Stretching DNA by electric field and flow field in microfluidic devices: An experimental validation to the devices designed with computer simulations

We examined the performance of three microfluidic devices for stretching DNA. The first device is a microchannel with a contraction, and the remaining two are the modifications to the first. The modified designs were made with the help of computer simulations [C. C. Hsieh and T. H. Lin, Biomicrofluidics 5(4), 044106 (2011) and C. C. Hsieh, T. H. Lin, and C. D. Huang, Biomicrofluidics 6, 044105 (2012)] and they were optimized for operating with electric field. In our experiments, we first used DC electric field to stretch DNA. However, the experimental results were not even in qualitative agreement with our simulations. More detailed investigation revealed that DNA molecules adopt a globular conformation in high DC field and therefore become more difficult to stretch. Owing to the similarity between flow field and electric field, we turned to use flow field to stretch DNA with the same devices. The evolution patterns of DNA conformation in flow field were found qualitatively the same as our prediction based on electric field. We analyzed the maximum values, the evolution and the distributions of DNA extension at different Deborah number in each device. We found that the shear and the hydrodynamic interaction have significant influence on the performance of the devices.     

Simulation of conformational preconditioning strategies for electrophoretic stretching of DNA in a microcontraction

We have used Brownian dynamics-finite element method to examine two conformational preconditioning approaches for improving DNA stretching in a microcontraction for the purpose of direct gene analysis. The newly proposed "pre-stretching" strategy is found to significantly improve the degree of DNA extension at the exit of the contraction. On the other hand, applying an oscillating extensional field to DNA yields no preconditioning effect. Detailed analysis of the evolution of DNA extension and conformation reveals that the success of our "pre-stretching" strategy relies on the "non-local" effect that cannot be predicted using simple kinematics analysis. In other words, accurate prediction can only be obtained using detailed simulations. Comparing to the existing preconditioning strategies, our "pre-stretching" method is easy to implement while still providing a very good performance. We hope that the insight gained from this study can be useful for future design of biomicrofluidic devices for DNA manipulation.     

协同创新网络演化模型及仿真研究——基于类DNA翻译过程

在综合协同创新网络基本属性和独有特质的基础上,通过刻画外界刺激转变过程和网络异质主体行为,构建出以异质性主体为网络要素、以刺激-反应机制为演化机理的协同创新网络类DNA翻译过程模型。运用系统仿真方法,分析了从协同创新网络的拓扑结构变动规律,知识元素和网络拓扑结构的耦合演化关系,网络异质主体的角色作用及主体开放程度与知识流动效率的关系等多个角度渐次深入地分析了协同创新网络演化过程中网络结构变动特点及其与知识元素、主体要素间深层次地交互作用关系。结果表明：协同创新网络发展过程中会多次涌现小世界特性,但程度、原因不尽相同;技术知识和网络结构存在协同演化现象;强势企业始终是协同创新网络的主导;主体开放程度对技术知识流动效率提升幅度有很大影响。强化企业在技术创新中的主体地位,并增强异质性主体间的开放程度,是提高协同创新绩效的有力保障。     

Rapid detection of natriuretic peptides by a microfluidic LabChip analyzer with DNA aptamers: Application of natriuretic peptide detection

Rapid detection of brain natriuretic peptide (BNP) concentration can be used for the diagnosis of acute heart failure and for the evaluation of the effectiveness of a clinical therapy. We used the systematic evolution of ligands by exponential enrichment method to develop DNA aptamers for BNP whose sequences were determined by cloning method and consensus sequence analysis. A total of eight conserved sequences was identified. By combining the fluorescent-labeled aptamers with fast protein lab-on-chip analysis, we could achieve quantification of BNP concentrations with high speed, sensitivity, and specificity.     

Convergent genomic signatures of high-altitude adaptation among domestic mammals

Abundant and diverse domestic mammals living on the Tibetan Plateau provide useful materials for investigating adaptive evolution and genetic convergence. Here, we used 327 genomes from horses, sheep, goats, cattle, pigs and dogs living at both high and low altitudes, including 73 genomes generated for this study, to disentangle the genetic mechanisms underlying local adaptation of domestic mammals. Although molecular convergence is comparatively rare at the DNA sequence level, we found convergent signature of positive selection at the gene level, particularly the EPAS1 gene in these Tibetan domestic mammals. We also reported a potential function in response to hypoxia for the gene C10orf67, which underwent positive selection in three of the domestic mammals. Our data provide an insight into adaptive evolution of high-altitude domestic mammals, and should facilitate the search for additional novel genes involved in the hypoxia response pathway.     

