Tamura模型下DNA序列点突变熵性质的研究

【目的】研究在较复杂的核苷酸替换模型,即Tamura模型下DNA序列中4种核苷酸频率随世代变化的规律,以得到序列熵的性质,为了解生物进化机理奠定基础。【方法】在Shannon信息熵理论基础上,利用La-grange乘数法进行理论证明,并用Mathematica软件模拟了Tamura模型下DNA序列中4种核苷酸组成的变化规律和序列熵的变化过程。【结果】DNA序列在Tamura模型下发生突变,各核苷酸频率随世代变化逐渐趋于平衡,且序列熵趋于最大值。【结论】核苷酸突变具有保熵性,验证了前人生物是朝着多样性增大的方向发展进化的结论。     

苏姜猪Lrh-1基因PCR-SSCP多态性及其与产仔数的关系

为深入研究苏姜猪肝受体类似物质-1(Lrh-1)基因的多态性及其与产仔数性状间相关性,依据NCBI数据库中猪Lrh-1基因核酸序列设计2对引物,采用聚合酶链式反应-单链构象多态性(PCR-SSCP)方法对苏姜猪Lrh-1基因进行多态性检测。检测结果显示,引物P1 PCR扩增产物存在7种SSCP条带型,共有4个碱基突变位点,分别为27287662、27287593、27287535和27287511位;引物P2 PCR扩增产物存在2种SSCP条带型,碱基突变位于27423038位;将扩增序列与猪Lrh-1CDS区进行比对分析,其中27287662、27287593和27423038位的碱基突变位于配体结合域(LBD)区内,且突变均属同义突变,表明LBD区对于Lrh-1基因功能稳定具有重要作用;不同碱基突变位点的基因频率经群体遗传学分析,除27287511位点处于群体不平衡状态(P0.05)外,其他位点均达群体平衡状态(P0.05);Lrh-1基因P1和P2扩增区SSCP不同类型苏姜猪第1胎和第2胎平均产仔数间无显著差异(P0.05)。     

绵羊MC1R和Agouti基因多态性与毛色性状的关联分析

[目的]MC1R和Agouti基因作为动物毛色主要候选基因,在调控黑色素的合成、参与毛色形成过程中起关键作用。研究绵羊MC1R和Agouti基因单核苷酸多态性,旨在探究MC1R和Agouti基因单核苷酸多态性与绵羊毛色的关系。[方法]随机采集特定杂交模式群体中黑色和白色绵羊的颈静脉血样各30份,提取DNA,并用PCR技术扩增MC1R和Agouti基因cDNA序列,测序获得目的片段碱基序列,比对后筛选分析MC1R和Agouti基因编码区SNPs位点,用SHEsis在线软件对单碱基突变位点连锁不平衡和单倍型分析。[结果]结果表明,受试群体中检测到的MC1R基因中有5个碱基突变位点,其中3个同义突变,2个错义突变;Agouti基因中检测到外显子4上有2个碱基突变位点,其中1个同义突变,1个错义突变。关联分析表明,Agouti基因中的2个突变位点及MC1R基因中的2个错义突变与被毛表型不相关(P0.05),MC1R基因中的3个同义突变位点与毛色性状显著相关(P0.05)。连锁不平衡发现,MC1R基因5个突变位点之间的连锁程度较强,单倍型分析表明,该群体中有8种单倍型组合,其中TGTGT和TGCTT与毛色显著相关(P0.05)。[结论]Agouti基因外显子的单核苷酸突变多态性与其被毛不相关,MC1R基因3个同义突变位点和2个单倍型组合与毛色性状相关。     

黔北麻羊LHβ基因多态性及其与产羔数的相关性分析

采用直接测序法检测LHβ基因在黔北麻羊中的单核苷酸多态性,以探讨促黄体素β亚基基因多态性与黔北麻羊产羔数的关系,以及该基因对黔北麻羊繁殖力的影响。结果表明:LHβ基因检测到2个突变位点,在外显子2第414位点发生了由C→T碱基突变,导致苏氨酸突变为甲硫氨酸;检测到AA、Aa 2种基因型。A等位基因频率为0.933 4,a等位基因频率为0.066 7,2种基因型之间产羔数差异均不显著(P0.05)。在内含子2第718位点发生了由G→A碱基突变,检测到BB、Bb 2种基因型。B等位基因频率为0.950 0,b等位基因频率为0.0500,2种基因型之间产羔数差异均不显著(P0.05)。     

