γ-Glutamylcysteine Production by Escherichia coli B Cells Dosed with the γ-Glutamylcysteine Synthetase Gene

Molecular studies on the evolution and systematics of fungi have been established primarily based on the neutral theory by analyzing neutral mutations in some defined segments of housekeeping genes as genetic markers. Such an approach is, however, hardly applicable for analyzing ancient evolutionary radiations. In the present study, we looked for DNA sequences characterizing higher taxa, and discovered a unique macroevolutionary genomic marker, megB1, that specifies the phylum Basidiomycota. megB1 is an approximately 500-bp DNA element, which is defined by terminal sequences and five internal segments conserved throughout the phylum. megB1 resides on the rDNA intergenic spacer 1 (IGS1) from 27 species of 10 Basidiomycota genera examined. While megB1 was not found in IGS1 from the other 92 species of the 27 Basidiomycota genera, several genera representing them carry megB1 in some other genomic regions. No known taxonomic criteria fit into the classification on the basis of whether megB1 resides on rDNA. Neighbor-joining analysis of the megB1 sequence, however, properly assigned species to their respective genera. Thus far, megB1 has not been found in any genomic or genetic databases currently available for other phyla. These results suggest that megB1 may have emerged upon the occurrence of Basidiomycota, and that this phylum evolved thereafter leaving this element conserved throughout their further differentiation. megB1 may be a novel genomic marker useful in the analysis of ancient through the latest evolutionary radiation in Basidiomycota.     

子囊菌的一个新目Umbilicariales J.C. Wei & Q.M. Zhou

本文基于核糖体SSU rDNA序列对石耳科Umbilicariaceae的系统地位进行了研究.将所获得的石耳科地衣中6个种的SSU rDNA序列与GenBank中其它地衣型及非地衣型真菌的相关序列进行比对用于系统发育研究.结果表明长期以来系统地位不够明确而暂时被置于茶渍目Lecanorales的石耳科不能被包括在茶渍目中,分子数据支持成立石耳目Umbilicariales.基于分子数据并结合形态学和解剖学特征描述了新目Umbilicariales J.C. Wei & Q.M. Zhou(Lecanoromycetes,Ascomycota).     

子囊菌的一个新目Umbilicariales J.C.Wei & Q.M.Zhou

本文基于核糖体SSU rDNA序列对石耳科Umbilicariaceae的系统地位进行了研究.将所获得的石耳科地衣中6个种的SSU rDNA序列与GenBank中其它地衣型及非地衣型真菌的相关序列进行比对用于系统发育研究.结果表明长期以来系统地位不够明确而暂时被置于茶渍目Lecanorales的石耳科不能被包括在茶渍目中,分子数据支持成立石耳目Umbilicariales.基于分子数据并结合形态学和解剖学特征描述了新目Umbilicariales J.C. Wei ＆ Q.M. Zhou（Lecanoromycetes,Ascomycota）.     

CHROMOPHYTE PLASTID 16S RIBOSOMAL RNA GENES FOUND IN A CLONE LIBRARY FROM ATLANTIC OCEAN SEAWATER

In recent years, the cloning of ribosomal RNA genes from natural plankton communities has provided insight into the biodiversity of marine bacterioplankton. Small eukaryotic phytoplankton, like bacterioplankton, can be difficult to cultivate or identify routinely by morphological characteristics. We used bacteria-specific 16S rRNA primers to amplify genes from picoplankton samples collected on 0.2–μm filters by filtration from a depth of 10 m in the pelagic region over the continental shelf off Cape Hatteras, North Carolina. Nucleic acid sequencing and probe hybridization revealed that chromophyte plastid genes comprised 25% of the genes in a library of 170 clones. The plastid genes belonged to two groups within the Chromophyta: the Prymnesiophyceae and the Bacillariophyceae. Comparisons revealed substantial diversity among the bacillariophyte gene sequences, but the species from which the genes originated could not be identified because few sequences from cultured bacillariophytes are available. The prymnesiophyte genes could not be identified either, although they were most similar (similarity = 0.94) to plastid genes from the coccolithophorid Emiliania huxleyi (Lohmann) Hay and Mohler strain PML92D. These results provide evidence of abundant chromophyte plastid 16S rRNA genes in the water over the continental shelf off Cape Hatteras. The results also suggest that plastid 16S rRNA genes may provide suitable genetic markers for studying phytoplankton biodiversity and biogeography .     