技术冲击与企业网络演化的时机和方向——激光光盘行业的案例

以1995~2008年激光光盘行业的战略联盟网络为对象,采用纵向案例研究方法,从企业网络演化的时机和方向考察网络演化过程。以行业关键事件作为分析企业网络演化时机的"时间窗口",通过结构强化效应和结构弱化效应来分析企业网络演化方向。我们认为,企业网络演化是企业网络对行业中发生的关键事件作出的反应,这些事件可能会强化网络结构或者弱化网络结构。通过分析行业关键事件的特征,可以事先识别出这些事件对网络结构的影响,从而使管理者能够采取适当的战略行为塑造网络结构,为企业获取竞争优势创造有利的外部环境。     

Two decades of suspect evidence for adaptive molecular evolution—negative selection confounding positive-selection signals

There has been a large literature in the last two decades affirming adaptive DNA sequence evolution between species. The main lines of evidence are from (i) the McDonald-Kreitman (MK) test, which compares divergence and polymorphism data, and (ii) the phylogenetic analysis by maximum likelihood (PAML) test, which analyzes multispecies divergence data. Here, we apply these two tests concurrently to genomic data of Drosophila and Arabidopsis. To our surprise, the >100 genes identified by the two tests do not overlap beyond random expectation. Because the non-concordance could be due to low powers leading to high false negatives, we merge every 20–30 genes into a ‘supergene’. At the supergene level, the power of detection is large but the calls still do not overlap. We rule out methodological reasons for the non-concordance. In particular, extensive simulations fail to find scenarios whereby positive selection can only be detected by either MK or PAML, but not both. Since molecular evolution is governed by positive and negative selection concurrently, a fundamental assumption for estimating one of these (say, positive selection) is that the other is constant. However, in a broad survey of primates, birds, Drosophila and Arabidopsis, we found that negative selection rarely stays constant for long in evolution. As a consequence, the variation in negative selection is often misconstrued as a signal of positive selection. In conclusion, MK, PAML and any method that examines genomic sequence evolution has to explicitly address the variation in negative selection before estimating positive selection. In a companion study, we propose a possible path forward in two stages—first, by mapping out the changes in negative selection and then using this map to estimate positive selection. For now, the large literature on positive selection between species has to await reassessment.     

Structural and dynamic properties of linker histone H1 binding to DNA

Found in all eukaryotic cells, linker histones H1 are known to bind to and rearrange nucleosomal linker DNA. In vitro, the fundamental nature of H1∕DNA interactions has attracted wide interest among research communities-from biologists to physicists. Hence, H1∕DNA binding processes and structural and dynamical information about these self-assemblies are of broad importance. Targeting a quantitative understanding of H1 induced DNA compaction mechanisms, our strategy is based on using small-angle x-ray microdiffraction in combination with microfluidics. The usage of microfluidic hydrodynamic focusing devices facilitates a microscale control of these self-assembly processes, which cannot be achieved using conventional bulk setups. In addition, the method enables time-resolved access to structure formation in situ, in particular, to transient intermediate states. The observed time dependent structure evolution shows that the H1∕DNA interaction can be described as a two-step process: an initial unspecific binding of H1 to DNA is followed by a rearrangement of molecules within the formed assemblies. The second step is most likely induced by interactions between the DNA and the H1's charged side chains. This leads to an increase in lattice spacing within the DNA∕protein assembly and induces a decrease in the correlation length of the mesophases, probably due to a local bending of the DNA.     

