Ribosomal DNA gene and phylogenetic relationships of Diplura and lower Hexapods

The monophyly of Diplura and its phylogenetic relationship with other hexapods are important for understanding the phylogeny of Hexapoda. The complete 18SrRNA gene and partial 28SrRNA gene (D3-D5 region) from 2 dipluran species (Campodeidae and Japygidae), 2 proturan species, 3 collembolan species, and 1 locust species were sequenced. Combining related sequences in GenBank, phylogenetic trees of Hexapoda were constructed by MP method using a crustacean Artemia salina as an outgroup. The results indicated that: (i) the integrated data of 18SrDNA and 28SrDNA could provide better phylogenetic information, which well supported the monophyly of Diplura; (ii) Diplura had a close phylogenetic relationship to Protura with high bootstrap support.

Reconstructing the evolutionary history of China: A caveat about inferences drawn from ancient DNA

The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modem data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (similar to 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modem populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed.

Mitochondrial DNA Haplogroups M7b1 ' 2 and M8a Affect Clinical Expression of Leber Hereditary Optic Neuropathy in Chinese Families with the m.11778G -> A Mutation

Leber hereditary optic neuropathy (LHON) is the most extensively studied mitochondrial disease, with the majority of the cases being caused by one of three primary mitochondrial DNA (mtDNA) mutations. Incomplete disease penetrance and gender bias are two

Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: Implications for the peopling of South Asia

To resolve the phylogeny of the autochthonous mitochondrial DNA (mtDNA) haplogroups of India and determine the relationship between the Indian and western Eurasian mtDNA pools more precisely, a diverse subset of 75 macrohaplogroup N lineages was chosen fo

More evidence for non-maternal inheritance of mitochondrial DNA?

Background: A single case of paternal co-transmission ofmitochondrial DNA (mtDNA) in humans has been reported so far. Objective: To find potential instances of non-maternal inheritance of mtDNA. Methods: Published medical case studies (of single patients) were searched for irregular mtDNA patterns by comparing the given haplotype information for different clones or tissues with the worldwide mtDNA database as known to date-a method that has proved robust and reliable for the detection of flawed mtDNA sequence data. Results: More than 20 studies were found reporting clear cut instances with mtDNAs of different ancestries in single individuals. As examples, cases are reviewed from recent published reports which, at face value, may be taken as evidence for paternal inheritance of mtDNA or recombination. Conclusions: Multiple types (or recombinant types) of quite dissimilar mitochondrial DNA from different parts of the known mtDNA phylogeny are often reported in single individuals. From re-analyses and corrigenda of forensic mtDNA data, it is apparent that the phenomenon of mixed or mosaic mtDNA can be ascribed solely to contamination and sample mix up.

Phantom mutation hotspots in human mitochondrial DNA

Phantom mutations are systematic artifacts generated in the course of the sequencing process. Contra common belief these artificial mutations are nearly ubiquitous in sequencing results, albeit at frequencies that may vary dramatically. The amount of artifacts depends not only on the sort of automated sequencer and sequencing chemistry employed, but also on other lab-specific factors. An experimental study executed on four samples under various combinations of sequencing conditions revealed a number of phantom mutations occurring at the same sites of mitochondrial DNA (mtDNA) repeatedly. To confirm these and identify further hotspots for artifacts, > 5000 mtDNA electropherograms were screened for artificial patterns. Further, > 30000 published hypervariable segment 1 sequences were compared at potential hotspots for phantom mutations, especially for variation at positions 16085 and 16197. Resequencing of several samples confirmed the artificial nature of these and other polymorphisms in the original publications. Single-strand sequencing, as typically executed in medical and anthropological studies, is thus highly vulnerable to this kind of artifacts. In particular, phantom mutation hotspots could easily lead to misidentification of somatic mutations and to misinterpretations in all kinds of clinical mtDNA studies.

Analysis of mitochondrial DNA variants in Japanese patients with schizophrenia

To test the hypothesis that mitochondrial DNA (mtDNA) variants contribute to the susceptibility to schizophrenia, we sequenced the entire mtDNAs from 93 Japanese schizophrenic patients. Three non-synonymous homoplasmic variants in subunit six of the ATP s

DNA拓扑异构酶Ⅱ与ⅠA的进化分析

DNA拓扑异构酶与断开DNA链和改变其拓扑结构有关。先前的研究认为,拓扑异构酶TypeⅡB是由TypeⅡA通过基因的复制、重组和缺失所造成。然而,本研究结果则显示,TypeⅠA与TypeⅡB的进化关系较近,而TypeⅡA与TypeⅡB的关系较远。因此,TypeⅡB可能是由TypeⅠA演化而来,或者说,TypeⅡB是TypeⅠA在古细菌中的特化形式;TypeⅡB可能是由TypeⅡA通过形成TypeⅠA后演化而成的,而不是由TypeⅡA直接通过基因的复制、重组和缺失所造成。在由TypeⅡA演化成为TypeⅠA,最后演化为TypeⅡB的过程中,DNA拓扑异构酶的催化机制也发生了变化从需要金属离子的协助,演化到了不需要镁离子的存在协助其催化。

