Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses

Background

Members of the genera Prevotella, Veillonella and Fusobacterium are the predominant culturable obligate anaerobic bacteria isolated from periodontal abscesses. When determining the cumulative number of clinical anaerobic isolates from periodontal abscesses, ambiguous or overlapping signals were frequently encountered in 16S rRNA gene sequencing chromatograms, resulting in ambiguous identifications. With the exception of the genus Veillonella, the high intra-chromosomal heterogeneity of rrs genes has not been reported.

Methods

The 16S rRNA genes of 138 clinical, strictly anaerobic isolates and one reference strain were directly sequenced, and the chromatograms were carefully examined. Gene cloning was performed for 22 typical isolates with doublet sequencing signals for the 16S rRNA genes, and four copies of the rrs-ITS genes of 9 Prevotella intermedia isolates were separately amplified by PCR, sequenced and compared. Five conserved housekeeping genes, hsp60, recA, dnaJ, gyrB1 and rpoB from 89 clinical isolates of Prevotella were also amplified by PCR and sequenced for identification and phylogenetic analysis along with 18 Prevotella reference strains.

Results

Heterogeneity of 16S rRNA genes was apparent in clinical, strictly anaerobic oral bacteria, particularly in the genera Prevotella and Veillonella. One hundred out of 138 anaerobic strains (72%) had intragenomic nucleotide polymorphisms (SNPs) in multiple locations, and 13 strains (9.4%) had intragenomic insertions or deletions in the 16S rRNA gene. In the genera Prevotella and Veillonella, 75% (67/89) and 100% (19/19) of the strains had SNPs in the 16S rRNA gene, respectively. Gene cloning and separate amplifications of four copies of the rrs-ITS genes confirmed that 2 to 4 heterogeneous 16S rRNA copies existed.

Conclusion

Sequence alignment of five housekeeping genes revealed that intra-species nucleotide similarities were very high in the genera Prevotella, ranging from 94.3–100%. However, the inter-species similarities were relatively low, ranging from 68.7–97.9%. The housekeeping genes rpoB and gyrB1 were demonstrated to be alternative classification markers to the species level based on intra- and inter-species comparisons, whereas based on phylogenetic tree rpoB proved to be reliable phylogenetic marker for the genus Prevotella.     

慈姑45S rDNA和端粒序列检测及核型分析

以45S r DNA和拟南芥型端粒序列为探针对慈姑(Sagittaria trifolia L.)有丝分裂中期染色体进行单色和双色荧光原位杂交分析,并用银染方法检测慈姑45S r DNA位点的表达,最后结合染色体测量数据和45S r DNA杂交信号建立慈姑的核型。结果显示,慈姑的单倍基因组总长度为76.9±1.38μm,最长染色体为11.55±0.10μm,最短染色体为4.54±0.27μm;慈姑的核型公式为:2n=22=2m+2sm+14st+4t,核型不对称性参数CI、A1、A2、As K(%)、AI分别为19.86±11.06、0.72、0.27、78.82、15.29,核型属于Stebbins类型中的3B型。慈姑具有3对45S r DNA位点,分别位于第8、9、10号染色体的短臂末端。拟南芥型端粒序列的杂交信号出现在慈姑每一条染色体的长、短臂末端。银染检测到6个Ag-NOR和6个核仁,表明3对45S r DNA位点在间期核都有表达。本研究结果为药食兼用植物慈姑提供了分子细胞遗传学基础资料。     

植物排放甲烷的研究进展

甲烷是一种重要的大气痕量气体,参与全球变暖和大气化学作用。传统上已知的甲烷生物排放源只有专性厌氧的原核生物即甲烷产生菌。然而近年来有研究发现,植物在好氧条件下能通过一种未知的机理排放甲烷,即非微生物机制产生甲烷。本文对植物排放甲烷的研究进展进行了综述,并提出了今后应加强研究的方面。     

Two New Diophrys‐Like Genera and Their Type Species,Apodiophrys ovalis n. g., n. sp. and Heterodiophrys zhui n. g., n. sp. (Ciliophora: Euplotida), with Notes on Their Molecular Phylogeny

ABSTRACT. Based on both morphological and molecular information, two new euplotid genera Apodiophrys n. g. and Heterodiophrys n. g. are described in the present paper. Apodiophrys n. g. is defined as sculptured Diophryinae with bipartite adoral zone; frontoventral cirri arranged in Diophrys‐pattern; marginal cirri located in two clearly separated groups. Heterodiophrys n. g. is recognizable by the combination of Diophrys‐like frontoventral cirri and the unique structure of several marginal cirri that are arranged in a long row. The type species for both new genera, Apodiophrys ovalis n. sp. and Heterodiophrys zhui n. sp., collected from southern China sea, are described. The small subunit rRNA (SSU rRNA) gene sequences for both new taxa are determined. Phylogenetic analyses based on these data indicate that Apodiophrys is most closely related to Paradiophrys, which then clusters with Uronychia species. Thus, Apodiophrys–Paradiophrys is separated from other typical Diophrys‐like genera in the SSU rRNA gene trees. The new genus Heterodiophrys is basal to the sister group of Diophrys–Diophryopsis, hence belongs to the “core”Diophrys‐complex.     

