The dimeric Mcm8–9 complex of Xenopus laevis likely has a conserved function for resistance to DNA damage

The success of Imatinib mesylate (STI571, Gleevec) in treating chronic myeloid leukemia (CML) is, to date, the crowning achievement of targeted molecular therapy in cancer. Nearly 90% of newly diagnosed patients treated with Imatinib in the chronic phase of the disease achieve a complete cytogenetic response. However, more than 95% of these patients retain detectable levels of BCR-ABL mRNA and patients discontinuing Imatinib therapy almost invariably relapse, demonstrating that an Imatinib insensitive population of leukemia-initiating cells (LICs) persists in nearly all patients. These findings underscore the need for treatments specifically targeting the leukemia-initiating population of CML cells. While mounting evidence suggests that the LIC in the chronic phase of CML is the BCR-ABL positive hematopoietic stem cell, several recent publications suggest that during CML blast crisis, a granulocyte-macrophage progenitor (GMP) population also acquires LIC properties through activation of the β-catenin pathway. Characterization of these cells and evaluation of their sensitivity to Imatinib is critical to our understanding and treatment of CML blast crisis.     

Molecular markers for systematic identification and population genetics of the invasive Ponto‐Caspian freshwater gammarid Dikerogammarus villosus (Crustacea,Amphipoda)

The Ponto‐Caspian amphipod, Dikerogammarus villosus, is an invasive species of many European rivers. First, we show that size difference of nrDNA ITS1 allows discriminating D. villosus from Dikerogammarus bispinosus, a closely related but morphologically hardly distinguishable species. Second, we present two types of polymorphic markers for D. villosus, three microsatellites and two single nucleotide polymorphisms (SNPs) of mtDNA COI gene, which were scored by polymerase chain reaction‐single strand conformational polymorphism (PCR‐SSCP). These markers will be very useful in studying population genetics of D. villosus.     

Mcm10 plays an essential role in origin DNA unwinding after loading of the CMG components

The CMG complex composed of Mcm2-7, Cdc45 and GINS is postulated to be the eukaryotic replicative DNA helicase, whose activation requires sequential recruitment of replication proteins onto Mcm2-7. Current models suggest that Mcm10 is involved in assembly of the CMG complex, and in tethering of DNA polymerase α at replication forks. Here, we report that Mcm10 is required for origin DNA unwinding after association of the CMG components with replication origins in fission yeast. A combination of promoter shut-off and the auxin-inducible protein degradation (off-aid) system efficiently depleted cellular Mcm10 to <0.5% of the wild-type level. Depletion of Mcm10 did not affect origin loading of Mcm2-7, Cdc45 or GINS, but impaired recruitment of RPA and DNA polymerases. Mutations in a conserved zinc finger of Mcm10 abolished RPA loading after recruitment of Mcm10. These results show that Mcm10, together with the CMG components, plays a novel essential role in origin DNA unwinding through its zinc-finger function.     

Phylogeny of the genus<Emphasis Type="Italic">Goodyera</Emphasis> (Orchidaceae; Cranichideae) in Korea based on nuclear ribosomal DNA ITS region sequences

We sequenced the nuclear ribosomal internal transcribed spacer (ITS) regions to determined the phylogenetic relationships of the severalGoodyera species in Korea and to measure the extent of their differentiation region. ITS 1 was 238 to 239 bp long while ITS 2 was 258 to 259 bp. The 5.8S coding region was 156 bp long. Sequence divergences among species, calculated by Kimura’s two- parameter method, ranged from 0.0 to 5.4%. The most parsimonious tree, with a consistency index of 0.935 and a retention index of 0.937, was produced with 337 steps. Our ITS sequence results demonstrate the monophyly of KoreanGoodyera and support previous morphological, geographical, and RAPD data analyses.     