Vannella epipetala n. sp. isolated from the leaf surface of Spondias mombin (Anacardiaceae) growing in the dry forest of Costa Rica

As part of a Microbial Observatory of Caterpillars located in the Area de Conservacíon Guanacaste (ACG) in northwestern Costa Rica, we isolated a novel species of the genus Vannella associated with the food of the caterpillars of the saturniid moth Rothschildia lebeau, namely the leaves of the dry forest deciduous tree Spondias mombin (Anacardiaceae). The new species can be distinguished from other described species of the genus by the presence of a plasmalemma coated with a thickened, osmiophilic lamina containing glycostyles, and by its unusual habitat, the leaf surfaces or phylosphere of S. mombin. We further established the novelty of our isolate by sequencing its nuclear small-subunit (SSU) rRNA gene and inferring its phylogenetic position among all other currently sequenced members of the genera Vannella and Platyamoeba. Our results reveal that our isolate shares most recent common ancestry with three strains of Platyamoeba placida, the type species of the genus Platyamoeba. Despite this placement, the isolate clearly possesses glycostyles that are the hallmark of the genus Vannella. In addition to the cultured isolate, we also present a closely related sequence from a SSU rRNA gene clone library constructed from a DNA extract of leaf-wash of S. mombin with sterile water.     

Relationships among orders and families of marsupials based on 12S ribosomal DNA sequences and the timing of the marsupial radiation

Part of the mitochondrial 12S ribosomal RNA gene was amplified and sequenced for 26 marsupials. Multiple alignments for these sequences as well as seven additional sequences taken from GenBank were obtained using CLUSTAL. PAUP was used for phylogenetic analysis and to obtain random tree-length distributions. Analyses were performed with and without phylogenetic constraints. Our results clearly show that 12S rDNA contains phylogenetic signal at and above the ordinal level and is thus appropriate for addressing phylogenetic questions deep in the mammalian tree. Standard parsimony analyses provide some support for a clade containing diprotodontians, dasyurids,Dromiciops, andNotoryctes; transversion parsimony analysis suggests the possible inclusion of peramelids as well. Within the Diprotodontia, vombatids and phascolarctids cluster together on transversion parsimony and phalangerids may be associated with this clade. The enigmatic tarsipedids are apparently part of a clade that also contains pseudocheirids, petaurids, and acrobatids. The 12S sequences suggest that the origination of extant marsupial orders peaked 15 million years later than the equivalent taxonomic diversification of extant placental orders and may be entirely post-Cretaceous. Families of diprotodontian marsupials originated during the Eocene and early Oligocene, which is consistent with previous single-copy DNA hybridization results.     

Delimitation of the Thoracosphaeraceae (Dinophyceae), including the calcareous dinoflagellates, based on large amounts of ribosomal RNA sequence data

The phylogenetic relationships of the Dinophyceae (Alveolata) are not sufficiently resolved at present. The Thoracosphaeraceae (Peridiniales) are the only group of the Alveolata that include members with calcareous coccoid stages; this trait is considered apomorphic. Although the coccoid stage apparently is not calcareous, Bysmatrum has been assigned to the Thoracosphaeraceae based on thecal morphology. We tested the monophyly of the Thoracosphaeraceae using large sets of ribosomal RNA sequence data of the Alveolata including the Dinophyceae. Phylogenetic analyses were performed using Maximum Likelihood and Bayesian approaches. The Thoracosphaeraceae were monophyletic, but included also a number of non-calcareous dinophytes (such as Pentapharsodinium and Pfiesteria) and even parasites (such as Duboscquodinium and Tintinnophagus). Bysmatrum had an isolated and uncertain phylogenetic position outside the Thoracosphaeraceae. The phylogenetic relationships among calcareous dinophytes appear complex, and the assumption of the single origin of the potential to produce calcareous structures is challenged. The application of concatenated ribosomal RNA sequence data may prove promising for phylogenetic reconstructions of the Dinophyceae in future.     

