Molecule cascades

Carbon monoxide molecules were arranged in atomically precise configurations, which we call "molecule cascades," where the motion of one molecule causes the subsequent motion of another, and so on in a cascade of motion similar to a row of toppling dominoes. Isotopically pure cascades were assembled on a copper (111) surface with a low-temperature scanning tunneling microscope. The hopping rate of carbon monoxide molecules in cascades was found to be independent of temperature below 6 kelvin and to exhibit a pronounced isotope effect, hallmarks of a quantum tunneling process. At higher temperatures, we observed a thermally activated hopping rate with an anomalously low Arrhenius prefactor that we interpret as tunneling from excited vibrational states. We present a cascade-based computation scheme that has all of the devices and interconnects required for the one-time computation of an arbitrary logic function. Logic gates and other devices were implemented by engineered arrangements of molecules at the intersections of cascades. We demonstrate a three-input sorter that uses several AND gates and OR gates, as well as the crossover and fan-out units needed to connect them.     

适配体的研究进程与思考

适配体（aptamer）是指利用指数富集的配体系统进化（SELEX）技术，从人工合成的寡核苷酸文库中筛选获得的能够与靶分子特异结合的短单链DNA和RNA分子。筛选得到的适配体可以与DNA，RNA，蛋白质或其它靶分子结合，影响这些靶分子的性质，从而起到改变与靶分子相关的生物学功能的效果。而且研究发现，适配体在与靶分子相互作用时，不仅序列，它们所形成的三维结构也尤其重要。同时，适配体在生物医药研究方面显示出广阔的应用前景。介绍了适配体的发展历程，以及一些典型适配体的生物学功效。提出了RNA适配体三维结构在与靶分子进行相互作用时可能发挥重要作用，以期为RNA适配体的筛选提供理论思考。     

Model-driven engineering of RNA devices to quantitatively program gene expression

The models and simulation tools available to design functionally complex synthetic biological devices are very limited. We formulated a design-driven approach that used mechanistic modeling and kinetic RNA folding simulations to engineer RNA-regulated genetic devices that control gene expression. Ribozyme and metabolite-controlled, aptazyme-regulated expression devices with quantitatively predictable functions were assembled from components characterized in vitro, in vivo, and in silico. The models and design strategy were verified by constructing 28 Escherichia coli expression devices that gave excellent quantitative agreement between the predicted and measured gene expression levels (r = 0.94). These technologies were applied to engineer RNA-regulated controls in metabolic pathways. More broadly, we provide a framework for studying RNA functions and illustrate the potential for the use of biochemical and biophysical modeling to develop biological design methods.     

适配体的研究进程与思考*

 适配体（aptamer）是指利用指数富集的配体系统进化（SELEX）技术，从人工合成的寡核苷酸文库中筛选获得的能够与靶分子特异结合的短单链DNA和RNA分子。筛选得到的适配体可以与DNA，RNA，蛋白质或其它靶分子结合，影响这些靶分子的性质，从而起到改变与靶分子相关的生物学功能的效果。而且研究发现，适配体在与靶分子相互作用时，不仅序列，它们所形成的三维结构也尤其重要。同时，适配体在生物医药研究方面显示出广阔的应用前景。介绍了适配体的发展历程，以及一些典型适配体的生物学功效。提出了RNA适配体三维结构在与靶分子进行相互作用时可能发挥重要作用，以期为RNA适配体的筛选提供理论思考。     

Design and implementation of an electronic mobile poultry production documentation system

Documentation is a major component of any traceability system where traceability is defined in the ISO Regulation 8402:1994 as the ability to trace the history, application and location of what is under consideration. Traceability systems are record keeping systems designed to track the flow of product or product attributes through the production process or supply chain. All international supply chains are forced to comply with traceability requirements. In this paper, we develop and implement an end-to-end mobile application prototype that traces the poultry production. This application consists of front-end and back-end systems. At the front-end, the worker uses a GPRS enabled handheld device (cell phone, PDA, etc.) to capture information on poultry operations collected at a remote chicken farm and transmit it to a back-end server in the main office. Through customized application the back-end server analyses all information received from the front-end and based on a built-in business process and business rules, intelligently updates various stakeholders of any breach of bio-security measures that requires immediate attention. The proposed system administrators can also access this application via Internet for management decision making. The back-end system consists of web server, defined business application logic and database server.     

