Microcalorimetry as a possible tool for phylogenetic studies of Tetrahymena

Using isothermal microcalorimetry, the growth power-time curves of three strains of Tetrahymena were determined at 28°C. Their Euclidean distances and cluster analysis diagram were obtained by using two thermokinetic parameters (r and Q_log), which showed that T. thermophila BF₁ and T. thermophila BF₅ had a closer relationship. Compared with the single molecular biomarker (ITS1) method, microcalorimetry wasmaybe a simpler, more sensitive andmore economic technique in the phylogenetic studies of Tetrahymena species.     

<Emphasis Type="Italic">X</Emphasis>-Trees and Weighted Quartet Systems

In this note, we consider a finite set X and maps W from the set $ \mathcal{S}_{2|2} (X) $ of all 2, 2- splits of X into $ \mathbb{R}_{\geq 0} $. We show that such a map W is induced, in a canonical way, by a binary X-tree for which a positive length $ \mathcal{l} (e) $ is associated to every inner edge e if and only if (i) exactly two of the three numbers W(ab|cd),W(ac|bd), and W(ad|cb) vanish, for any four distinct elements a, b, c, d in X, (ii) $ a \neq d \quad\mathrm{and}\quad W (ab|xc) + W(ax|cd) = W(ab|cd) $ holds for all a, b, c, d, x in X with #{a, b, c, x} = #{b, c, d, x} = 4 and $ W(ab|cx),W(ax|cd) $ > 0, and (iii) $ W (ab|uv) \geq \quad \mathrm{min} (W(ab|uw), W(ab|vw)) $ holds for any five distinct elements a, b, u, v, w in X. Possible generalizations regarding arbitrary $ \mathbb{R} $-trees and applications regarding tree-reconstruction algorithms are indicated.AMS Subject Classification: 05C05, 92D15, 92B05.     

黄鳝DEAD-box家族PL10基因的克隆与序列分析

通过PCR克隆的方法，从黄鳝(Monopterus albus)中得到两个PL10基因的cDNA片段Mo PL10A和Mo PL10B，长度均为1．127kb，推测其编码375个氨基酸的蛋白片段．结合其他PL10类同源物序列，对这两条cDNA进行了分析和初步的功能推测．根据此片段的氨基酸序列构建的系统发育树与形态分类结果一致．在不同组织中的RT—PCR结果表明Mo PL10A和Mo PL10B的mRNA在各组织中的分布有差异．     

A Novel Insight into the Perfect Phylogeny Problem

One of the classical problem in computational biology is the character compatibility problem or perfect phylogeny problem. A standard formulation of this problem in terms of two closely related questions is the following. Given a data set consisting of a finite set X and a set

SNPlexing the human Y-chromosome: a single-assay system for major haplogroup screening

SNPs are one of the main sources of DNA variation among humans. Their unique properties make them useful polymorphic markers for a wide range of fields, such as medicine, forensics, and population genetics. Although several high-throughput techniques have been (and are being) developed for the vast typing of SNPs in the medical context, population genetic studies involve the typing of few and select SNPs for targeted research. This results in SNPs having to be typed in multiple reactions, consuming large amounts of time and of DNA. In order to improve the current situation in the area of human Y-chromosome diversity studies, we decided to employ a system based on a multiplex oligo ligation assay/PCR (OLA/PCR) followed by CE to create a Y multiplex capable of distinguishing, in a single reaction, all the major haplogroups and as many subhaplogroups on the Y-chromosome phylogeny as possible. Our efforts resulted in the creation of a robust and accurate 35plex (35 SNPs in a single reaction) that when tested on 165 human DNA samples from different geographic areas, proved capable of assigning samples to their corresponding haplogroup.     

Phylogenetic characterization of a mixed microbial community capable of degrading carbon tetrachloride

Two bacterial communities (NO92 and GBS) capable of degrading carbon tetrachloride (CT) were enriched from in-house CT-contaminated water. These communities are able to degrade CT in the presence of toluene. To characterize the community structure and diversity, one enrichment (NO92) was subjected to 16S ribosomal RNA (rRNA) gene-based molecular analysis. The 16S rRNA genes were amplified from the bulk genomic community DNA and cloned into plasmid vectors. Unique 16S rRNA gene clones, i.e., phylotypes, were detected by four tetrameric restriction enzymes. Together, 123 16S rRNA gene clones were obtained; thirty-one showed different restriction fragment length polymorphism (RFLP) patterns. About 73% of the clones belong to two dominant RFLP patterns. Phylogenetic analysis based on the partial 16S rRNA gene sequences of 10 major phylotypes showed that all the phylotypes that were sequenced were affiliated with the high G+C Gram-positive bacteria. Whereas seven of the phylotypes (∼80% of the clones) were closely related to Rhodococcus, the other three (∼5% of the clones) were related to Curtobacterium. These results suggest that this CT-degrading community is diverse but is predominated by closely related bacterial groups.     