伊犁马MCT1基因多态性与速度性能的关联性分析

【目的】研究伊犁马MCT1基因多态性与速度性能的关联性,为专门化用途速度马的选种育种提供技术支撑。【方法】以50匹参加2 000 m速度赛的2岁伊犁马为研究对象,运用DNA直接测序法筛选伊犁马MCT1基因第2、3外显子的突变位点,分析其多态性位点以及与伊犁马2 000 m比赛成绩的关联性。【结果】在伊犁马MCT1基因第2外显子上发现一个SNP位点,在伊犁马MCT1基因第3外显子上没有发现突变位点,在g.52168582处,碱基T突变为碱基G,此突变位点为错义突变,该突变导致其编码氨基酸由苯丙氨酸变为亮氨酸,属于中度多态位点,处于Hardy-Weinberg平衡状态,共存在TT、TG、GG 3种基因型,TT基因平均速度高于GG和TG基因型平均速度,且TT基因型平均速度显著高于GG基因型平均速度(P<0.05)。【结论】在伊犁马MCT1基因第2外显子g.52168582T>G处TT基因型更有利于伊犁马2 000 m比赛速度。     

牦牛FSHR基因第10外显子的序列测定及比较研究

为探讨牦牛FSHR基因的序列特征,揭示该基因的变异和对家畜产子率的意义,应用PCR克隆技术,测定了牦牛、中国西门塔尔牛和小尾寒羊的FSHR基因第10外显子+1393+2125位点间序列,进行了比较研究。结果表明:三畜种扩增区段的序列长度一致,但存在碱基突变,碱基变异率分别为:牦牛与中国西门塔尔牛1.12 %;牦牛与小尾寒羊2.88 %;中国西门塔尔牛与小尾寒羊2.59 %。牦牛序列与中国西门塔尔牛序列间有2处错义突变;牦牛序列与小尾寒羊序列有5处错义突变,错义突变位点数多于中国西门塔尔牛与小尾寒羊序列间的错义突变位点数。三畜种的碱基错义突变数目与它们产双胎率高低的趋势相一致。错义突变导致的第660位点氨基酸替换,牦牛和中国西门塔尔牛以可磷酸化的丝氨酸替代了小尾寒羊的苯丙氨酸。     

玉米DNA诱导的水稻变异株特异序列分析

为了解外源DNA导入对受体水稻基因组DNA序列的影响,探索受体基因组发生碱基变异的规律,为外源DNA诱导水稻变异的研究提供数据。利用改良的花粉管通道法将玉米基因组DNA导入水稻受体日本晴中,获得的2个水稻变异株B1和B2,经AFLP分析,得到14条特异条带,对其序列分析发现:14条特异序列测序共得到3 791个碱基,其中有144个碱基发生了突变,碱基总突变率为3.80%。特异带的产生是由于限制性内切酶识别序列的碱基或选择性碱基发生突变,或DNA片段的插入或缺失所致。发生单碱基突变的频次显著高于双碱基突变、连续三碱基突变和连续多碱基插入或缺失。发生碱基置换的位点频率(87.04%)显著高于碱基的插入(3.70%)和缺失(9.26%)。在碱基置换中,转换的频率(76.47%)显著高于颠换(23.53%)。上述结果表明,外源DNA导入水稻细胞可诱导受体碱基发生突变,且发生碱基置换的位点频率最高,在碱基置换中以转换为主。     

枯草芽胞杆菌果糖基转移酶基因的克隆及其序列分析

利用自行设计的引物,在枯草芽孢杆菌基因组内获得果糖基转移酶基因,基因和相应蛋白序列分析发现.该基因共1 422个碱基,编码473个氨基酸,与GenBank注册的sacB基因序列有89%的相似性;全长序列有152突变碱基,共造成18个氨基酸的错义突变,但没引起酶保守活性位点的关键氨基酸突变.这结果为后期表达特异连接α1→2糖苷键的果糖基转移酶或者该基因的定点突变打下基础.     

