Extensive variation in chromosome number and genome size in sexual and parthenogenetic species of the jumping‐bristletail genus Machilis (Archaeognatha)

Parthenogenesis in animals is often associated with polyploidy and restriction to extreme habitats or recently deglaciated areas. It has been hypothesized that benefits conferred by asexual reproduction and polyploidy are essential for colonizing these habitats. However, while evolutionary routes to parthenogenesis are manifold, study systems including polyploids are scarce in arthropods. The jumping‐bristletail genus Machilis (Insecta: Archaeognatha) includes both sexual and parthenogenetic species, and recently, the occurrence of polyploidy has been postulated. Here, we applied flow cytometry, karyotyping, and mitochondrial DNA sequencing to three sexual and five putatively parthenogenetic Eastern‐Alpine Machilis species to investigate whether (1) parthenogenesis originated once or multiply and (2) whether parthenogenesis is strictly associated with polyploidy. The mitochondrial phylogeny revealed that parthenogenesis evolved at least five times independently among Eastern‐Alpine representatives of this genus. One parthenogenetic species was exclusively triploid, while a second consisted of both diploid and triploid populations. The three other parthenogenetic species and all sexual species were diploid. Our results thus indicate that polyploidy can co‐occur with parthenogenesis, but that it was not mandatory for the emergence of parthenogenesis in Machilis. Overall, we found a weak negative correlation of monoploid genome size (Cx) and chromosome base number (x), and this connection is stronger among parthenogenetic species alone. Likewise, monoploid genome size decreased with elevation, and we therefore hypothesize that genome downsizing could have been crucial for the persistence of alpine Machilis species. Finally, we discuss the evolutionary consequences of intraspecific chromosomal rearrangements and the presence of B chromosomes. In doing so, we highlight the potential of Alpine Machilis species for research on chromosomal and genome‐size alterations during speciation.     

基于结构信息的RNA多序列比对

多序列比对是生物信息学中重要的基础研究内容,对各种RNA序列分析方法而言,这也是非常重要的一步。不像DNA和蛋白质,许多功能RNA分子的序列保守性要远差于其结构的保守性,因此,对RNA的分析研究要求其多序列比对不仅要考虑序列信息,而且要充分考虑到其结构信息。本文提出了一种考虑了结构信息的同源RNA多序列比对算法,它先利用热力学方法计算出每条序列的配对概率矩阵,得到结构信息,由此构造各条序列的结构信息矢量,结合传统序列比对方法,提出优化目标函数,采用动态规划算法和渐进比对得到最后的多序列比对。试验证实该方法的有效性。     

Recent progress in 8igenomic research of liver cancer

Along the course of occurrence and development of liver cancer, the corresponding somatic cells accumulate some important genetic variations. These variations may be divided into two categories. For the genetic changes closely related to etiology of liver cancer, the well-known cases include insertion and integration of the hepatitis B virus (HBV) DNA after infection, and mutations at site 249 of the tumor suppressor gene p53 induced by exposure to aflatoxin B1. The secondary genetic changes include amplification and deletion of certain chromosome regions, mutations in p53 at the sites other than 249, as well as the mutational activation of the Wnt/β-catenin signal pathway. The tumor cells with these genetic variations may gradually become the dominant clones under evolutionary selection. Besides, identification of genetic susceptible against risk of liver malignancy is also an important aspect of research in this field. Supported by the National Natural Science Foundation of China (Grant No. 30425019)     

A review on data mining and continuous optimization applications in computational biology and medicine

An emerging research area in computational biology and biotechnology is devoted to mathematical modeling and prediction of gene‐expression patterns; it nowadays requests mathematics to deeply understand its foundations. This article surveys data mining and machine learning methods for an analysis of complex systems in computational biology. It mathematically deepens recent advances in modeling and prediction by rigorously introducing the environment and aspects of errors and uncertainty into the genetic context within the framework of matrix and interval arithmetics. Given the data from DNA microarray experiments and environmental measurements, we extract nonlinear ordinary differential equations which contain parameters that are to be determined. This is done by a generalized Chebychev approximation and generalized semi‐infinite optimization. Then, time‐discretized dynamical systems are studied. By a combinatorial algorithm which constructs and follows polyhedra sequences, the region of parametric stability is detected. In addition, we analyze the topological landscape of gene‐environment networks in terms of structural stability. As a second strategy, we will review recent model selection and kernel learning methods for binary classification which can be used to classify microarray data for cancerous cells or for discrimination of other kind of diseases. This review is practically motivated and theoretically elaborated; it is devoted to a contribution to better health care, progress in medicine, a better education, and more healthy living conditions. Birth Defects Research (Part C) 87:165–181, 2009. © 2009 Wiley‐Liss, Inc.     