Biochemistry of information storage in the nervous system

The use of molecular biological approaches has defined new mechanisms that store information in the mammalian nervous system. Environmental stimuli alter steady-state levels of messenger RNA species encoding neurotransmitters, thereby altering synaptic, neuronal, and network function over time. External or internal stimuli alter impulse activity, which alters membrane depolarization and selectively changes the expression of specific transmitter genes. These processes occur in diverse peripheral and central neurons, suggesting that information storage is widespread in the neuraxis. The temporal profile of any particular molecular mnemonic process is determined by specific kinetics of turnover and by the geometry of the neuron resulting in axonal transport of molecules to different synaptic arrays at different times. Generally, transmitters, the agents of millisecond-to-millisecond communication, are subject to relatively long-lasting changes in expression, ensuring that ongoing physiological function is translated into information storage.     

新疆南疆三地州农牧民农业信息需求意愿实证研究

通过对新疆南疆三地州3644户农牧民的实地走访和问卷调查,对农牧民的农业信息需求现状、制约农牧民信息需求的因素进行实证研究和科学评估,以便于相关信息传播机构以农牧民信息需求为中心来改善信息服务供给状况,提高信息服务质量,进而满足农牧民的农业信息需求,推进农村信息化进程,推动农村经济发展。     

Stretchable and foldable silicon integrated circuits

We have developed a simple approach to high-performance, stretchable, and foldable integrated circuits. The systems integrate inorganic electronic materials, including aligned arrays of nanoribbons of single crystalline silicon, with ultrathin plastic and elastomeric substrates. The designs combine multilayer neutral mechanical plane layouts and "wavy" structural configurations in silicon complementary logic gates, ring oscillators, and differential amplifiers. We performed three-dimensional analytical and computational modeling of the mechanics and the electronic behaviors of these integrated circuits. Collectively, the results represent routes to devices, such as personal health monitors and other biomedical devices, that require extreme mechanical deformations during installation/use and electronic properties approaching those of conventional systems built on brittle semiconductor wafers.     

Dicer蛋白分子的进化与结构研究进展

Dicer蛋白在RNA干扰(RNA interference,RNAi)途径中起着非常重要的作用,不同生物来源的Dicer蛋白在数量和结构上均存在着一定的差异.在植物界的生物进化过程中,Dicer蛋白的数量逐渐增多,功能逐步出现分化;而在动物界的生物进化过程中,Dicer蛋白的数量逐渐减少,功能却逐步整合.不同Dice...     

Step-by-step engineered multiparticle entanglement

After quantum particles have interacted, they generally remain in an entangled state and are correlated at a distance by quantum-mechanical links that can be used to transmit and process information in nonclassical ways. This implies programmable sequences of operations to generate and analyze the entanglement of complex systems. We have demonstrated such a procedure for two atoms and a single-photon cavity mode, engineering and analyzing a three-particle entangled state by a succession of controlled steps that address the particles individually. This entangling procedure can, in principle, operate on larger numbers of particles, opening new perspectives for fundamental tests of quantum theory.     

灌区野外手动闸门智能测控仪的设计与实现

灌区野外手动闸门智能测控仪是针对我国农业灌区野外闸门分布分散、不具备供电条件、计量和控制手段落后等现状展开研究而取得的研究成果。测控仪采用了国际最先进的弹片微型计算机技术、TM信息卡技术、智能算法技术、自动化控制技术进行了装置的研究设计。成功研制出的野外手动闸门测控仪全面解决了灌区闸门水量科学计量及智能监控的难题。     

REDUNDANCY AND BIOLOGICAL AGING

The relationship between aging and organizational redundancy in biological systems was investigated from the standpoint of information theory. A mortality rate function derived for a randomly deteriorating redundant system approximates observed mortality rates more closely than does the Gompertz function and indicates that variations in redundancy among various mammalian species could account for their widely different rates of aging.     

