发展中的mRNA差别显示技术

随着ＰＣＲ技术的出现（１９８５）,在分子生物学界又相继出现了两个很有影响的新技术──ＲＡＰＤ技术（１９９０）和ｍＲＮＡ差示法（１９９２）,前者用于分子标记,后者用于基因分离。ｍＲＮＡ差示法的生物学基础是基因的差别表达,既：单个细胞中表达的基因仅占基因总数的１５％。这种基因的差别表达决定了生命的所有过程,如：发育和分化、对逆境的反应、细胞分裂、老化等,图一给出了该方法最初的技术路线。提取要比较的两种或两种以上样品的ｍＲＮＡｓ,分别逆转录成ｃＤＮＡｓ,经过ＰＣＲ扩增后,直接进行测序胶电泳即可识别有差别的ｍＲＮＡ。其中、关键的是ＰＣＲ扩增时两个引物的设计．３＇端引物Ｏｌｉｇｏ（ｄＴ）ＭＮ很容易与具有Ｎ＇Ｍ＇－ｐｏｌｙ（Ａ）－３＇末端的大多数ｍＲＮＡ结合,进行ｃＤＮＡ的逆转录合成。Ｍ、Ｎ提供锚定位点,防止３＇端引物在ｐｏｌｙ（Ａ）序列不同位置上的随机结合。５＇端为１０个碱基的随机引物。这个经验上的碱基数值较理论的６－７个碱基（表一）更能满足测序胶电泳要求的条件：分子大小在５００ｂｐ左右,每条泳道上条带数在１００条左右。该方法近年来又有如下改进：一、ＰＣＲ退火温度由４２℃改为４０℃,可在保证特异性的同时,增加泳道上的     

Toward the systems biology of vesicle transport

Systems biology aims to study complex biological processes, such as intracellular traffic, as a whole. Systematic genome-wide assays have the potential to identify the transport machinery, delineate pathways and uncover the molecular components of physiological processes that influence trafficking. A goal of this approach is to create predictive models of intracellular trafficking pathways that reflect these relationships. In this review, we highlight current genome-wide technologies of particular relevance to vesicle transport and describe recent applications of these technologies in the framework of systems biology. Systems approaches hold great promise for placing trafficking pathways in their cellular contexts.     

Pathway and ontology analysis: emerging approaches connecting transcriptome data and clinical endpoints

The increasing use of gene expression profiling offers great promise in clinical research into disease biology and its treatment. Along with the ability to measure changing expression levels in thousands of genes at once, comes the challenge of analyzing and interpreting the vast sets of data generated. Analysis tools are evolving rapidly to meet such challenges. The next step is to interpret observed changes in terms of the biological properties or relationships underlying them. One powerful approach is to make associations between the genes that are under investigation and well-known biochemical or signaling pathways, and further to assess the significance of such associations. Similarly, genes can be mapped to standardized biological categories via an ontology resource. We discuss these approaches and several web-based resources and tools designed to facilitate such analyses. This information can be used to facilitate understanding and to help design more focused experiments for validating the relevance and importance of these biological pathways and processes in human disease and therapeutics.     

The uncertain road towards genomic medicine

Cheap, high-throughput approaches to generating biological data are transforming biology into a data-driven science and promise to similarly transform medicine. However, the road to genomic medicine is paved with challenges and uncertainty.     

Can heavy isotopes increase lifespan? Studies of relative abundance in various organisms reveal chemical perspectives on aging

Stable heavy isotopes co‐exist with their lighter counterparts in all elements commonly found in biology. These heavy isotopes represent a low natural abundance in isotopic composition but impose great retardation effects in chemical reactions because of kinetic isotopic effects (KIEs). Previous isotope analyses have recorded pervasive enrichment or depletion of heavy isotopes in various organisms, strongly supporting the capability of biological systems to distinguish different isotopes. This capability has recently been found to lead to general decline of heavy isotopes in metabolites during yeast aging. Conversely, supplementing heavy isotopes in growth medium promotes longevity. Whether this observation prevails in other organisms is not known, but it potentially bears promise in promoting human longevity.     

Are biologists in 'future shock'? Symbiosis integrates biology across domains

The study of symbiosis is quintessential systems biology. It integrates not only all levels of biological analysis--from molecular to ecological--but also the study of the interplay between organisms in the three domains of life. The development of this field is still in its early stages, but so far, the findings promise to revolutionize the way we view the biotic world. This Essay outlines some of the challenges facing the field and the implications of its development for all of biology.     

Solid-state magic-angle spinning NMR of membrane proteins and protein-ligand interactions

Structural biology is developing into a universal tool for visualizing biological processes in space and time at atomic resolution. The field has been built by established methodology like X-ray crystallography, electron microscopy and solution NMR and is now incorporating new techniques, such as small-angle X-ray scattering, electron tomography, magic-angle-spinning solid-state NMR and femtosecond X-ray protein nanocrystallography. These new techniques all seek to investigate non-crystalline, native-like biological material. Solid-state NMR is a relatively young technique that has just proven its capabilities for de novo structure determination of model proteins. Further developments promise great potential for investigations on functional biological systems such as membrane-integrated receptors and channels, and macromolecular complexes attached to cytoskeletal proteins. Here, we review the development and applications of solid-state NMR from the first proof-of-principle investigations to mature structure determination projects, including membrane proteins. We describe the development of the methodology by looking at examples in detail and provide an outlook towards future 'big' projects.     

