花斑无须鲶(Ageneiosus marmoratus)全基因组微卫星分布特征研究

根据NCBI已公布的花斑无须鲶全基因组序列,利用MISA软件对花斑无须鲶全基因组的6种完整型微卫星进行筛选并分析其分布特征. 结果如下:在花斑无须鲶全基因组(约1.03Gb)中符合条件的微卫星序列共336 037个,丰度为326个/Mb. 微卫星总长度为7 720 686 bp,占花斑无须鲶全基因组的0.75%. 其中二碱基类型的微卫星数目最多,为145 318个,占微卫星总数的43.24%,其次分别为单碱基(37.12%)、三碱基(11.00%)、四碱基(7.39%)、五碱基(1.04%)和六碱基(0.21%). 花斑无须鲶全基因组微卫星中的优势碱基类别按照数量从高到低排列依次为A、AC、AG、AT、AAT、AAAT、TATC、AAG、AAC和TGA,共有305 243个,占微卫星总数的 90.84%,A、T碱基在微卫星中占绝对优势.     

Expression of green fluoscrescent protein gene in Sclerotinia sclerotiorum

Protoplasts of the pathogenic plant fungus,Sclerotinia sclerotiorum,were transformed using the pPGF plasmid,which contains green fluorescent protein gene,under the control of Aspergillus nidulans regulatory sequences. The pPGF plasmid was introduced by PEG/CaCl2 treatment. Positive transformants were harvested with hygromycin B (HYG) resistance as selective marker,and then were observed with green fluorescence phenomena in response to blue light,which suggested that GFP gene was cloned into genome DNA of S. sclerotiorum. The transformants were verified mitotically stable by Southern blotting analysis and passage culturing. This study is developed as an initial step for further research into infection mechanisms of S. sclerotiorum to plants and interactions with bio-control fungus.     

应用基因组重排技术提高普那霉素产量

将普那霉素产生菌——始旋链霉菌ND-23的孢子和原生质体经紫外线诱变后获得高产突变菌株,其中高产突变株SP-S73的产量达到356 mg/L,比出发菌株提高了31%.在上述增产突变株中选取4株作为基因组重排的出发亲本,对它们进行了4轮基因组重排育种,筛选得到了高产重排菌株,其中1株重排菌株G-211的普那霉素产量为832 mg/L,比产量最高的亲本菌株提高了134%,比原始出发菌株ND-23(272 mg/L)提高了206%.通过研究高产菌株和出发菌株ND-23在5 L罐上的发酵过程,发现普那霉素产生菌的生物合成属于非生长耦合型;其高产菌株G-211在合成产物的时期对还原糖和氨基氮的消耗量均大于原始菌株ND-23,这些结果将为高产菌株发酵条件优化和发酵放大研究提供有价值的参考.     

Metagenomics: Facts and Artifacts,and Computational Challenges

Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. By enabling an analysis of populations including many (so-far) unculturable and often unknown microbes, metagenomics is revolutionizing the field of microbiology, and has excited researchers in many disciplines that could benefit from the study of environmental microbes, including those in ecology, environmental sciences, and biomedicine. Specific computational and statistical tools h...     

New Generations: Sequencing Machines and Their Computational Challenges

New generation sequencing systems are changing how molecular biology is practiced. The widely promoted ＄1000 genome will be a reality with attendant changes for healthcare, including personalized medicine. More broadly the genomes of many new organisms with large samplings from populations will be commonplace. What is less appreciated is the explosive demands on computation, both for CPU cycles and storage as well as the need for new computational methods. In this article we will survey some of these develo...     

快速的致病基因分析方法

目前通过IBD定位研究致病基因首先需要检测IBD片段,然后利用得到的IBD关系进行关联检测来定位致病基因,但是寻找IBD片段需要较长时间。提出了一种新的算法FADG,通过分析IBS和IBD的关系找出候选IBD片段,然后定义评价函数分别对病例组和对照组进行分析,差异最大的SNP位点就是致病位点。通过对GAW15提供的类风湿关节炎模拟数据的五个主要的致病位点和GS生成的模拟数据进行分析,实验结果与数据给定的致病位点一致;与已有的方法进行对比表明该算法在能找到正确位点的基础上效率较高;最后选择了RA数据中两条染色体分别进行permutation测试,验证算法得到致病位点的可信度,进一步排除所得结果假阳性的可能性。     

巨龙竹基因组DNA的提取及RAPD反应条件的优化

用改良CTAB法从巨龙竹硅胶干燥的叶片中提取基因组DNA，成功地进行RAPD扩增，通过正交法以RAPD反应条件优化。6个试验因子的最适条件为：模板DNA1－1.5ng/μl，引物0.8-1.0μmol/L,dNTPs0.1-0.5mmol/L,Mg^2 2.0-2.5mmol/L,Taq酶0.5-1.0U，退火温度35－36℃。     

比较基因组揭示广西酸菜乳杆菌碳水化合物活性酶谱

微生物中的碳水化合物活性酶(carbohydrate active enzymes,CAZymes)具有降解植物组织的作用,相对于真菌,目前对于乳杆菌的CAZymes研究还比较少.该研究从广西酸菜中筛选获得了3株产CAZymes的乳杆菌,并通过二代测序技术比较其编码基因.16S rRNA测序结果表明3株乳杆菌分别是La...     

基于机器学习的基因组微卫星状态探测方法综述

[目的]探讨机器学习在基因组微卫星状态检测方法中的应用及未来研究方向.[文献范围]本文收集了微卫星状态检测方法相关文献.[方法]首先简要介绍微卫星状态检测的意义和常用的检测手段,其次对目前主流的基于机器学习的检测方法进行详细介绍,最后展望未来机器学习在微卫星状态检测领域中的研究方向.[结果]基于机器学习的检测方法从大量...