Optical projection tomography as a tool for 3D microscopy and gene expression studies

Current techniques for three-dimensional (3D) optical microscopy (deconvolution, confocal microscopy, and optical coherence tomography) generate 3D data by "optically sectioning" the specimen. This places severe constraints on the maximum thickness of a specimen that can be imaged. We have developed a microscopy technique that uses optical projection tomography (OPT) to produce high-resolution 3D images of both fluorescent and nonfluorescent biological specimens with a thickness of up to 15 millimeters. OPT microscopy allows the rapid mapping of the tissue distribution of RNA and protein expression in intact embryos or organ systems and can therefore be instrumental in studies of developmental biology or gene function.     

Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins

Synthetic genetic devices that interface with native cellular pathways can be used to change natural networks to implement new forms of control and behavior. The engineering of gene networks has been limited by an inability to interface with native components. We describe a class of RNA control devices that overcome these limitations by coupling increased abundance of particular proteins to targeted gene expression events through the regulation of alternative RNA splicing. We engineered RNA devices that detect signaling through the nuclear factor κB and Wnt signaling pathways in human cells and rewire these pathways to produce new behaviors, thereby linking disease markers to noninvasive sensing and reprogrammed cellular fates. Our work provides a genetic platform that can build programmable sensing-actuation devices enabling autonomous control over cellular behavior.     

农业机械多媒体决策支持系统的研究

为了帮助农民及农机管理部门了解各种农机具的信息，进行辅助决策、咨询和农机发展需求预测，我们采用多媒体技术，将系统分析、预测和辅助决策与数据库技术有机地结合起来，实现了数据库和模型库的互联，在windows环境下开发了一个农业机械多媒体决策支持系统。它能对各种农业机械进行多媒体信息管理和技术经济适应性分析，为农机管理部门科学预测和决策提供了依据，同时，我们还输入了浙江省主要的各类农机具的多媒体信息，其实际应用效果良好。     

Fermionic bell-state analyzer for spin qubits

We propose a protocol and physical implementation for partial Bell-state measurements of Fermionic qubits, allowing for deterministic quantum computing in solid-state systems without the need for two-qubit gates. Our scheme consists of two spin qubits in a double quantum dot where the two dots have different Zeeman splittings and resonant tunneling between the dots is only allowed when the spins are antiparallel. This converts spin parity into charge information by means of a projective measurement and can be implemented with established technologies. This measurement-based qubit scheme greatly simplifies the experimental realization of scalable quantum computers in electronic nanostructures.     

Enzyme-free nucleic acid logic circuits

Biological organisms perform complex information processing and control tasks using sophisticated biochemical circuits, yet the engineering of such circuits remains ineffective compared with that of electronic circuits. To systematically create complex yet reliable circuits, electrical engineers use digital logic, wherein gates and subcircuits are composed modularly and signal restoration prevents signal degradation. We report the design and experimental implementation of DNA-based digital logic circuits. We demonstrate AND, OR, and NOT gates, signal restoration, amplification, feedback, and cascading. Gate design and circuit construction is modular. The gates use single-stranded nucleic acids as inputs and outputs, and the mechanism relies exclusively on sequence recognition and strand displacement. Biological nucleic acids such as microRNAs can serve as inputs, suggesting applications in biotechnology and bioengineering.     

