Development of a DNA sensor using a molecular logic gate

This communication reports the increase in fluorescence resonance energy transfer (FRET) efficiency between two laser dyes in the presence of deoxyribonucleic acid (DNA). Two types of molecular logic gates have been designed where DNA acts as input signal and fluorescence intensity of different bands are taken as output signal. Use of these logic gates as a DNA sensor has been demonstrated.     

动物转基因技术的新进展

到目前为止,原核注射是最可靠,也是使用最广泛的动物转基因方法.但该方法存在整合效率太低及不能定点整合的问题.在过去的20年里,出现了一些新的转基因方法,包括精子介导、反转录病毒介导、携带外源基因体细胞的核移植、ＥＳ细胞基因打靶技术等.但这些方法都未能根本地解决存在的问题.最近的一些文献中报道转基因技术在原有方法的基础上做出了改进后,取得了突破性进展.     

肝纤维化基因治疗的进展

肝硬化是慢性肝病晚期的组织学改变 ,以纤维组织大量增生和肝小叶结构无序化为特征 ,因此又称肝纤维化。近年来随着分子生物学的发展 ,肝纤维化的分子机制逐渐得以阐明 ,从而使肝纤维化的基因治疗成为可能。肝纤维化的基因治疗主要起到阻止纤维化发展、刺激肝细胞分裂和肝组织结构重建三方面的作用。目前 ,常用的方法一般是通过缺陷病毒 (如腺病毒 )转入特定的细胞因子和酶 (如肝细胞生长因子、转化生长因子β1受体、基质金属蛋白酶等 )的基因 ,通过靶细胞表达这些因子作用于受损的肝脏 ,达到延缓和治愈肝纤维化的目的     

基于DNA分子的现代人起源研究35年回顾与展望

1983年,有学者首次发表现代人线粒体DNA进化树,认为现代人可能起源自亚洲。1987年,又有学者按照分子钟假说得到线粒体在10-20万年前出自非洲的推论。随后,以分子钟为前提的Y染色体和常染色体DNA研究也支持了出非洲的结论,该结论逐渐成为分子进化领域的主流理论。2010年,对尼安德特人常染色体基因组的研究指出其对现代人有遗传贡献,这颠覆了人们先前关于现代人只来源自非洲,其他大洲的当地古人被完全取代的认知。目前,单地区起源说已经被修正为同化说。尽管学界对非洲人遗传多样性最高这一现象有共识,但是对该现象的不同解读却可以得出两种迥然不同的结果,现代人出亚洲说和出非洲说。大量研究证实基因组的大部分序列是有功能的,并处在遗传变异水平的饱和态,这质疑了中性理论以及由它推导的现代人出非洲说的合理性,而中性理论的提出恰恰是用来解释并非普遍存在的分子钟的。近年来已经有研究者从新理论的角度解读遗传多样性的饱和态和线性态,人们对现代人起源的认识将会进一步加深完善。     

Small RNAs in development - insights from plants

microRNAs (miRNAs) and small interfering RNAs (siRNAs), which constitute two major classes of endogenous small RNAs in plants, impact a multitude of developmental and physiological processes by imparting sequence specificity to gene and genome regulation. Although lacking the third major class of small RNAs found in animals, Piwi-interacting RNAs (piRNAs), plants have expanded their repertoire of endogenous siRNAs, some of which fulfill similar molecular and developmental functions as piRNAs in animals. Research on plant miRNAs and siRNAs has contributed invaluable insights into small RNA biology, thanks to the highly conserved molecular logic behind the biogenesis and actions of small RNAs. Here, I review progress in the plant small RNA field in the past two years, with an emphasis on recent findings related to plant development. I do not recount the numerous developmental processes regulated by small RNAs; instead, I focus on major principles that have been derived from recent studies and draw parallels, when applicable, between plants and animals.     

用分子遗传学及免疫学方法控制鱼类寄生性甲藻

寄生性甲藻,例如Amyloodiniumocellatum,给鱼类养殖带来严重的危害。虽然,近年来针对Amyloodinium的药物治疗有一些新的进展,如使用氯喹、过氧化氢和3,N泛影葡胺拉沙洛西等,然而,含铜类药物仍然是最有效的。近年来分子遗传学和免疫学的进展,使得我们能够更好地了解寄生性甲藻的流行病学及其防治方法。分子系统学研究认为某些寄生性甲藻,如Amyloodiniumocellatum,可以聚类为高度同源性的一支;而其它的如Piscinoodiniumpillulare,则可以认为不止一种或更高的分类阶元。这些分子分析也发展出一些高灵敏的检测技术,可以检测出环境中极少量的寄生性甲藻。通过对Amyloodinium的免疫学研究表明,鱼类能对寄生物的感染产生强烈的高度特异的保护性免疫应答,其中主要是抗体介导的免疫应答。鱼体皮肤和鳃也能表达内源非特异性多肽抗生素(类组蛋白),它们能对Amyloodinium造成致命的破坏。利用这些特异或非特异的免疫防御,将更有助于我们控制这些具有严重危害性的寄生性甲藻     