乳糖操纵子介导的半乳糖苷酶在转基因动物中的应用前景

细菌的乳糖操纵子可以在哺乳动物中调控基因的表达,修饰阻抑物基因和操纵基因可调控阻抑物诱导能力及其对操纵基因的亲和力,更好的适应高等动物的内环境。半乳糖苷酶对乳糖操纵子系统有正向调控作用,利用乳糖操纵子在转基因动物中可诱导性调控半乳糖苷酶基因的表达,能有效的提高转基因动物利用半乳糖苷、吸收营养物质的能力。以下从乳糖操纵子的结构功能、乳糖阻抑物功能活性的基因调控、操纵基因的功能以及其在哺乳动物的应用现状四个方面,结合半乳糖苷酶的生理功能和其在转基因动物中应用两个方面进行综述,对乳糖操纵子介导的半乳糖苷酶在转基因动物中的应用效果和前景进行了分析探讨。     

基于多分类支持向量机的基因表达系列分析

基因表达系列分析(Serial analysis of gene expression,SAGE)是一种基因表达数据,反映了细胞内的动态变化。模式识别和可视化方法是分析SAGE数据的基本工具,但是由于缺乏描述数据的统计特性,传统的聚类分析技术不适用于SAGE数据的分析。本文提出了一种基于多分类和支持向量机的SAGE数据的分析法。经过对模拟数据和人类癌症SAGE数据的分析,基于径向基核函数的多分类支持向量机算法"一对一"(one-against-one,OAO)算法提供了比PoissonC和PoissonS更好的分类结果。     

Exogenous H<Subscript>2</Subscript>O<Subscript>2</Subscript> improves the chilling tolerance of manilagrass and mascarenegrass by activating the antioxidative system

The effect of foliar pretreatment by hydrogen peroxide (H₂O₂) at low concentrations of 0, 5, 10, and 15 mM on the chilling tolerance of two Zoysia cultivars, manilagrass (Zoysia matrella) and mascarenegrass (Zoysia tenuifolia), was studied. The optimal concentration for H₂O₂ pretreatment was 10 mM, as demonstrated by the lowest malondialdehyde (MDA) content and electrolyte leakage (EL) levels and higher protein content under chilling stress (7°C/2°C, day/night). Prior to initiation of chilling, exogenous 10 mM H₂O₂ significantly increased catalase (CAT), ascorbate peroxidase (APX), glutathione-dependent peroxidases (GPX), and glutathione-S-transferase (GST) activities in manilagrass, and guaiacol peroxidase (POD), APX, and glutathione reductase (GR) activities in mascarenegrass, suggesting that H₂O₂ may act as a signaling molecule, inducing protective metabolic responses against further oxidative damage due to chilling. Under further stress, optimal pretreatments alleviated the increase of H₂O₂ level and the decrease of turfgrass quality, and improved CAT, POD, APX, GR, and GPX activities, with especially significant enhancement of APX and GPX activities from the initiation to end of chilling. These antioxidative enzymes were likely the important factors for acquisition of tolerance to chilling stress in the two Zoysia cultivars. Our results showed that pretreatment with H₂O₂ at appropriate concentration may improve the tolerance of warm-season Zoysia grasses to chilling stress, and that manilagrass had better tolerance to chilling, as evaluated by lower MDA and EL, and better turfgrass quality, regardless of the pretreatment applied.     

留学生组织学全英文教学的探索与实践

我教研室已承担留学生组织学教学多年,在对留学生进行组织学全英文授课的教学实践中,为了提高教学质量,我们从课程安排、教材选用、教学方法、教学手段以及考试与成绩等方面进行了的探索和改革,并对留学生教学中遇到的语言交流问题进行分析,总结了提高外语水平的经验.本文就留学生组织学教学的探索与实践作了介绍,以便大家互相交流经验,共同提高.     

肝炎后肝硬化患者肝癌发生的保护因素与危险因素研究

目的:通过回顾性病例对照研究,探讨多种因素在病毒性肝炎后肝化门静脉高压症患者HCC发生过程中的作用以及脾切除是否抑制了肝癌的发生进程。方法:收集第四军医大学西京医院病案统计室检索2002年1月～2008年12月之间出院诊断为病毒性肝炎后(HBV/HCV)肝硬化门脉高压的病例2300余例,收集所有病例的一般资料,临床及实验室检查数据,影象学检查结果,以及在治疗过程中的脾切除手术史。采用病例对照,按年龄、性别两个指标进行1:1配对,根据研究对象是否合并HCC将其分为合并HCC组(组1),未合并HCC组(组2),采用SPSS17.0进行单因素分析及多因素logistic回归分析。结果:描述性统计结果显示,两组的ALB、AST、TP、ALP、GGT等差异有统计学意义(P<0.05),而PLT、ALT、TBIL等在两组间差异无统计学意义(P>0.05)。将单因素分析有意义的研究因素纳入多因素logistic回归方程得知,AST、ALP、GGT异常升高增加了肝癌发生的危险性,而行脾切除和门奇断流术明显降低了肝癌发生的危险性,仅为无手术患者肝癌发生危险性的57.1%(OR:0.571,95%CI:0.394～0.825)。...     

大鼠去神经支配脾脏内淋巴细胞ERK表达变化的研究

目的:探讨脾脏神经支配与免疫功能关系.方法:清洁级成年雄性SD大鼠20只,随机分成实验组、对照组.手术切除实验组10只大鼠脾脏神经纤维,饲养1周后取出脾脏,4%多聚甲醛固定,石蜡切片行HE染色及ABC免疫组织化学染色.结果:(1)HE染色两组大鼠脾脏结构结构清晰,动脉周围淋巴鞘内淋巴细胞密集成团状,红髓内可见大量红细胞,在去除大鼠脾脏神经支配的实验组较对照组脾脏大体结构无明显变化;(2)两组脾脏淋巴细胞均有ERK表达,对照组正常脾脏表达ERK阳性细胞占16.2%,实验组仅占6.0%.实验组脾脏内表达ERK阳性细胞数量明显低于对照组,差异具有显著性(P＜0.01),同时ERK表达量也低于对照组,且差异具有显著性(P＜0.01).结论:在去除神经支配后,脾脏内淋巴细胞增殖活性明显降低,在一定程度上影响到脾脏免疫功能.