天敌胁迫下食饵种群动态模型的突变分析

在Logistic模型的基础上增加天敌的胁迫项,构造了天敌胁迫下食饵种群的动态模型。在食饵种群的增长量和天敌的捕食量达到动态平衡的情况下,推导出食饵种群动态的尖角突变模型。运用突变分析的方法,解释了食饵种群在天敌胁迫下也有可能爆发的生态现象。尖角突变模型中的复合控制变量无需坐标转化即可判断系统所处的状态。从理论上解决了以往研究复合控制变量时参数转化的问题。参数简化后可得到折叠突变模型。     

崇仁麻鸡PepT1基因多态性与饲料转化率的关联分析

试验以60～120日龄崇仁麻鸡为试验材料,根据鸡PepT1基因序列设计引物,采用PCR产物直接测序方法检测PepT1基因单核苷酸多态性,并通过对序列碱基的通读以及峰图的鉴定进行基因型分析,探讨PepT1基因多态性与崇仁麻鸡饲料转化率之间的关系。结果共检测到3个SNP位点,且均为沉默突变。其中在PepT1基因外显子4第95处发生了单碱基的改变(G→A),这个突变产生3种基因型(AA,AB和BB),在PepT1基因外显子6第64处和第70处上发现两处突变(分别是由C→G和A→G),且这两处突变具有同一性,这两个突变产生2种基因型(AA,AB)。用POPGENE 32软件分析PepT1基因的多态信息,PV1位点在崇仁麻鸡上表现为中度多态,PV2位点为低度多态位点,且它们均处于Hardy-Weinberg平衡中。通过SPSS 17.0对崇仁麻鸡PepT1基因各SNPs基因型与饲料转化效率进行相关性分析,发现PepT1基因PV1位点的三种基因型和PV2位点的两种基因型与崇仁麻鸡饲料转化效率均没有显著相关性(P>0.05)。     

纯血马和百色马IGF1R基因蛋白编码区序列的多态性分析

[目的]研究纯血马和百色马IGF1R基因成熟蛋白编码区序列的多态性,为揭示马矮小性状的分子机理和马的分子育种提供理论参考。[方法]采集纯血马和百色马的血样各57份,按常规酚仿法抽提DNA。利用DNA混合池和PCR产物直接测序的方法检测IGF1R基因的多态位点,利用PCR-RFLP技术分析这些多态位点在纯血马和百色马中的基因型及其频率分布。[结果]在马IGF1R基因的第2、第5和第16外显子上存在4个多态位点,其中突变179627 T→C为纯血马和百色马共有,且两者在基因型频率上差异不显著;突变212077 G→A为纯血马所独有;突变406 T→C和212 110 G→A为百色马所独有。[结论]马IGF1R基因的多态位点可能与百色马的矮小和纯血马的高大有关。     

第一产业内部产值结构变化及主要驱动因子研究——以成都市为例

第一产业是基础产业,其内部也存在各行业的经济竞争。引入了信息熵的概念,更好地反映了第一产业内部产值结构的变化。经过对熵值的小波变换,提取了各熵值变化的突变点。在对突变点分析之后得出,国家政策和特大自然灾害是影响第一产业内部产值结构的因素,并针对现在第一产业内部产值结构的现状提出了对策。     

Strand-biased spreading of mutations during somatic hypermutation

Somatic hypermutation (SHM) is a major means by which diversity is achieved in antibody genes, and it is initiated by the deamination of cytosines to uracils in DNA by activation-induced deaminase (AID). However, the process that leads from these initiating deamination events to mutations at other residues remains poorly understood. We demonstrate that a single cytosine on the top (nontemplate) strand is sufficient to recruit AID and lead to mutations of upstream and downstream A/T residues. In contrast, the targeting of cytosines on the bottom strand by AID does not lead to substantial mutation of neighboring residues. This strand asymmetry is eliminated in mice deficient in mismatch repair, indicating that the error-prone mismatch repair machinery preferentially targets top-strand uracils in a way that promotes SHM during the antibody response.     

