遗传多样性的分子检测

生物多样性的保护和可持续利用是维持全球经济稳定和发展的重要因素,也是保持我们赖以生存环境的重要内容。为了实现这一目的,必须尽快建立一套对生物多样性认识和检测的有效方法,逐步认清全球生物多样性的基本状况。本文论述了生物多样性特别是物种间和物种内多样性的几种主要检测方法,着重介绍分子标记的最新进展及比较基因组学的兴起在生物多样性研究中的广泛应用。     

修正非齐次马尔可夫模型应用的研究

修正非齐次模型是在齐次模型和非齐次模型基础上提出的适用于蛋白质编码区的马尔可夫模型。此模型可以用来分析生物物种进化和基因突变,模型中的马尔可夫度与序列进化水平相关联,转移矩阵与基因突变相关联。本文通过比较7类不同物种-1度马尔可夫链的含量,验证了生物物种进化反映在密码子使用上的特征;通过密码子位点间转移矩阵的计算,分析了基因突变在密码子不同位点上发生的可能性。     

用于鉴别大西洋鲑和虹鳟的生物传感检测方法

旨在开发用于水产品物种鉴定的检测方法,以鉴别虹鳟(Oncorhynchus mykiss)假冒大西洋鲑(Salmo salar)的现象。根据大西洋鲑和虹鳟基因组序列相似性比对结果,在核基因肌红蛋白基因区设计了三对聚合酶链式反应扩增引物,分别为大西洋鲑特异性引物、虹鳟特异性引物和鲑鳟通用引物。在上游引物5'端标记生物素分子,使扩增产物被亲和素修饰的电极表面捕获锚定,在下游引物5'端标记二茂铁分子,使扩增产物带有电化学信号。基于以上方法构建了电化学生物传感体系,通过循环伏安信号检测特定扩增引物,从而能够鉴别样品是否来源于大西洋鲑或虹鳟。本研究构建的电化学生物传感检测方法具有准确、清洁的特点,能够用于成鱼、鱼苗、鱼卵、鱼肉及其加工制品的物种鉴定,并能够从混有其他物种DNA的样品如鱼泥中成功检测鱼肉DNA的物种来源。     

分子伴侣的功能和应用

本文综述了分子伴侣的分类、功能、作用机理、研究现状及应用前景。分子伴侣是在生物大分子的折叠、组装、转运及降解等过程中起协助作用,参与协助抗原的呈递和遗传物质的复制、转录及构象的确立,但自身并不发生任何变化的一大类广泛存在于生物体内的蛋白质分子。随着对分子伴侣的进一步研究和相关知识的不断深入,分子伴侣在生物产品开发、物种改良、抗衰老,疾病预防、诊断和治疗以及环境监测方面具有广阔的前景。     

分子信标核酸检测技术研究进展

介绍了分子信标设计和分子信标核酸检测原理、技术特性和在基因突变大规模自动化检测中的应用. 分子信标是一种基于荧光共振能量转移现象设计的发卡型寡核苷酸探针,空间结构上呈茎环结构, 环序列是与靶核酸互补的探针,茎序列由与靶序列无关的互补序列构成,茎的一端连上荧光分子,另一端连上淬灭分子.通过空间结构改变决定分子信标发射荧光特性,从而对核酸进行定量检测. 分子信标技术具有操作简单、敏感、特异、可对核酸进行液相实时检测和对活体内核酸动态进行检测等特点,已应用于HIV辅助受体基因等基因突变的大规模自动化检测,是一种新型核酸定量检测技术.     

肠道感知与生物适应性

肠道(gut)是机体与外界交流的重要器官，吸收营养并排出废物，在维持机体稳态和生理功能方面起着至关重要的作用。肠道中存在丰富的细胞类型和神经信号分子，研究表明，肠道细胞上的特定受体能够被食物激活，从而感知味道和营养成分，并将信息直接或间接向大脑传递。肠道感知(intestinal perception)是自然界多种生物中普遍存在的感觉系统，具有物种保守性。因此，肠道感知相关的研究，对理解物种的进化和生物在自然界中的适应性机制具有重要意义。本文对肠道不同物质感知的分子及环路机制的研究现状进行了简要综述，为进一步研究肠-脑轴神经环路在生物个体进化中的作用及生物的物种-环境共生进化的理论提供依据。     

基因芯片技术在植物基因克隆中的应用研究进展

基因芯片是以预先设计的方式将大量的生物讯息密码(寡核苷酸、cDNA、基因组DNA等)固定在玻片、硅片等固相载体上组成的密集分子阵列.基因芯片技术本质是生物信号的平行分析,它利用核酸分子杂交原理,通过荧光标记技术检测杂交亲和与否,再经过计算机分析处理可迅速获得所需信息.由于其具有高通量、微型化、连续化、自动化、快速和准确等特点,已引起国际国内广泛的关注和重视,在许多领域得到了广泛的应用.本文简述了基因芯片的概念,技术特点及主要分类,着重对其在基因表达水平检测,基因突变和多态性的分析,基因组DNA分析,后基因组学研究以及转基因农作物检测等方面进行阐述,并说明其存在的问题及展望.     

