Isolation and partial amino acid sequencing of the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from three species of orchid

Small subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) have been purified from 3 species of orchid in the genus Cymbidium by gel filtration followed by preparative sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and electroelution. The samples were subjected to amino acid composition analysis and partial N-terminal amino acid sequencing. The sequencing data clearly confirm that one of the species examined is the hybrid offspring of a cross between the other two.     

基于比较基因组学的高地芽孢杆菌6ww6分子标识筛选及其快速鉴定

【目的】高地芽孢杆菌(Bacillus altitudinis) 6ww6是一株根际耐盐促生菌,可以作为微生物肥料的优选菌种。为了加强菌种知识产权保护,建立菌株快速检测方法。【方法】本研究通过基因组比对分析、TBLASTn检索、NR库检索验证并剔除有其他同源的结果序列,最终得到菌株6ww6的孤儿基因,设计引物进行PCR鉴定。【结果】筛选出5个特异性基因J939_13195、J9319_05960、J9319_13355、J9319_05965和J9319_13350。引物5960F和5960R可以单一性扩增出菌株6ww6的目的基因J9319_05960,确定其为菌株6ww6的特异性分子标识。【结论】本研究确定了菌株6ww6的唯一性身份编码,建立了以比较基因组学和孤儿基因为基础的菌株水平上的鉴定方法。该方法具有快速、精确、能鉴定到菌株水平的优点,对于有价值微生物的知识产权保护提供了有力的抓手。     

A robust six-miRNA prognostic signature for head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) remains a major health problem worldwide. We aimed to identify a robust microRNA (miRNA)-based signature for predicting HNSCC prognosis. The miRNA expression profiles of HNSCC were obtained from The Cancer Genome Atlas (TCGA) database. The TCGA HNSCC cohort was randomly divided into the discovery and validation cohort. A miRNA-based prognostic signature was built up based on TGCA discovery cohort, and then further validated. The downstream targets of prognostic miRNAs were subjected to functional enrichment analyses. The role of miR-1229-3p, a prognosis-related miRNA, in tumorigenesis of HNSCC was further evaluated. A total of 305 significantly differentially expressed miRNAs were found between HNSCC samples and normal tissues. A six-miRNA prognostic signature was constructed, which exhibited a strong association with overall survival (OS) in the TCGA discovery cohort. In addition, these findings were successfully confirmed in TCGA validation cohort and our own independent cohort. The miRNA-based signature was demonstrated as an independent prognostic indicator for HNSCC. A risk signature-based nomogram model was constructed and showed good performance for predicting the OS for HNSCC. The functional analyses revealed that the downstream targets of these prognostic miRNAs were closely linked to cancer progression. Mechanistically, in vitro analysis revealed that miR-1229-3p played a tumor promoting role in HNSCC. In conclusion, our study has developed a robust miRNA-based signature for predicting the prognosis of HNSCC with high accuracy, which will contribute to improve the therapeutic outcome.     

Distribution and characterization of simple sequence repeats in Gossypium raimondii genome

Simple sequence repeats (SSRs) can be derived from the complete genome sequence. These markers are important for gene mapping as well as marker-assisted selection (MAS). To develop SSRs for cotton gene mapping, we selected the complete genome sequence of Gossypium raimondii, which consisted of 4447 non-redundant scaffolds. Out of 775.2 Mb sequence examined, a total of 136,345 microsatellites were identified with a density of 5.69 kb per SSR in the G. raimondii genome leading to development of 112,177 primer pairs. The distributions of SSRs in the genome were non-random. Among the different motifs ranging from 1 to 6 bp, penta-nucleotide repeats were most abundant (30.5%), followed by tetra-nucleotide repeats (18.2%) and di-nucleotide repeats (16.9%). Among all identified 457 motif types, the most frequently occurring repeat motifs were poly-AT/TA, which accounted for 79.8% of the total di-nt SSRs, followed by AAAT/TTTA with 51.5% of the total tetra-nucleotede. Further, 18,834 microsatellites were detected from the protein-coding genes, and the frequency of gene containing SSRs was 46.0% in 40,976 genes of G. raimondii. These genome-based SSRs developed in the present study will lay the groundwork for developing large numbers of SSR markers for genetic mapping, gene discovery, genetic diversity analysis, and MAS breeding in cotton.     