Viral infection and host defense

Double-stranded RNA, made as an intermediary substance in the replication of most, if not all, viruses, may play a much more important role in the pathogenesis and the recovery from virus infections than has hitherto been suspected. Apparently, dsRNA is used by both the challenge virus and the host cell in an attempt to gain "molecular control." Double-stranded RNA exerts a set of effects, which may be well balanced, not only at the level of the individual cell but also at the complex assemblage of these cells termed the organism (Fig. 1). In the cell, interferon synthesis is triggered, although interferon mRNA translation may not occur if dsRNA shuts off protein synthesis too quickly. In the whole organism, the disease severity will depend on how certain toxic reactions evoked by infection (such as cell necrosis and fever) are counterbalanced by an increase in the host defense mechanisms (for example, immune responsiveness and interferon production). Many aspects of the response, relating to either progress of, or recovery from, the disease, can be explained on the basis of a dsRNA. In addition to drawing attention to the biodynamic role of dsRNA, our hypothesis suggests specific experimental vectors designed to enhance our information on the molecular basis of the morbid process which occurs with viral infection. Finally, we suggest that, although the dsRNA molecule may be viewed as a rather simple unit structure, the opportunity for further diversity in the biological activity of a given dsRNA molecule always exists. Namely, each deviation from a perfectly double-helical arrangement introduces the possibility for emphasizing one biological reactivity at the expense of another. This latter structure-activity property may partially account for the extreme apparent diversity, commonly encountered, in the presentations of virologic illness. Appendix note added in proof. Subsequent to submission of this text, we have found that the potent mitogen effect of dsRNA for lymphocytes (murine and human) is also exquisitively sensitive to the fidelity in base pairing of the input polymer pair (59). For example, infrequent "loops" (one nucleotide per 20 base pairs) in an otherwise perfectly helical rI(n) (.) rC(n) molecule [for example, rI(n) (.) r(C(19,)U)(n)] strongly changes its mitogenic properties. This observation, which supports our thesis that a "fine structure" term can be developed for other reactions triggered by dsRNA's in biological systems, emphasizes that diverse biological effects may be encountered with an ostensibly uniform family of dsRNA's.     

RNA二级结构预测方法

RNA是一类具有重要生物学功能的生物大分子,它是遗传信息由DNA到蛋白质的中间传递体.RNA二级结构预测方法可以分为基于热力学的预测方法和基于系统发生学的预测方法两大类.本文就RNA二级结构预测的方法进行了综述,介绍了最低自由能预测法、配分函数预测法、协同变异预测法、随机上下文无关语法预测法等4种预测方法以及它们的优缺点.     

基于现代信息技术的蔬菜安全预警与追溯平台建设

【目的】借助现代信息技术,实现蔬菜从生产到销售整个环节质量安全的预警与追溯。【方法】以蔬菜为研究对象,以国家蔬菜生产基地--寿光市为示范区,围绕寿光市蔬菜质量安全监管和溯源管理的信息化需求,采用WebGIS、物联网、条码识别、数据库等多种现代信息技术,研究蔬菜物流数据的采集和存储形式,并探索蔬菜质量安全预警与追溯平台的建设。【结果】结合物联网数据采集技术,采用SQLServer2008作为前台建立了一套属性数据库,包括产地蔬菜数据、蔬菜加工环节数据、蔬菜运输环节数据、蔬菜销售环节数据等。利用GIS功能制作了一套蔬菜质量安全相关空间数据,包括山东省道路图、寿光市采样点图、寿光市土壤养分图等。在此基础上,建立了一套切实有效的蔬菜质量安全预警与追溯平台。平台设计结合各种信息技术及寿光市蔬菜安全生产业务的需要,同时充分考虑数据的保密性和用户的需求,将平台划分为四大模块：数据查询、蔬菜质量安全预警、蔬菜质量安全追溯、辅助工具。实现的功能主要包括：蔬菜信息录入编辑,蔬菜产品信息及运送信息查询、地理坐标查询,实时预警,蔬菜质量安全追溯,蔬菜空间立体信息展示,蔬菜物流运输路径优化,蔬菜产地土壤养分统计,蔬菜产地土壤养分插值,网络视频监控等。其中实时预警功能利用物联网实时获取数据的特点,将采集的坐标、温度、湿度、时间等信息传送到平台服务器,该平台对蔬菜的温度、湿度、保质期等进行实时监测、预警,确保蔬菜的质量安全;蔬菜质量安全追溯功能根据蔬菜条形码和记载的物流坐标,在地图上对物流配送路径进行追溯;路径分析功能可以根据蔬菜运输的出发地和目的地进行路径的最优设计;蔬菜空间立体信息展示功能可以实现从土壤到地面再到大气的整个垂直面的立体化展示,是空间、时间不同节点信息数据的立体化集成。【结论】本研究充分利用GIS技术更形象地展示了蔬菜从开始种植到最后销售所有环节的信息,对蔬菜质量安全管理的提升有很大的帮助,一定程度上对政府相关部门监管蔬菜安全起到了很好的辅助决策功能。