南极硅藻生物多样性及生态分布研究进展

南极硅藻在南极生态系统中起着至关重要的作用, 是南极食物网的基石, 其物种多样性、群落结构特征直接或间接影响南极生态系统的稳定性。根据近30 年来国内、外有关南极硅藻的多样性和生物地理学研究, 综述了海冰硅藻的种类组成和分布特点, 南极湖泊硅藻的物种构成特征及附生硅藻和共生硅藻多样性的研究进展, 为南极硅藻的生物多样性研究、分子生态学研究、生物地理学研究开发和利用提供参考依据。     

环境DNA metabarcoding及其在生态学研究中的应用

环境DNA metabarcoding(eDNA metabarcoding)是指利用环境样本(如土壤、水、粪便等)中分离的DNA进行高通量的多个物种(或高级分类单元)鉴定的方法。近年来,该方法引起了学者的广泛关注,逐渐应用于生物多样性研究、水生生物监测、珍稀濒危物种和外来入侵物种检测等生态学领域。介绍环境DNA metabarcoding的含义和研究方法;重点介绍环境DNA metabarcoding在物种监测、生物多样性研究和食性分析等生态学领域中的应用;总结环境DNA metabarcoding应用于生态学研究领域面临的挑战并对该方法的发展进行展望。     

分子绝对进化速率与物种分歧时间之间的定量关系

通过对美国国家生物技术信息中心数据库Gen Bank提供的一些蛋白质和核苷酸序列进行比对和分析,发现生物分子绝对进化速率k与进化时间或物种分歧时间t之间存在下列定量关系:lnk=-Ea/Rt+lnK0,式中Ea为位点突变活化能,k0为分子极限绝对进化速率,R为常数,并对其生物学意义进行了初步的探讨;数据分析还揭示出物种的分子极限绝对进化速率与进化时间或物种分歧时间之间也服从相似的定量公式,也就是说生物分子进化过程可能同时受到序列位点突变和控制物种分子极限绝对进化速率进化的两个"分子钟"作用,即存在"双重分子钟"现象。     

eNOS基因多态性与神经管畸形的研究进展

神经管畸形(neural tube defects,NTDs)是一类常见的出生缺陷,严重威胁着妇女儿童的身心健康和人口素质的提高,给社会的发展带来沉重负担,可引起孕妇流产、婴儿死亡和终生残疾。NTDs可分为无脑儿、脑膨出和脊柱裂三种类型,其病因和具体的发病机制尚不清楚。国内外多数研究认为,NTDs是一种由基因的多态性和环境因素所引起的严重的基因突变,还不能用一种单一原因来解释该病的发生。目前的研究热点是易感基因与NTDs的关系,内皮型一氧化氮合酶(endothelial nitric oxide synthase,eNOS)基因最近已被认为是导致NTDs发生的重要候选基因。eNOS基因的点突变或成串突变可以导致酶活性的变化,使eNOS的表达上调,引起NO分泌的异常,促进神经元的凋亡,进而导致大脑的发育异常。本文从eNOS基因多态性与NTDs的相关性研究进行综述。     

CIP耐药的铜绿假单胞菌两种分子耐药机制关系的研究

目的探讨环丙沙星（CIP）耐药的铜绿假单胞菌临床分离株主动外排药物与gyrA、parC基因突变的关系。方法联合碳酰氰基-对-氯苯腙（CCCP）和CIP对CIP耐药的铜绿假单胞菌株进行主动外排阳性株和阴性株的筛选,并对这些菌株的gyrA,parC基因进行聚合酶链式反应-限制性片段长度多态性分析（PCR—RFLP）。结果57％（55／97）的CIP耐药菌株最小抑菌浓度（MIC）可被逆转,gyrA单基因突变率为65％,gyrA和pa-C双基因突变率为35％,未发现parC单基因突变的菌株。主动外排阳性组与阴性组gyrA、parC基因突变情况差异无显著性。结论在本地区铜绿假单胞菌对CIP的耐药机制中,主动外排系统表达上调与抗菌药物作用靶位的改变均占有重要的地位,两者可能是并存的两种相对独立的机制。     

Mutations, mutation rates, and evolution at the hypervariable VNTR loci of Yersinia pestis

VNTRs are able to discriminate among closely related isolates of recently emerged clonal pathogens, including Yersinia pestis the etiologic agent of plague, because of their great diversity. Diversity is driven largely by mutation but little is known about VNTR mutation rates, factors affecting mutation rates, or the mutational mechanisms. The molecular epidemiological utility of VNTRs will be greatly enhanced when this foundational knowledge is available. Here, we measure mutation rates for 43 VNTR loci in Y. pestis using an in vitro generated population encompassing approximately 96,000 generations. We estimate the combined 43-locus rate and individual rates for 14 loci. A comparison of Y. pestis and Escherichia coli O157:H7 VNTR mutation rates and products revealed a similar relationship between diversity and mutation rate in these two species. Likewise, the relationship between repeat copy number and mutation rate is nearly identical between these species, suggesting a generalized relationship that may be applicable to other species. The single- versus multiple-repeat mutation ratios and the insertion versus deletion mutation ratios were also similar, providing support for a general model for the mutations associated with VNTRs. Finally, we use two small sets of Y. pestis isolates to show how this general model and our estimated mutation rates can be used to compare alternate phylogenies, and to evaluate the significance of genotype matches, near-matches, and mismatches found in empirical comparisons with a reference database.     