Ion channels: molecular targets of neuroactive insecticides

Many of the insecticides in current use act on molecular targets in the insect nervous system. Recently, our understanding of these targets has improved as a result of the complete sequencing of an insect genome, i.e., Drosophila melanogaster. Here we examine the recent work, drawing on genetics, genomics and physiology, which has provided evidence that specific receptors and ion channels are targeted by distinct chemical classes of insect control agents. The examples discussed include, sodium channels (pyrethroids, p,p′-dichlorodiphenyl-trichloroethane (DDT), dihydropyrazoles and oxadiazines); nicotinic acetylcholine receptors (cartap, spinosad, imidacloprid and related nitromethylenes/nitroguanidines); γ-aminobutyric acid (GABA) receptors (cyclodienes, γ-BHC and fipronil) and L-glutamate receptors (avermectins). Finally, we have examined the molecular basis of resistance to these molecules, which in some cases involves mutations in the molecular target, and we also consider the future impact of molecular genetic technologies in our understanding of the actions of neuroactive insecticides.     

An Insight into Biomolecular Flexibility: Its Measuring,Modeling and Regulating on Function at Single Molecule Level

The protein structure-function paradigm implies that the structure of a protein defines its function. Crystallization techniques such as X-ray, electron microscopy (EM) and nuclear magnetic resonance (NMR) have been applied to resolve the crystal structure of numerous proteins, provided beautiful and informative models of proteins. However, proteins are not intrinsically in static state but in dynamic state, which is lack in crystal models. The protein flexibility, a key mechanical property of proteins, plays important roles in various biological processes, such as ligand-receptor interaction, signaling transduction, substrate recognition and post-translational modifications. Advanced time-resolved crystallography has been developed recent years to visualize and characterize the dynamic of proteins and reviewed in literatures. In the present review, we will focus on the single-molecule based techniques and theoretical methods in determining the flexibility of proteins, exhibit some interest examples of proteins and DNA molecular flexibility to their functions, and provide an insight in molecular flexibility from the biomechanics point of view.     

Molecular Clock Calibrations and Metazoan Divergence Dates

It has recently been argued that living metazoans diverged over 800 million years ago, based on evidence from 22 nuclear genes for such a deep divergence between vertebrates and arthropods (Gu 1998). Two ``internal' calibration points were used. However, only one fossil divergence date (the mammal–bird split) was directly used to calibrate the molecular clock. The second calibration point (the primate–rodent split) was based on molecular estimates that were ultimately also calibrated by the same mammal–bird split. However, the first tetrapods that can be assigned with confidence to either the mammal (synapsid) lineage or the bird (diapsid) lineage are approximately 288 million years old, while the first mammals that can be assigned with confidence to either the primate or the rodent lineages are 65 million years old, or 85 million years old if ferungulates are part of the primate lineage and zhelestids are accepted as ferungulate relatives. Recalibration of the protein data using these fossil dates indicates that metazoans diverged between 791 and 528 million years ago, a result broadly consistent with the palaeontological documentation of the ``Cambrian explosion.' The third, ``external' calibration point (the metazoan–fungal divergence) was similarly problematic, since it was based on a controversial molecular study (which in turn used fossil dates including the mammal–bird split); direct use of fossils for this calibration point gives the absurd dating of 455 million years for metazoan divergences. Similar calibration problems affect another recent study (Wang et al. 1999), which proposes divergences for metazoans of 1000 million years or more: recalibrations of their clock again yields much more recent dates, some consistent with a ``Cambrian explosion' scenario. Molecular clock studies have persuasively argued for the imperfection of the fossil record but have rarely acknowledged that their inferences are also directly based on this same record. Received: 26 January 1999 / Accepted: 14 April 1999     

人类细胞色素P450与药物氧化代谢遗传多态性分子机制的研究现状

近年,在表型及基因型上均发现存在药物氧化代谢多态性,特别是对于人类细胞色素Ｐ４５０氧化酶与药氧化代谢遗传多态性的关系进行了深入的研究。有关ＣＹＰ２Ｄ６、ＣＹＰ２Ｃ１９等的突变已大多被鉴定;ＣＹＰ１Ａ１、ＣＹＰ１Ａ２等在表型存在多态性而确切的遗传机制尚不清楚。     