α-葡萄糖苷酶抑制剂的构效关系

为建立抑制剂与α 葡萄糖苷酶之间的构效关系 ,按照Dixon的方法测定了多种糖及糖衍生物的抑酶性 .共出现 3种Dixon曲线 ,分别代表了 3种不同的酶结合方式 .这些糖和糖衍生物的结构变化 (如羟基构象、C 1位取代基、聚合度等的变化 )都会影响其与酶的结合能力 .结果表明 ,与酶有高结合力的物质需要满足一定的结构要求 ,如恰当的羟基构象、阳离子、共价连接的环形成的半椅状或椅状构型等     

肾综合征出血热纯化疫苗的SDS-PAGE分析

为了证明蛑综合征出血热纯化疫苗的主要成分坦病毒蛋白,采用出血热纯化疫苗经浓缩后进行SDS－PAGE和Western-blotting分析。结果 经SDS－PAGE显示,肾综合征出血热纯化疫苗有三条蛋白带,分子量分别约为70kD、55kD和50kD,与汉坦病毒三种结构蛋白（糖蛋白G1、G2和核蛋白NP）的分子量相符;经Western-blotting显示,分子量50kD的蛋白带反应阳性,分子量70kD和55kD的蛋白带无反应,认定出血热纯化疫苗的主要成分为汉坦病毒蛋白,主要由G1、G2和NP三种结构蛋白构成。     

Prediction of the coding sequences of mouse homologues of KIAA gene: II. The complete nucleotide sequences of 400 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries.

We have accumulated information of the coding sequences of uncharacterized human genes, which are known as KIAA genes, and the number of these genes exceeds 2000 at present. As an extension of this sequencing project, we recently have begun to accumulate mouse KIAA-homologous cDNAs, because it would be useful to prepare a set of human and mouse homologous cDNA pairs for further functional analysis of the KIAA genes. We herein present the entire sequences of 400 mouse KIAA cDNA clones and 4 novel cDNA clones which were incidentally identified during this project. Most of clones entirely sequenced in this study were selected by computer-assisted analysis of terminal sequences of the cDNAs. The average size of the 404 cDNA sequences reached 5.3 kb and that of the deduced amino acid sequences from these cDNAs was 868 amino acid residues. The results of sequence analyses of these clones showed that single mouse KIAA cDNAs bridged two different human KIAA cDNAs in some cases, which indicated that these two human KIAA cDNAs were derived from single genes although they had been supposed to originate from different genes. Furthermore, we successfully mapped all the mouse KIAA cDNAs along the genome using a recently published mouse genome draft sequence.     

红系细胞中Cre重组酶介导的位点特异性片段交换

Cre介导的片段交换技术利用重组酶Cre的位点特异性重组特性 ,在基因组的特定位点进行靶片段与目的片段的交换。运用互为反向的Lox位点 ,在鼠红白血病MEL细胞中进行靶载体的整合和交换载体的交换 ,探讨在特定的染色质环境下红系特异性顺式作用元件的功能。电穿孔转染MEL细胞后从含有潮霉素 (hygromycin)的选择性半固体培养基中挑取MEL细胞单克隆 ,通过PCR和Southern杂交鉴定整合完整性和拷贝数 ,获得三种整合有靶载体p1L HyTk L1 β EGFP neo的细胞株A ,B和D。交换载体pL1 HS2 1L(含有 732 bp的人β 珠蛋白基因簇 5′DNaseI高敏位点 2核心片段 )和Cre表达载体pBS185共转染细胞株A ,9 (1,3 二羟 2丙氧甲基 )鸟嘌呤 (gancyclovir)负筛选后挑取单细胞克隆A HS。PCR检测显示HS2片段以反方向进行了交换。流式细胞仪分析显示平均的荧光细胞百分比 (2 .4 2 % )低于未交换的细胞株A (35 .94 % )。A HS中EGFP的低表达可能是处于非容许方向的HS2片段出现方向依赖性基因沉默所致。     

GDNF缺失突变体的设计及其结构与功能关系(英文)

研究了GDNF结构与功能的关系 .基于鼠源GDNF的晶体结构 ,利用计算机SGIIndigo2(R4 4 0 0 )工作站和InsightⅡ (95.5)蛋白质分析软件模拟了人GDNF三维结构 ,设计了GDNF分子的两个缺失突变体ΔN1 2 8和ΔN78 90 .以野生型GDNFcDNA作为模板 ,用PCR法得到编码缺失突变体的DNA片段 .将大肠杆菌作为表达系统 ,使缺失突变体GDNF在大肠杆菌中表达 ,对表达产物纯化和复性后进行生物活性测定 .两株突变体在大肠肝菌中获得了高效表达 ,纯化后的GDNF突变体ΔN1 2 8可以与存在于KG 1a细胞表面的受体结合 ,但不能促进 8日龄鸡胚背根节突起的生长 .突变体ΔN78 90既不能与受体结合 ,同时也失去了促背根节突起生长的功能 .说明GDNF分子的N端氨基酸对分子的生物学活性很重要 ,但对分子与受体GDNFR α的结合并不是必需的 ,而分子中的螺旋区对分子与受体的结合以及生物学活性都必不可少 .