酯表现出偏爱性;其催化水解反应的最适温度为40℃,最适p H7.5;40℃下的半衰期为15.72 min,在p H 7.0-8.0的条件下,具有较好的稳定性。【结论】lip C24的编码产物为一个45 k Da蛋白,具有明显的脂肪酶活性,为中温中性脂肪酶。     

Rumen Bacterial Diversity of 80 to 110-Day-Old Goats Using 16S rRNA Sequencing

The ability of rumen microorganisms to use fibrous plant matter plays an important role in ruminant animals; however, little information about rumen colonization by microbial populations after weaning has been reported. In this study, high-throughput sequencing was used to investigate the establishment of this microbial population in 80 to 110-day-old goats. Illumina sequencing of goat rumen samples yielded 101,356,610 nucleotides that were assembled into 256,868 reads with an average read length of 394 nucleotides. Taxonomic analysis of metagenomic reads indicated that the predominant phyla were distinct at different growth stages. The phyla Firmicutes and Synergistetes were predominant in samples taken from 80 to 100-day-old goats, but Bacteroidetes and Firmicutes became the most abundant phyla in samples from 110-day-old animals. There was a remarkable variation in the microbial populations with age; Firmicutes and Synergistetes decreased after weaning, but Bacteroidetes and Proteobacteria increased from 80 to 110 day of age. These findings suggested that colonization of the rumen by microorganisms is related to their function in the rumen digestive system. These results give a better understanding of the role of rumen microbes and the establishment of the microbial population, which help to maintain the host’s health and improve animal performance.     

隐甲藻深层培养产生二十碳五烯酸的研究

二十碳五烯酸 (Ｃ2 0 :5 ,Ｅｉｃｏｓａｐｅｎｔａｅｎｏｉｃａｃｉｄ ,简称ＥＰＡ)是一种重要的ω 3系列人体必需多不饱和脂肪酸 (Ｐｏｌｙｕｎ ｓａｔｕｒａｔｅｄｆａｔｔｙａｃｉｄｓ,ＰＵＦＡ) [1～ 2 ] 。自从Ｄｙｅｒｂｅｒｇｅ等人报道了二十碳五烯酸对防止和治疗血栓、关节硬化、抗炎症、抗癌、促进脑组织发育等方面具有明显效果以来 ,人们对它的营养和医药价值及生产方法进行了广泛的研究[3～ 6] 。目前 ,二十碳五烯酸主要来源于深海鱼油 ,但其产量不稳定 ,纯化工艺复杂且含有难以消除的鱼腥味 ,难以满足市场的需求。由于二十碳五…     

A strategy for fusion expression and preparation of functional glucagon-like peptide-1 (GLP-1) analogue by introducing an enterokinase cleavage site

KGLP-1, a 31-amino acid glucagon-like peptide-1 (GLP-1) analogue, has a great therapeutic potential for anti-diabetes. In this work, a strategy for expression and purification of functional KGLP-1 peptide has been established. KGLP-1 cDNA was fused with glutathione S-transferase (GST), with an enterokinase cleavage site in the fusion junction. The recombinant fusion protein GST–KGLP-1 was affinity purified via the GST-tag, and then digested with enterokinase. The resulting GST part as well as the enzymes were eliminated by ultra-filtration followed by size exclusion chromatograph. The yield of purified KGLP-1 was approximately 12.1 mg/L, with purity of 96.18 %. The recombinant KGLP-1 was shown to have similar bioactivity as native GLP-1 when evaluated in a Chinese hamster ovary cell line expressing a GLP-1 receptor-egfp reporter gene.     