Transposition of cloned P elements into Drosophila germ line chromosomes

Recombinant DNA carrying the 3-kilobase transposable element was injected into Drosophila embryos of a strain that lacked such elements. Under optimum conditions, half of the surviving embryos showed evidence of P element-induced mutations in a fraction of their progeny. Direct analysis of the DNA of strains derived from such flies showed them to contain from one to five intact 3-kilobase P elements located at a wide variety of chromosomal sites. DNA sequences located outside the P element on the injected DNA were not transferred. Thus P elements can efficiently and selectively transpose from extrachromosomal DNA to the DNA of germ line chromosomes in Drosophila embryos. These observations provide the basis for efficient DNA-mediated gene transfer in Drosophila.     

Gene body-specific methylation on the active X chromosome

Differential DNA methylation is important for the epigenetic regulation of gene expression. Allele-specific methylation of the inactive X chromosome has been demonstrated at promoter CpG islands, but the overall pattern of methylation on the active X(Xa) and inactive X (Xi) chromosomes is unknown. We performed allele-specific analysis of more than 1000 informative loci along the human X chromosome. The Xa displays more than two times as much allele-specific methylation as Xi. This methylation is concentrated at gene bodies, affecting multiple neighboring CpGs. Before X inactivation, all of these Xa gene body-methylated sites are biallelically methylated. Thus, a bipartite methylation-demethylation program results in Xa-specific hypomethylation at gene promoters and hypermethylation at gene bodies. These results suggest a relationship between global methylation and expression potentiality.     

Repeat-induced G-C to A-T mutations in Neurospora

In the Neurospora genome duplicate sequences are detected and altered in the sexual phase. Both copies of duplicate genes are inactivated at high frequency, whether or not they are linked. Restriction sites change, and affected sequences typically become heavily methylated. To characterize the alterations of the DNA, duplicated sequences were isolated before and after one or more sexual cycles. DNA sequencing and heteroduplex analyses demonstrated that the process (termed RIP) produces exclusively G-C to A-T mutations. Changes occur principally at sites where adenine is 3' of the changed cytosine. A sequence duplicated at a distant site in the genome lost approximately 10 percent of its G-C pairs in one passage through a cross. A closely linked duplication of the same sequence that was passed twice through a cross lost about half of its G-C pairs. The results suggest a mechanism for the RIP process.     

Parallel association of Fos and Jun leucine zippers juxtaposes DNA binding domains

The protein products of the fos and jun proto-oncogenes form a heterodimeric complex that participates in a stable high affinity interaction with DNA elements containing AP-1 binding sites. The effects of deletions and point mutations in Fos and Jun on protein complex formation and DNA binding have been examined. The data suggest that Fos and Jun dimerize via a parallel interaction of helical domains containing a heptad repeat of leucine residues (the leucine zipper). Dimerization is required for DNA binding and results in the appropriate juxtaposition of basic amino acid regions from Fos and Jun, both of which are required for association with DNA.     

TDP-43 mutations in familial and sporadic amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a fatal motor neuron disorder characterized pathologically by ubiquitinated TAR DNA binding protein (TDP-43) inclusions. The function of TDP-43 in the nervous system is uncertain, and a mechanistic role in neurodegeneration remains speculative. We identified neighboring mutations in a highly conserved region of TARDBP in sporadic and familial ALS cases. TARDBPM337V segregated with disease within one kindred and a genome-wide scan confirmed that linkage was restricted to chromosome 1p36, which contains the TARDBP locus. Mutant forms of TDP-43 fragmented in vitro more readily than wild type and, in vivo, caused neural apoptosis and developmental delay in the chick embryo. Our evidence suggests a pathophysiological link between TDP-43 and ALS.     

DNA looping generated by DNA bending protein IHF and the two domains of lambda integrase

The multiprotein-DNA complexes that participate in bacteriophage lambda site-specific recombination were used to study the combined effect of protein-induced bending and protein-mediated looping of DNA. The protein integrase (Int) is a monomer with two autonomous DNA binding domains of different sequence specificity. Stimulation of Int binding and cleavage at the low affinity core-type DNA sites required interactions with the high affinity arm-type sites and depended on simultaneous binding of the sequence-specific DNA bending protein IHF (integration host factor). The bivalent DNA binding protein is positioned at high affinity sites and directed, by a DNA bending protein, to interactions with distant lower affinity sites. Assembly of this complex is independent of protein-protein interactions.