Towards a systems biology approach to study type II/IV secretion systems

Many gram-negative bacteria produce thin protein filaments, named pili, which extend beyond the confines of the outer membrane. The importance of these pili is illustrated by the fact that highly complex, multi-protein pilus-assembly machines have evolved, not once, but several times. Their many functions include motility, adhesion, secretion, and DNA transfer, all of which can contribute to the virulence of bacterial pathogens or to the spread of virulence factors by horizontal gene transfer. The medical importance has stimulated extensive biochemical and genetic studies but the assembly and function of pili remains an enigma. It is clear that progress in this field requires a more holistic approach where the entire molecular apparatus that forms the pilus is studied as a system. In recent years systems biology approaches have started to complement classical studies of pili and their assembly. Moreover, continued progress in structural biology is building a picture of the components that make up the assembly machine. However, the complexity and multiple-membrane spanning nature of these secretion systems pose formidable technical challenges, and it will require a concerted effort before we can create comprehensive and predictive models of these remarkable molecular machines.     

Towards a systems biology approach to study type II/IV secretion systems

Many gram-negative bacteria produce thin protein filaments, named pili, which extend beyond the confines of the outer membrane. The importance of these pili is illustrated by the fact that highly complex, multi-protein pilus-assembly machines have evolved, not once, but several times. Their many functions include motility, adhesion, secretion, and DNA transfer, all of which can contribute to the virulence of bacterial pathogens or to the spread of virulence factors by horizontal gene transfer. The medical importance has stimulated extensive biochemical and genetic studies but the assembly and function of pili remains an enigma. It is clear that progress in this field requires a more holistic approach where the entire molecular apparatus that forms the pilus is studied as a system. In recent years systems biology approaches have started to complement classical studies of pili and their assembly. Moreover, continued progress in structural biology is building a picture of the components that make up the assembly machine. However, the complexity and multiple-membrane spanning nature of these secretion systems pose formidable technical challenges, and it will require a concerted effort before we can create comprehensive and predictive models of these remarkable molecular machines.     

溶藻微生物的研究进展

溶藻微生物在防治有害藻类水华中的作用和潜力,已受到学者的广泛关注.综述溶藻微生物(主要是溶藻细菌和噬藻体)的溶藻作用机制,量效关系及分子生物学.阐述溶藻微生物对蓝藻水华治理存在的问题,并对溶藻微生物作为潜在的控藻因子进行展望.     

植物对重金属耐性的分子生态机理

植物适应重金属元素胁迫的机制包括阻止和控制重金属的吸收、体内螯合解毒、体内区室化分隔以及代谢平衡等。近年来,随着分子生物学技术在生态学研究中的深入应用,控制这些过程的分子生态机理逐渐被揭示出来。菌根、根系分泌物以及细胞膜是控制重金属进入植物根系细胞的主要生理单元。外生菌根能显著提高寄主植物的重金属耐性,根系分泌物通过改变根际pH、改变金属物质的氧化还原状态和形成络合物等机理减少植物对重金属的吸收。目前,控制菌根和根系分泌物重金属抗性的分子生态机理还不清楚。但细胞膜跨膜转运器已得到深入研究,相关金属离子转运器被鉴定和分离,一些控制基因如铁锌控制运转相关蛋白(ZIP)类、自然抵抗相关巨噬细胞蛋白(Nramp)类、P_1B-type ATPase类基因已被发现和克隆。金属硫蛋白(MTs)、植物螯合素(PCs)、有机酸及氨基酸等是植物体内主要的螯合物质,它们通过螯合作用固定金属离子,降低其生物毒性或改变其移动性。与MTs合成相关的MT-like基因已经被克隆,PCs合成必需的植物螯合素合酶(PCS), 即γ-Glu-Cys二肽转肽酶(γ-ECS) 的编码基因已经被克隆,控制麦根酸合成的氨基酸尼克烟酰胺(NA)在重金属耐性中的作用和分子机理也被揭示出来。ATP 结合转运器(ABC)和阳离子扩散促进器(CDF) 是植物体内两种主要膜转运器,通过它们和其它跨膜方式,重金属被分隔贮藏于液泡内。控制这些蛋白转运器合成的基因也已经被克隆,在植物中的表达证实其与重金属的体内运输和平衡有关。热休克蛋白(HSP)等蛋白类物质的产生是一种重要的体内平衡机制,其分子机理有待进一步研究。重金属耐性植物在这些环节产生了相关响应基因或功能蛋白质,分子克隆和转基因技术又使它们在污染治理上得到了初步的应用。     