Genetics of the peroxidase isoenzymes in Petunia

Summary As detected by starch gel electrophoresis, the fast moving anodal group of peroxidase isoenzymes, the PRXa complex, of a Petunia homozygous for the encoding gene can be made up of one to four bands, depending on the tissue sampled, the age of the tissue and of the plant, and the genetic background. Additional evidence is presented showing that the PRXa complex is encoded by one structural gene, prxA, rather than by tandem duplicated genes. On the basis of electrophoretic variation in Petunia hybrida and related species, five prxA alleles were found. A prxA internal site mutation was found recognized by the absence of recombination between the mutation that affected the temporal programme of the gene and the mutation that altered the mobility of the enzyme. By a three-point test, the gene prxA was located on chromosome III and found to be linked to the genes Mf1 and Ht1 in the order prxA-Mf1-Ht1. The construction of a trisomic III triply heterozygous for prxA confirmed the location of prxA.     

Duplication and divergence: the evolution of nematode globins

In common with many other groups, nematodes express globins with unknown functions. Nematode globin-like genes can be divided into class 1 globins, similar to vertebrate myoglobins, and a wide range of additional classes. Here we show that class 1 nematode globins possess a huge amount of diversity in gene sequence and structure. There is evidence for multiple events of gene duplication, intron insertion and loss between species, and for allelic variation effecting both synonymous and non-synonymous sites within species. We have also examined gene expression patterns in class I globins from a variety of species. The results show variation in the degree of gene expression, but the tissue specificity and temporal specificity of expression may be more conserved in the phylum. Because the structure-function relationships for the binding and transport of oxygen by globins are well understood, the consequences of genetic variation causing amino acid changes are explored. The gene family shows great promise for discovering unique insights into both structure-function relationships of globins and their physiologial roles.     

结核分枝杆菌eis基因突变与氨基糖苷耐药的研究

目的：探讨结核分枝杆菌eis基因突变与氨基糖苷耐药之间的相互关系。方法：以本室保存的35株已确定耐一线药物（异烟肼、利福平、乙胺丁醇、链霉素）的结核分支杆菌为研究对象,应用BECTEC960测定其二线药物（阿米卡星、卡那霉素）的耐药情况,同时应用基因测序的方法测定结核分枝杆菌eis基因突变情况,分析eis基因突变与氨基糖苷耐药之间的相互关系。结果：氨基糖苷耐药的部分结核分杆杆菌中,eis基因487位碱基出现突变,相应的163位氨基酸密码子由CGT突变为CAT,即由缬氨酸变为异亮氨酸。结论：eis基因V163I突变（缬氨酸变为异亮氨酸）可能与结核分枝杆菌耐氨基糖苷类药物有关。     

Towards a quantitative understanding of horizontal gene transfer: a kinetic model

In this work, we present a simple kinetic model of horizontal gene transfer. It describes the processes of gene duplication, mutation, gene transfer and the regulation of the total size of the genome for genetically homogeneous prokaryotic species or strains. The emerging nonlinear system of first-order differential equations can be linearized at the stationary point. For selected models, we give an analytical solution for the number of foreign and native genes within a species. We identify a regime characterized by a fast gene transfer rate and species with a mixed genome, a slow gene transfer regime with pure organisms, and a crossover region. The data are compared to experiments, and the biological implications of our model are discussed.     

Subfunctionalization: How often does it occur? How long does it take?

The mechanisms responsible for the preservation of duplicate genes have been debated for more than 70 years. Recently, Lynch and Force have proposed a new explanation: subfunctionalization--after duplication the two gene copies specialize to perform complementary functions. We investigate the probability that subfunctionalization occurs, the amount of time after duplication that it takes for the outcome to be resolved, and the relationship of these quantities to the population size and mutation rates.     

ISOLATION BY DISTANCE IN EQUILIBRIUM AND NON-EQUILIBRIUM POPULATIONS

It is shown that for allele frequency data a useful measure of the extent of gene flow between a pair of populations is , which is the estimated level of gene flow in an island model at equilibrium. For DNA sequence data, the same formula can be used if F_ST is replaced by N_ST. In a population with restricted dispersal, analytic theory shows that there is a simple relationship between M? and geographic distance in both equilibrium and non-equilibrium populations and that this relationship is approximately independent of mutation rate when the mutation rate is small. Simulation results show that with reasonable sample sizes, isolation by distance can indeed be detected and that, at least in some cases, non-equilibrium patterns can be distinguished. This approach to analyzing isolation by distance is used for two allozyme data sets, one from gulls and one from pocket gophers.