DNA 水平自然选择作用的检测

上个世纪60 年代, Kimura 提出的“中性进化”假说使经典的达尔文自然选择学说遭遇了前所未有 的挑战。但新近的研究表明: 在DNA 水平, 越来越多的证据支持“自然选择”的进化理论。这些研究成果得益 于近年来大量群体和基因组DNA 数据的积累, 以及理论群体遗传学的发展。在DNA 水平检测选择作用是否存 在的方法包括两大类: 种内多态性检验和种间差异度检验。前者以Tajima (1989) 提出的D 检验为代表, 后者 大都基于“中性条件下, 种内与种间进化速率一致”的原理。这些方法以中性假说作为零假设, 结合统计检验 方法分析DNA 数据, 被称为“中性检验”。这些方法对于解决一些有关进化的基础理论问题和人类遗传学及生 物信息学的深入研究都具有重要意义。本文介绍几个应用广泛的检测方法, 以使国内的读者了解它们的基本思 路和操作方法。

家鸡和原鸡的线粒体DNA多态性比较

本文运用１１种限制性内切酶分析了家鸡（茶花鸡、尼西鸡、大理漾濞黄鸡）和原鸡共１０只个体的线粒体ＤＮＡ限制性片段长度多态性（ＲＦＬＰ），平均每个个体检测到的片段为４０条左右。但仅发现３种变异的限制性格局，即ＳｔｕＩ－Ｂ，ＥｃａＵ－Ｂ和ＥｃｏＲＩ－Ｂ。其中ＳｔｕＩ─Ｂ和ＳｃａＩ─Ｂ为首次报道，而且均为原鸡所特有，ＥｃｏＲＩ─Ｂ则为大理漾濞黄鸡所特有。茶花鸡和尼西鸡拥有完全相同的限制性格局。经过计算，原鸡与茶花─尼西鸡的遗传距离为０．３２％，与漾濞黄鸡的遗传距离为０．４８％。上述结果提示，受试原鸡所代责的云南孟连亚群体可能是一个较为特殊的群体，应受到保护和注意。

云南保种山羊线粒体DNA限制性酶切研究

　采用碱变性法,提取来自云南省不同地区4个保种山羊的13个个体的线粒体DNA(mtDNA),并用ApaⅠ,AvaⅠ,BamHⅠ,BclⅠ,BcIⅠ，BglⅡ,ClaⅠ,DraⅠ, EcoRⅠ,EcoRⅤ,HaeⅠ,HindⅢ,KpnⅠ,PstⅠ,PvuⅡ,SacⅠ,SalⅠ,SmaⅠ,StuⅠ和XhoⅠ等20种限制性内切酶进行酶切分析。结果发现它们的线粒体DNA的分子量大 小约为15.8Kb；不同限制性内切酶的酶切位点分别为：DraⅠ有7个酶切位点，AvaⅢ有6个酶切位点，EcoRⅤ和StuⅠ共有5个酶切位点，HindⅡ和HaeⅡ有4个酶 切位点，BamHⅠ,BglⅡ,PstⅠ和PvuⅡ有3个酶切位点，ApaⅠ，ClaⅠ有两个酶切位点，其余有1个酶切位点。各保种山羊间未发现变异，说明云南的4个保种山 羊极可能来自于共同的母性祖先。

λ噬菌体DNA形成三链辫状结构的序列搜索

该文按照三碱基体中碱基的配合原则, 通过对λ噬菌体 DNA 核苷酸序列作计算机深度搜索. 在理论上建立了三链辫状结构模型。

DNA三链结构模型和能力学研究

该文按照用 STM 得到的一种变性 DNA 三链辫状结构图象, 用分子建筑术分别构建了三链辫状结构和三链螺旋结构的分子模型. 经过运用共轭梯度法优化后, 作了能量分析, 进而讨论了它们的稳定性和结构特征。

真核生物DNA甲基化作用与基因突变(英文)

迄今为止, 不少人认为5-甲基胞嘧啶的存在可能是基因突变的“热点”. 然而, 事实上5-甲基胞嘧啶作为一种稀有碱基, 本来就是许多真核生物 DNA 的正常组分. 它的存在也是真核生物DNA的特征之一. 作者几年来所作的理论研究表明, 5-甲基胞嘧啶不可能是基因突变的“热点”. 由胞嘧啶甲基化成为5-甲基胞嘧啶, 再经水解脱氨成为胸腺嘧啶的反应(C→m~(5)C→T)在正常生理条件下是不太可能发生的. 在真核生物DNA中, G—C碱基对转变为A—T碱基对的反应可能是由互变异构碱基配对或其它因素引起的。

一种改进的动物线粒体DNA提取方法

线粒体 DNA (mtDNA)已被广泛用于动物群体遗传学和进化生物学的研究, 并取得了许多有意义的结果. 有效的 mtDNA 提取方法无疑是开展这方面研究的前提. 关于动物 mtDNA 的提取方法, 国内外已有不少报导. 概括起来, 可分为: 1)氯化铯超速离心法, 2)柱层析法, 3)DNase法, 4)碱变性法. 该文报道了一种改进的碱变性提取法, 与其它方法相比, 具有应用范围广、简便、经济等优点。