分子系统学原理及其在林木上的应用

综述了林木分子系统学的是新研究进展,分析了现代分子生物学方法的不断改进给林木系统学研究带来的革命性进展,阐述了RAPD,cpDNA,rDNA等在林木分子系统学研究中的应用及取得的成果,评述了各种不同分子标记的适用范围以及对相关基因进化规律的认识,同时提出了这些分子标记在分子系统学研究中应注意的一些问题。     

分子系统学在微体古生物及相关领域中的应用

核酸（ＤＮＡ和ＲＮＡ）和蛋白等生物大分子（尤其是它们的序列资料）可作为重要的生物性状用于系统分类和演化等主题的研究。相对于形态学性状而言,分子性状不仅是前者的补充,而且具有许多前者无法比拟的优点;比如ＤＮＡ作为遗传信息的直接载体能较准确地反映生物类群之间的系统发生关系、信息量巨大、易于定量化和进行计算机分析等等。分子古生物研究包含两个方面：一、发掘化石生物分子,以提供历史生物界演化过程中的直接遗传学证据以及检验分子演化速率等方面的独特数据;二、利用现代分子生物学数据,探讨化石生物界的系统发生问题。上述两个研究方向均已成为当今演化生物学领域的热点。有孔虫等具有重要化石记录的微体生物的分子系统学研究已经开始。随着现生的和化石的生物分子资料的逐渐积累,预期在不久的将来,分子资料将成为微体古生物研究中不可缺少的重要数据之一。     

Naturalists, Molecular Biologists, and the Challenges of Molecular Evolution

Biologists and historians often present natural history and molecular biology as distinct, perhaps conflicting, fields in biological research. Such accounts, although supported by abundant evidence, overlook important areas of overlap between these areas. Focusing upon examples drawn particularly from systematics and molecular evolution, I argue that naturalists and molecular biologists often share questions, methods, and forms of explanation. Acknowledging these interdisciplinary efforts provides a more balanced account of the development of biology during the post-World War II era. This revised version was published online in July 2006 with corrections to the Cover Date.     

常用核基因序列在双翅目昆虫系统学中的研究进展

双翅目昆虫分为长角亚目和短角亚目,前者主要类群包括蚊、蠓、蛉和蚋,后者主要类群为虻类和蝇类。国内外学者对双翅目昆虫形态分类和分子系统发育关系研究均较多。本文整理总结了几种主要核基因在双翅目昆虫进化和系统发育关系的研究资料,结果显示:双翅目的单系性得到了众多形态学、生物学和分子数据的支持,多数系统发育研究认为传统的长角亚目为并系,短角亚目是一个单系,其主要类群舞虻下目、环裂类、有缝组和有瓣蝇类均为单系,但非环裂类、无缝组为并系,无瓣类可能为并系;基本搞清了有重要医学意义和与环境关系密切的类群,特别是有瓣蝇类各科类群分类系统的进化关系;双翅目昆虫发生辐射进化的三个分支节点时间即:低等双翅目(蚊类)2.2亿年、低等短角亚目(虻类)1.8亿年、有缝组(蝇类)6500万年;大量双翅目昆虫自然生命史历经吸血性、植食性和寄生性,有2.6亿年以上的演化历程。从相关核基因研究中总结出:18SrRNA、28SrRNA和CAD基因能很好的解决高级阶元从目到属的系统发育问题;EF-1ɑ基因和White基因更适合从科到属水平的分类阶元;ITS基因一般应用在从属到种水平的低级分类阶元,并被广泛应用到双翅目昆虫分子系统学研究中。