A Chemometry of Aldrovanda vesiculosa L. (Waterwheel,Droseraceae) Populations

The genus Aldrovanda is a Palaeogene element containing a single extant species, Aldrovanda vesiculosa L. This aquatic carnivorous herb has a very wide range of distribution, natively covering four continents; however, it is a critically endangered aquatic plant species worldwide. Previous studies revealed that A. vesiculosa had an extremely low genetic variation. The main aim of the present paper is to explore, using chemometric tools, the diversity of 16 A. vesiculosa populations from various sites from four continents (Eurasia, Africa, Australia). Using chemometric data as markers for genetic diversity, we show the relationships of 16 A. vesiculosa populations from various sites, including four continents. Phytochemical markers allowed the identification of five well-supported (bootstrap > 90%) groups among the 16 populations sampled. The principal component analysis data support the idea that the strongly related African (Botswana) and Australian (Kimberley, NT, NW Australia) populations are the most distant ones, separated from the European and Asian ones. However, considering the five Australian populations sampled, three are nested within the Eurasian group. The chemometric data are correlated positively with the geographical distances between the samples, which suggests a tendency toward isolation for the most distant populations.     

On the complexity of SNP block partitioning under the perfect phylogeny model

Recent technologies for typing single nucleotide polymorphisms (SNPs) across a population are producing genome-wide genotype data for tens of thousands of SNP sites. The emergence of such large data sets underscores the importance of algorithms for large-scale haplotyping. Common haplotyping approaches first partition the SNPs into blocks of high linkage-disequilibrium, and then infer haplotypes for each block separately. We investigate an integrated haplotyping approach where a partition of the SNPs into a minimum number of non-contiguous subsets is sought, such that each subset can be haplotyped under the perfect phylogeny model. We show that finding an optimum partition is -hard even if we are guaranteed that two subsets suffice. On the positive side, we show that a variant of the problem, in which each subset is required to admit a perfect path phylogeny haplotyping, is solvable in polynomial time.     

中国喇叭螺属的系统发育关系和生物地理学初探(肺螺亚纲:柄眼目:虹蛹螺科)

本文运用支序分析方法和H enn ig86软件探讨了柄眼目虹蛹螺科喇叭螺属中国种类的系统发育关系。中国喇叭螺属种类现已知17种,主要分布于我国长江流域和秦岭以南的地区。选择H.tubif erum和G.hung erf ord ianus作为外群,运用命令ie*对原始数据集进行运算,并进行逐步加权处理,结果共得到步长=115,C I值=74,R I值=90的同等简约树2株,选择其中具有较少未解决系统关系的一株作为支序分析的首选支序图。支序分析的结果将中国喇叭螺属的17个种初步分为两组:喇叭螺组和贝喇叭螺组。贝喇叭螺组包括B.p licid ens和B.hubeina,喇叭螺组包括剩余的15种。该结果与J.T he le(1931)将喇叭螺属分为喇叭螺指名亚属和贝喇叭螺亚属相符。根据首选支序图,运用扩散-隔离分析方法对该属的动物地理学进行了分析和讨论,认为中国喇叭螺属现有分布格局的形成可能与青藏高原的隆起有关。     

角蝾螺精子的超微结构

用透射电镜(TEM)技术研究了角蝾螺精子的超微结构.成熟精子包括头部和尾部.头部由啤酒瓶状顶体与柱状细胞核构成.顶体内含物分布均匀,电子密度稍低于细胞核;顶体下腔呈细长管状,基部扩大成喇叭形,内有颗粒状物质分布.细胞核物质致密,电子密度高;核的前、后端都有一V字形凹陷,分别为核前窝和核后窝.尾部包括中段和末段.中段由5个线粒体围绕近、远端中心粒构成;末段细长鞭状,由中央轴丝及外包的质膜组成,轴丝为典型的"9+2"结构.比较了角蝾螺精子与相关腹足类精子结构的异同,分析了角蝾螺精子在腹足类系统演化中的地位.