Systems biology in drug discovery

The hope of the rapid translation of 'genes to drugs' has foundered on the reality that disease biology is complex, and that drug development must be driven by insights into biological responses. Systems biology aims to describe and to understand the operation of complex biological systems and ultimately to develop predictive models of human disease. Although meaningful molecular level models of human cell and tissue function are a distant goal, systems biology efforts are already influencing drug discovery. Large-scale gene, protein and metabolite measurements ('omics') dramatically accelerate hypothesis generation and testing in disease models. Computer simulations integrating knowledge of organ and system-level responses help prioritize targets and design clinical trials. Automation of complex primary human cell-based assay systems designed to capture emergent properties can now integrate a broad range of disease-relevant human biology into the drug discovery process, informing target and compound validation, lead optimization, and clinical indication selection. These systems biology approaches promise to improve decision making in pharmaceutical development.     

计算系统生物学:理论、方法及在药物研发中的应用

计算系统生物学是一个多学科交叉的新兴领域,旨在通过整合海量数据建立其生物系统相互作用的复杂网络。数据的整合和模型的建立需要发展合适的数学方法和软件工具,这也是计算系统生物学的主要任务。生物系统模型有助于从整体上理解生物体的内在功能和特性。同时,生物网络模型在药物研发中的应用也越来越受到制药企业以及新药研发机构的重视,如用于特异性药物作用靶点的预测和药物毒性评估等。该文简要介绍计算系统生物学的常见网络和计算模型,以及建立模型所用的研究方法,并阐述其在建模和分析中的作用及面临的问题和挑战。     

Engineering life through Synthetic Biology

Synthetic Biology is a field involving synthesis of novel biological systems which are not generally found in nature. It has brought a new paradigm in science as it has enabled scientists to create life from the scratch, hence helping better understand the principles of biology. The viability of living organisms that use unnatural molecules is also being explored. Unconventional projects such as DNA playing tic-tac-toe, bacterial photographic film, etc. are taking biology to its extremes. The field holds a promise for mass production of cheap drugs and programming bacteria to seek-and-destroy tumors in the body. However, the complexity of biological systems make the field a challenging one. In addition to this, there are other major technical and ethical challenges which need to be addressed before the field realizes its true potential.     

Viroids:Small Probes for Exploring the Vast Universe of RNA Trafficking in Plants

Cell-to-cell and long-distance trafficking of RNA is a rapidly evolving frontier of integrative plant biology that broadly impacts studies on plant growth and development, spread of infectious agents and plant defense responses. The fundamental questions being pursued at the forefronts revolve around function, mechanism and evolution. In the present review, we will first use specific examples to illustrate the biological importance of cell-to-cell and long-distance trafficking of RNA. We then focus our discussion on research findings obtained using viroids that have advanced our understanding of the underlying mechanisms involved in RNA trafficking. We further use viroid examples to illustrate the great diversity of trafficking machinery evolved by plants, as well as the promise for new insights in the years ahead. Finally, we discuss the prospect of integrating findings from different experimental systems to achieve a systems-based understanding of RNA trafficking function, mechanism and evolution.     

Pharmacogenomics - it''s not just pharmacogenetics

New technologies in both combinatorial chemistry and combinatorial biology promise to unlock new opportunities for drug discovery and lead optimisation. Using such genome-based technologies to measure the dynamic properties of pharmacological systems, pharmacogenomics can now provide an objective measure of a drug's biological efficacy, including its potential adverse effects.     

Metals in biology: defining metalloproteomes

The vital nature of metal uptake and balance in biology is evident in the highly evolved strategies to facilitate metal homeostasis in all three domains of life. Several decades of study on metals and metalloproteins have revealed numerous essential bio-metal functions. Recent advances in mass spectrometry, X-ray scattering/absorption, and proteomics have exposed a much broader usage of metals in biology than expected. Even elements such as uranium, arsenic, and lead are implicated in biological processes as part of an emerging and expansive view of bio-metals. Here we discuss opportunities and challenges for established and newer approaches to study metalloproteins with a focus on technologies that promise to rapidly expand our knowledge of metalloproteins and metal functions in biology.     

The role of abiotic factors in the pupation of Thaumatotibia leucotreta Meyrick (Lepidoptera: Tortricidae) in the soil

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Revealing evolutionary pathways by fitness landscape reconstruction

The concept of epistasis has since long been used to denote non-additive fitness effects of genetic changes and has played a central role in understanding the evolution of biological systems. Owing to an array of novel experimental methodologies, it has become possible to experimentally determine epistatic interactions as well as more elaborate genotype-fitness maps. These data have opened up the investigation of a host of long-standing questions in evolutionary biology, such as the ruggedness of fitness landscapes and the accessibility of mutational trajectories, the evolution of sex, and the origin of robustness and modularity. Here we review this recent and timely marriage between systems biology and evolutionary biology, which holds the promise to understand evolutionary dynamics in a more mechanistic and predictive manner.