鸡爪槭种下分类群的DNA条形码筛选

槭属鸡爪槭(Acer palmatum Thunb.)是北温带广泛分布的一类园艺观赏树种,由于频繁的种内杂交渐渗导致其种下分类群的形态性状特征趋同,致使传统的形态学分类难以准确鉴定,新兴的DNA条形码技术为快速、准确的鉴定鸡爪槭种下分类群提供了新的思路。本研究采用5个叶绿体DNA片段(rpl16、psbA-trnH、trnL-trnF、rbcL、matK)和核基因组ITS片段,运用PWG-distance和Tree-Building两种方法对鸡爪槭的8个分类群共32个个体进行DNA条形码分析。结果显示,单个叶绿体基因组片段(分辨率为0%~25%)或核rDNA ITS片段(12.5%)的分辨率较低,不同组合的叶绿体DNA片段(0%~62.5%)、叶绿体片段与核rDNA ITS片段(12.5%~50%)的分辨率则相对较高。其中,rpl16+psbA-trnH+trnL-trnF片段组合的分辨率最高(62.5%),较为符合DNA条形码快速、准确鉴定的要求,因此建议将其作为鸡爪槭种下分类群鉴定的DNA条形码。     

Genetic divergence and phylogenetic analysis of genus <Emphasis Type="Italic">Jatropha</Emphasis> based on nuclear ribosomal DNA ITS sequence

The genus Jatropha belongs to the family Euphorbiaceae having significant economic importance. The present investigation was undertaken with an aim to understand phylogenetic relationships among seven species (J. curcas, J. glandulifera, J. gossypifolia, J. integerrima, J. multifida, J. podagrica, and J. tanjorensis.) which are widely distributed in India, using nuclear ribosomal DNA ITS sequence (nrDNA ITS) and to compare the results with multilocus marker analysis systems reported earlier for the same genus. The size variation obtained among sequenced nrDNA ITS regions was narrow and ranged from 647 to 654 bp. The overall mean genetic distance (GD) of genus Jatropha was found to be 0.385. Highest interspecific GD (0.419) was found between J. glandulifera and J. multifida. The least interspecific GD (0.085) was found between J. gossypifolia and J. tanjorensis. The highest intraspecific GD was observed in J. podagrica (0.011) and least in J. gossypifolia (0.002). The phylogram obtained using nrDNA ITS sequence showed congruence with the phylograms obtained using multilocus markers system reported earlier with minor variations. The present study also strongly supports high phylogentic closeness of J. curcas and J. integerrima. The only exception found was J. podagrica which clustered with J. multifida in earlier based on multilocus marker analysis, was clustered with J. curcas in the present analysis. The sequence data generated in the present investigation will help for further studies in intraspecies population, and their phylogentic analysis, biogeographical, molecular evolution studies and also pave way for future phylogetic and/or evolution studies among the other groups belongs to the family Euphorbiaceae.     

真菌DNA条形码研究进展

DNA条形码（DNA barcode）是通过一段短的标准DNA片段实现物种的快速、准确和标准化鉴定。线粒体细胞色素C氧化酶亚基I（COI）基因作为动物的DNA条形码已广泛应用于物种鉴定中,在植物上已选定叶绿体rbcL和matK基因作为基本的DNA条形码。目前世界各国真菌学家正对不同的真菌类群进行不同基因片段的筛选与评价,并在第四届国际生命条形码大会上正式推荐了ITS作为真菌的首选DNA条形码。对国内外真菌DNA条形码的研究进展进行总结与分析,并展望真菌DNA条形码的应用前景。     

基于ITS序列西南地区不同居群薤白亲缘关系及其地理分布格局研究

该研究以西南地区分布的薤白(Allium macrostemon Bunge)为材料,对21个不同居群的薤白进行核糖体DNA的ITS序列测定,并结合GenBank相关序列,对27个不同居群薤白开展了系统分析,以探讨西南地区不同居群薤白的亲缘关系和生物地理分布格局。结果表明:(1)西南地区不同产区薤白nrDNA ITS序列长度介于607～638 bp之间,G+C含量为48%～52%,平均值为50%。(2)基于贝叶斯法和最大简约法构建的系统树均表明薤白为一单系群。(3)系统发育树分析结果显示,27个居群的薤白总体划分为a组和b组,其中位于西南地区东面的四川剑阁县、重庆巫溪县、贵州德江县和云南丘北县的薤白共同聚为a组,位于西南地区西面的四川汶川县、四川石棉县、四川江油市以及云南虎跳峡、云南昆明市、云南三坝的薤白归为b组。研究表明,nrDNA ITS序列可以鉴定不同地区薤白的亲缘关系。     

