Phylogenetic analysis of the family Thermaceae with an emphasis on signature position and secondary structure of 16S rRNA

The sequences of the 16S rRNA genes from 38 strains of the family Thermaceae were compared by alignment analysis. The genus-specific and species-specific base substitutions or base deletions (signature positions) were found in three hypervariable regions (in the helices 6, 10 and 17). The differentiation of secondary structures of the high variable regions in the 5' end (38-497) containing several signature positions further supported the concept. Based on the comparisons of the secondary structures in the segments of 16S rRNAs, a key to the species of the family Thermaceae was proposed. (C) 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.

Discovery of a male-biased mutant family and identification of a male-specific SCAR marker in gynogenetic gibel carp Carassius auratus gibelio

Gibel carp ( Carassius auratus gibelio) is a uniquely gynogenetic species with a minor ratio of males in natural habitats, but its male origin and sex determination mechanisms have been unknown. In this study, a male-biased mutant family was discovered from the gynogenetic gibel carp, and a male-specific SCAR marker was identified from the mutant family. Normal spermatogenesis was observed in the male testes by immuno. fluorescence histochemistry. Nearly identical AFLP profiles were observed between males and females, but a male-specific 86 bp AFLP fragment was screened by sex-pool bulked segregant analysis and individual screening. Based on the male-specific AFLP fragment, a total of 579 bp sequences were cloned by genome walking. Subsequently, a male-specific SCAR marker was designed, and the male-specific DNA fragment was confirmed to be steadily transmitted to the next generation and consistently detected only in males. (C) 2009 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.

水菖蒲的化学成分研究和忍冬属植物的色谱分析

本论文由三章组成。第一章阐述了藏药水菖蒲的化学成分研究，共分离鉴定了39个化学成分，其中6个为新化合物。第二章报道了几种忍冬属植物的HPLC、HPLC-MS、GC分析以及抑菌活性、重金属含量测定结果。第三章概述了菖蒲属植物的研究进展。 第一章报道了水菖蒲(Acorus calamus L.)化学成分的分离纯化与结构鉴定。采用正、反相硅胶柱层析等分离方法，从水菖蒲的根中共分离出41个化合物，通过红外、质谱、核磁共振及X-ray单晶衍射等波谱方法和模拟计算方法鉴定了其中39个化合物的结构，主要为倍半萜、苯丙素、甾体类化合物。其中含有5个新的倍半萜类化合物和1系列新的甾体皂苷衍生物。经波谱分析将它们的结构鉴定为 1b, 7a(H)-cadinane-4a, 6a, 10a-triol (1), (2R,6R,7S,9S)-1(10), 4-cadinadiene-2, 9-diol (2), 1a, 5b-guaiane-10a-O-ethyl-4b, 6b-diol (7), 6b, 7b(H)-cadinane-1a, 4a, 10a-triol (13)，(1R,4R,6S,10R)-1-hydroxy-7(11)-cadinen-5, 8-dione (14)， 4′-O-正n碳酰基-3-O- β-D-葡萄糖基谷甾醇(n=14, 16, 18, 22) (15)。 第二章包括四个部分。第一部分报道了忍冬属三种植物40个样品的HPLC测定和对主要活性成分绿原酸的定量分析结果，以及运用HPLC-MS技术对色谱图中8个峰进行指认。在此基础上，考察了种植和采收多个因素对绿原酸含量的影响。第二部分报道了忍冬属三种植物27个样品的GC分析，根据样品的挥发性成分的保留时间对不同样品进行了定性比较，并考察了花期及海拔高度对植物挥发性成分的影响。第三、四部分分别阐述了灰毡毛忍冬和红腺忍冬的体外抑菌活性研究和重金属含量测定结果。 第三章全面系统地概述了菖蒲属植物的化学成分和药理活性研究进展。 This dissertation is composed by three chapters. The first chapter elaborates the phytochemical investigation of Acorus calamus L. Thirty-nine compounds including six new compounds were isolated and identified. The second chapter reports the research on genus Lonicera by HPLC, HPLC-MS and GC. Antifungal activity and heavy metals measurement of genus Lonicera were reported. The third chapter is a review about the research progress on the plant family of Acorus. The first chapter focuses on the isolation and identification of chemical constituents from Acorus calamus L.. Forty-one compounds were isolated from the root of Acorus calamus L. by repeat column chromatography over normal and reversed phase silica gel, the structure of thirty-nine compounds was identified by spectroscopic methods and computational methods, including IR, MS, NMR and X-ray. Those compounds mainly belonged to sesquiterpene, phenylpropanoid and steroid. Among them, five are new sesquiterpenes and one series are new steroid glycoside derivatives. Their structure were suggested as 1b, 7a(H)-cadinane-4a, 6a, 10a-triol (1), (2R,6R,7S,9S)-1(10), 4-cadinadiene-2, 9-diol (2), 1a, 5b-guaiane-10a-O-ethyl-4b, 6b- diol (7), 6b, 7b(H)-cadinane-1a, 4a, 10a-triol (13), (1R,4R,6S,10R)-1-hydroxy-7(11)- cadinen-5, 8-dione (14), 4′-O-carbonyl-3-O-β-D-glucosyl-sitosterol (carbonyl = tetradecanoyl, hexadecanoyl, octadecyl, docosanoyl) (15). The second chapter consists of four parts. The first part reports the HPLC analysis of forty samples of the genus Lonicera, and the quantitative investigation of chlorogenic acid in these samples by HPLC analysis. Relationship between the content of chlorogenic acid in different samples and their planting conditions and harvesting time were discussed. Furthermore, eight compounds were identified or tentatively characterized based on their mass spectra and UV spectra profiles. The second part is about qualitative analysis of the volatile constituent in twenty-seven samples of genus Lonicera by GC. The effect of planting altitude and harvesting time on the volatile constituent was also investigated. The third and fourth parts describe the antifungal activity and content of some kinds of heavy metals of L. macranthoides Hand.-Mazz. and L. hypoglauca Miq.. The third chaspter is a review about the research progress of the plant family of Acorus.