A Bipartite Network-based Method for Prediction of Long Non-coding RNA–protein Interactions

As one large class of non-coding RNAs(nc RNAs), long nc RNAs(lncRNAs) have gained considerable attention in recent years. Mutations and dysfunction of lnc RNAs have been implicated in human disorders. Many lnc RNAs exert their effects through interactions with the corresponding RNA-binding proteins. Several computational approaches have been developed, but only few are able to perform the prediction of these interactions from a network-based point of view. Here,we introduce a computational method named lnc RNA–protein bipartite network inference(LPBNI). LPBNI aims to identify potential lnc RNA–interacting proteins, by making full use of the known lnc RNA–protein interactions. Leave-one-out cross validation(LOOCV) test shows that LPBNI significantly outperforms other network-based methods, including random walk(RWR)and protein-based collaborative filtering(Pro CF). Furthermore, a case study was performed to demonstrate the performance of LPBNI using real data in predicting potential lnc RNA–interacting proteins.     

Extrapolating the effect of deleterious nsSNPs in the binding adaptability of flavopiridol with CDK7 protein: a molecular dynamics approach

Background

Recent reports suggest the role of nonsynonymous single nucleotide polymorphisms (nsSNPs) in cyclin-dependent kinase 7 (CDK7) gene associated with defect in the DNA repair mechanism that may contribute to cancer risk. Among the various inhibitors developed so far, flavopiridol proved to be a potential antitumor drug in the phase-III clinical trial for chronic lymphocytic leukemia. Here, we described a theoretical assessment for the discovery of new drugs or drug targets in CDK7 protein owing to the changes caused by deleterious nsSNPs.

Methods

Three nsSNPs (I63R, H135R, and T285M) were predicted to have functional impact on protein function by SIFT, PolyPhen2, I-Mutant3, PANTHER, SNPs&GO, PhD-SNP, and screening for non-acceptable polymorphisms (SNAP). Furthermore, we analyzed the native and proposed mutant models in atomic level 10 ns simulation using the molecular dynamics (MD) approach. Finally, with the aid of Autodock 4.0 and PatchDock, we analyzed the binding efficacy of flavopiridol with CDK7 protein with respect to the deleterious mutations.

Results

By comparing the results of all seven prediction tools, three nsSNPs (I63R, H135R, and T285M) were predicted to have functional impact on the protein function. The results of protein stability analysis inferred that I63R and H135R exhibited less deviation in root mean square deviation in comparison with the native and T285M protein. The flexibility of all the three mutant models of CDK7 protein is diverse in comparison with the native protein. Following to that, docking study revealed the change in the active site residues and decrease in the binding affinity of flavopiridol with mutant proteins.

Conclusion

This theoretical approach is entirely based on computational methods, which has the ability to identify the disease-related SNPs in complex disorders by contrasting their costs and capabilities with those of the experimental methods. The identification of disease related SNPs by computational methods has the potential to create personalized tools for the diagnosis, prognosis, and treatment of diseases.

Lay abstract

Cell cycle regulatory protein, CDK7, is linked with DNA repair mechanism which can contribute to cancer risk. The main aim of this study is to extrapolate the relationship between the nsSNPs and their effects in drug-binding capability. In this work, we propose a new methodology which (1) efficiently identified the deleterious nsSNPs that tend to have functional effect on protein function upon mutation by computational tools, (2) analyze d the native protein and proposed mutant models in atomic level using MD approach, and (3) investigated the protein-ligand interactions to analyze the binding ability by docking analysis. This theoretical approach is entirely based on computational methods, which has the ability to identify the disease-related SNPs in complex disorders by contrasting their costs and capabilities with those of the experimental methods. Overall, this approach has the potential to create personalized tools for the diagnosis, prognosis, and treatment of diseases.

     

基因组数据库简介

本文以北京大学生物信息中心安装的3个国际著名基因组数据库GDB、GenoList和Ensembl为基础,介绍目前常用的基因组数据库,包括这些数据数据库的内容、数据格式、使用方法,以及用于构建上述数据库的数据库管理系统。 Abstract:A brief introduction to the genome databases GDB,GenoList and Ensembl is given.These databases,mirrored and maintained at the Centre of Bioinformatics,Peking University,provide useful information for genome research.