Development of Transformation System in Monascus Purpureus using an Autonomous Replication Vector with Aureobasidin A Resistance Gene

To enhance the variety of genetic tools and thus to promote molecular genetic study, aureobasidin A and its resistance gene were adopted as a new marker system together with the incorporation of the Gateway system to facilitate the introduction of long heterologous DNA fragments into Monascus purpureus. The minimum inhibitory concentration of aureobasidin A against Monascus was 0.05 μg/ml and a transformation efficiency of 17 colonies/μg DNA was obtained by the protoplast-PEG method with the vector pAUR316, containing the aureobasidin A resistance gene. Southern analysis of the transformants confirmed that pAUR316 exists as an independent vector, demonstrating that the AMA1 sequence acts as the autonomous replication sequence in M. purpureus. Through the use of the Gateway system, a polyketide synthase gene (7.8 kbp) responsible for citrinin biosynthesis was introduced. As a result, the transformants showed 1.5-fold higher production of citrinin than the wild-type strain. Received 21 September 2005; Revisions requested 5 October 2005; Revisions received 2 November 2005; Accepted 3 November 2005     

A likelihood framework to measure horizontal gene transfer

We suggest a likelihood-based approach to estimate an overall rate of horizontal gene transfer (HGT) in a simplified setting. To this end, we assume that the number of occurring HGT events within a given time interval follows a Poisson process. To obtain estimates for the rate of HGT, we simulate the distribution of tree topologies for different numbers of HGT events on a clocklike species tree. Using these simulated distributions, we estimate an HGT rate for a collection of gene trees representing a set of taxa. As an illustrative example, we use the "Clusters of Orthologous Groups of proteins" (COGs). We also perform a correction of the estimated rate taking into account the inaccuracies due to gene tree reconstructions. The results suggest a corrected HGT rate of about 0.36 per gene and unit time, in other words 11 HGT events have occurred on average among the 44 taxa of the COG species tree. A software package to estimate an HGT rate is available online (http://www.cibiv.at/software/hgt/).     

藏羚羊和藏野驴粪便真菌多样性比较研究

为探究西藏地区反刍动物(藏羚羊)和单胃草食动物(藏野驴)粪便中真菌群落结构,本研究采用ITS1区高通量测序方法分析西藏羌塘国家自然保护区藏羚羊和藏野驴新鲜粪便中真菌的多样性.结果表明:从5头藏羚羊新鲜粪便中共鉴定出5个门、15个纲、32个目、45个科和56个属的真菌;从5头藏野驴新鲜粪便中共鉴定出3个门、10个纲、18...     

Molecular diagnosis of Colletotrichum gloeosporioides causing Anthracnose/Dieback disease in Greater Yam (Dioscorea alata L.)

The Greater Yam (Dioscorea alata L.), a significant tropical tuber crop is highly affected by the anthracnose/dieback disease caused by Colletotrichum gloeosporioides, which greatly reduces the yield as well as market acceptability of the tubers. The different methods that could be used for proper identification of the pathogen by PCR were investigated. The studies indicate that species specific polymerase chain reaction assay based on highly conserved regions in ITS in the genome of the pathogen can be the best strategy for detection of this pathogen at species level. The use of genus specific primers was also successful in detection of Colletotrichum spp. The cloning and sequencing of evolutionarily conserved regions such as ITS, PelB and paralleling them with the available sequences in NCBI database is also costly but reliable approach. The various methods are elaborately tested and their use in diagnosis is discussed in detail.     

石耳属ITS条形码物种的快速鉴定

生物DNA条码是利用一个短的DNA标记进行生物的快速鉴定。以真菌界的石耳目、石耳科中的石耳属地衣的部分种类为材料,应用地衣共生菌的rDNA-ITS序列,对29种石耳属地衣进行鉴定,并初步探究其中部分种类特异的微型条码,为石耳属地衣的快速鉴定提供依据。