台湾乳白蚁肠道鞭毛虫群落结构及三种研究方法的比较

大量鞭毛虫栖息在低等白蚁肠道内, 是白蚁赖以生存的共生微生物。不同种类的鞭毛虫共同作用形成了一套降解食物的系统, 为宿主提供营养和能量。研究鞭毛虫群落结构是揭示其各组成种类生理功能的基础。利用形态特征进行物种鉴定受鞭毛虫生长发育阶段、 样品制备方法等多种因素的影响, 而基于分子标记的分子生物学方法能不受这些因素的制约来研究复杂的微生物群落。本研究结合形态特征鉴定和分子生物学方法研究台湾乳白蚁Coptotermes formosanus肠道鞭毛虫群落结构, 并对这些方法进行了比较。通过光学显微镜和扫描电子显微镜进行形态观察鉴定, 确定了台湾乳白蚁肠道内的3种鞭毛虫, 分别为伪披发虫Pseudotrichonympha grassii、 全鞭毛虫Holomastigotoides mirabile和旋披发虫Spirotrichonympha leidyi。18S rDNA文库限制性片段长度多态性分析较形态鉴定能够反映群落更复杂的物种多样性。利用光学显微镜进行细胞计数较18S rDNA文库克隆数能更准确地反映各种鞭毛虫数量, 每头工蚁肠道内平均含伪披发虫780±179头, 全鞭毛虫1 630±391头, 旋披发虫2 950±1 003头。本研究建立了光学显微镜形态鉴定和18S rDNA分子标记相结合调查鞭毛虫多样性和数量的方法, 为进一步研究白蚁肠道共生生物的功能奠定了基础。     

Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences

A total of 10 882 porcine microsatellite repeats were identified in genomic shotgun sequences from the Sino-Danish Pig Genome Sequencing Consortium (http://www.piggenome.dk). Of these, 4528 microsatellites were placed on a pig-human comparative map by blast analysis of porcine sequences against the human genome (blast cut-off threshold =1 x 10(-5)). All microsatellite sequences placed on the comparative map are accessible at http://www.animalgenome.org/QTLdb/pig.html. These sequences increase the number of identified microsatellites in the porcine genome by several orders of magnitude. They are a new resource of microsatellite sequences for generating markers to be used in linkage studies and in fine mapping and positional cloning of quantitative trait loci.     

Characterization and mapping of a novel mutant sms1 (senescence and male sterility 1) in rice

Plant senescence plays diverse important roles in development and environmental responses.However,the molecular basis of plant senescence is remained largely unknown.A rice spontaneous mutant with the character of early senescence and male sterility (sms) was found in the breeding line NT10-748.In order to identify the gene SMS1 and the underlying mechanism,we preliminarily analyzed physiological and biochemical phenotypes of the mutant.The mutant contained lower chlorophyll content compared with the wild t...     

Escherichia coli and enterococci are sensitive and reliable indicators for human,livestock and wildlife faecal pollution in alpine mountainous water resources

Aims: This study evaluated the applicability of standard faecal indicator bacteria (SFIB) for alpine mountainous water resources monitoring. Methods and Results: Escherichia coli, enterococci (ENTC) and Clostridium perfringens were investigated by standard or frequently applied phenotypic and genotypic methods in a broad range of animal and human faecal sources in a large alpine mountainous area. Clostridium perfringens occurred only in human, livestock and carnivorous source groups in relevant average concentrations (log 4·7–7·0 CFU g^?1) but not in herbivorous wildlife sources. Escherichia coli proved to be distributed in all faecal source groups with remarkably balanced average concentrations (log 7·0–8·4 CFU g^?1). Except for single faecal samples from the cattle source group, prevalence rates for ENTC source groups were generally >87% with average concentrations of log 5·3–7·7 CFU g^?1. To test the faecal indication capacity in the environment, faecal prevalence data were comparatively analysed with results from the concurrently performed multi‐parametric microbial source tracking effort on karst spring water quality from the investigated alpine mountainous catchment ( Reischer et al. 2008 ; Environ Microbiol 10:2598–2608). Conclusion: Escherichia coli and enterococci are reliable faecal indicators for alpine mountainous water resources monitoring, although E. coli is the more sensitive one. Clostridium perfringens did not prove to be an indicator of general faecal pollution but is suggested a conservative microbial source tracking marker for anthropogenic faecal influence. Significance and Impact of the Study: Applicability of SFIB is currently hotly debated. This is the first study providing comprehensive information on the applicability of SFIB at alpine mountainous habitats.     

Mg2+依赖性蛋白磷酸酶1δ的生物信息学分析

Mg2+依赖性蛋白磷酸酶1δ(protein phosphatase magnesium-dependent 1δ,PPM1D)作为肝癌潜在的预后标志物和治疗靶点,其致癌机制和预后价值仍未完全阐明。为了全面认识PPM1D,使用生物信息学方法,对PPM1D蛋白的序列同源性、组织表达、亚细胞定位、理化性质、空间结构及蛋白质相互作用网络进行分析。结果表明:人PPM1D基因编码605个氨基酸组成的多肽,与物种进化程度一致,属于PP2C蛋白超家族,是碱性不稳定的亲水蛋白,无信号肽和跨膜区域;PPM1D蛋白主要定位于细胞核内,其主要二级结构为随机卷曲,存在磷酸化、乙酰化、甲基化和泛素化位点,与PPM1D相互作用的蛋白主要是细胞周期检查点蛋白和细胞损伤修复相关蛋白。根据分析结果阐述了PPM1D蛋白与癌症的相关性以及PPM1D蛋白作为癌症标志物的理论基础,为进一步研究该蛋白及其参与的信号通路提供一定的借鉴和参考。