The role of natural selection in circadian behaviour: a molecular-genetic approach

Circadian rhythms (~24 h) in biochemistry, physiology and behaviour are found in almost all eukaryotes and some bacteria. The elucidation of the molecular components of the 24 h circadian clock in a number of model organisms in recent years has provided an opportunity to assess the adaptive value of variation in clock genes. Laboratory experiments using artificially generated mutants reveal that the circadian period is adaptive in a 24 h world. Natural genetic variation can also be studied, and there are a number of ways in which the signature of natural selection can be detected. These include the study of geographical patterns of genetic variation, which provide a first indication that selection may be at work, and the use of sophisticated statistical neutrality tests, which examine whether the pattern of variation observed is consistent with a selective rather than a neutral (or drift) scenario. Finally, examining the probable selective agents and their differential effects on the circadian phenotype of the natural variants provides the final compelling evidence for selection. We present some examples of how these types of analyses have not only enlightened the evolutionary study of clocks, but have also contributed to a more pragmatic molecular understanding of the function of clock proteins.     

分子遗传标记技术在蜻蜓目昆虫研究中的应用

分子生物学技术应用于昆虫系统学研究在近些年发展相当迅速。目前已出现了几十种分子遗传标记。该文简述了酯酶同工酶电泳、核酸序列分析以及AFLP、RAPD、核酸探针等分子生物学技术在蜻蜓目昆虫研究中的应用情况。     

中国跳鼠总科物种的系统分类学研究进展

近年来,随着分子系统学的发展以及荒漠地区物种多样性和分类学研究的深入,新的隐存种不断被发现,一些类群的分类地位也发生了变动。中国是世界上跳鼠总科(Dipodoidea)物种多样性最高的国家,通过对中国跳鼠总科物种的分类系统进行重新梳理和研究,确认跳鼠总科在中国有3科6亚科12属22种。证实中国分布有第五种蹶鼠——灰蹶鼠(Sicista pseudonapaea)。五趾跳鼠亚科原属Allactaga是一个并系群,应拆分为Allactaga、Orientallactaga、Scarturus三个属;原五趾跳鼠、巨泡五趾跳鼠、巴里坤跳鼠归于Orientallactaga属,小五趾跳鼠移入Scarturus属,且是一个包含隐存种的种团。大五趾跳鼠在我国仅有文献记载,其分布存疑。跳鼠亚科原三趾跳鼠努日亚种提升为种——塔里木跳鼠(Dipus deasyi);而准噶尔羽尾跳鼠(Stylodipus sungorus)在我国有分布。奇美跳鼠(Chimaerodipus auritus)是近年来在我国发现并命名的新属新种。     

Nonviral gene transfer to skeletal, smooth, and cardiac muscle in living animals

The study of muscle physiology has undergone many changes over the past 25 years and has moved from purely physiological studies to those intimately intertwined with molecular and cell biological questions. To ask these questions, it is necessary to be able to transfer genetic reagents to cells both in culture and, ultimately, in living animals. Over the past 10 years, a number of different chemical and physical approaches have been developed to transfect living skeletal, smooth, and cardiac muscle systems with varying success and efficiency. This review provides a survey of these methods and describes some more recent developments in the field of in vivo gene transfer to these various muscle types. Both gene delivery for overexpression of desired gene products and delivery of nucleic acids for downregulation of specific genes and their products are discussed to aid the physiologist, cell biologist, and molecular biologist in their studies on whole animal biology. electroporation; liposomes; plasmids; transfection; gene expression     

分子生物学技术在胃肠道微生态中应用研究进展

哺乳动物胃肠道中栖息着大量的微生物(主要为细菌),它们在营养、生理、免疫等方面对宿主起着有益作用。传统上,胃肠道菌群研究主要依靠培养技术。近来,一些基于16S rRNA(DNA)的分子生物学技术已被广泛应用于胃肠道菌群的研究,这些技术主要有16S rDNA克隆基因文库、16S rDNA指纹技术、定量PCR技术、荧光原位杂交技术及基因芯片技术等。对这些用于胃肠道微生态研究的分子生物学技术作一综述。     

Simple evolutionary pathways to complex proteins.

A recent paper in this journal has challenged the idea that complex adaptive features of proteins can be explained by known molecular, genetic, and evolutionary mechanisms. It is shown here that the conclusions of this prior work are an artifact of unwarranted biological assumptions, inappropriate mathematical modeling, and faulty logic. Numerous simple pathways exist by which adaptive multi-residue functions can evolve on time scales of a million years (or much less) in populations of only moderate size. Thus, the classical evolutionary trajectory of descent with modification is adequate to explain the diversification of protein functions.