企业知识产权能力演化路径——基于战略导向视角

知识产权能力是促进企业成长的重要动力,它受企业内外因共同影响。其中,企业战略导向对知识产权能力起到重要决定作用。本文从战略导向视角出发,分别论述了作为战略导向两个维度的市场导向、创业导向与知识产权能力演化之间的关联,并在此基础上进一步探讨了知识产权能力演化路径。本文选取沪深上市10年以上的28家计算机应用企业,运用散点图、多元回归等研究方法,系统分析企业知识产权能力演化路径。结果表明,战略导向与企业知识产权能力演化之间存在显著相关,进一步分析发现创业导向正向影响知识产权创造、运用能力,市场导向则正向影响知识产权运用能力。知识产权能力结构的演化伴随着企业战略导向的调整,不同战略导向会形成相应的知识产权能力结构。     

Measurements of DNA barcode label separations in nanochannels from time-series data

We analyzed time-series data for fluctuations of intramolecular segments of barcoded E. coli genomic DNA molecules confined in nanochannels with sizes near the persistence length of DNA. These dynamic data allowed us to measure the probability distribution governing the distance between labels on the DNA backbone, which is a key input into the alignment methods used for genome mapping in nanochannels. Importantly, this dynamic method does not require alignment of the barcode to the reference genome, thereby removing a source of potential systematic error in a previous study of this type. The results thus obtained support previous evidence for a left-skewed probability density for the distance between labels, albeit at a lower magnitude of skewness. We further show that the majority of large fluctuations between labels are short-lived events, which sheds further light upon the success of the linearized DNA genome mapping technique. This time-resolved data analysis will improve existing genome map alignment algorithms, and the overall idea of using dynamic data could potentially improve the accuracy of genome mapping, especially for complex heterogeneous samples such as cancer cells.     

Knowledge sources of entrepreneurship: Firm formation by academic,user and employee innovators

Innovative new ventures are at the heart of economic development, particularly when these startups are created by employee, academic, and user innovators. We synthesize across literature streams examining each phenomena to document distinctions between firms originating from different “knowledge contexts.” We then integrate the knowledge context into Teece's (1986) theoretical framework identifying factors that impact a firm's ability to profit from innovation. Doing so allows us to develop stylized facts and predictive propositions pertaining to differences in the innovative contributions, roles played in shaping industrial dynamics and evolution, and performance outcomes for startups stemming from the three entrepreneurial origins. These propositions provide unique insights into the causes of patterns of industry evolution, contribute to theory in the areas of entrepreneurship and industry evolution, and yield important policy and managerial implications.     

D-谷胱甘肽及其同分异构体稳定的水相碲化镉量子点制备及其荧光性质的研究

使用5-D-谷氨酰-D-半胱氨酰甘氨酸(D-谷胱甘肽)及其同分异构体1-L-谷氨酰-D-半胱氨酰甘氨酸作为稳定剂,在水溶液中合成了碲化镉(CdTe)量子点.通过控制反应回流时间,研究了在不同的反应时间内由2种同分异构体稳定的CdTe量子点的紫外光谱,发现分子结构的细微差别能够引起量子点的表面状态不同,进而导致制备的量子点荧光性质不同.通过荧光光谱研究了2种分子稳定CdTe纳米粒子荧光性质的差异,并结合紫外-可见光谱,讨论了引起2种CdTe量子点荧光性质不同的原因.     

The network of innovators in Jena: An application of social network analysis

We apply social network analysis methods to describe the evolution of the innovator network of Jena, Germany in the period from 1995 to 2001. We find this evolution to be directed towards an increasing focus on core competencies of the network. Further we analyse the network resulting from R&D cooperations and explain - by means of network regression techniques - that the job mobility of scientists and the technological overlap between the actors, rather than past cooperations, can best predict the resulting structure.     

企业文化中心法则构建机制研究

结合生物中心法则,提出了企业文化中心法则。企业文化的三个层次——核心价值观、制度/技术文化以及行为/形象文化分别对应于生物大分子DNA、RNA和蛋白质。企业文化三层次间也存在着信息复制、转录和转译的过程。企业文化中心法则的构建,为我们探讨企业文化层次要素间的信息传递、企业文化的运行演化规律以及构建良好的企业文化提供了新的视角和思路。     

Synchronization in complex networks under structural evolution

We investigate the effects of structural evolution on the stability of synchronized behavior in complex networks. By structural evolution we mean processes that change the topology of the network. In particular, we consider structural evolution as two simultaneous processes: on one hand, the topology changes according to an arbitrary switching law among a set of admissible patterns of connection; on the other hand, the strength of connection evolves according to an adaptive law. Our results show that by constraining the admissible patterns of connection, and using an adaptive law based on the difference between the nodes, we can guarantee the stability of the synchronized solution of the network despite structural changes. Additionally, we extend our results by considering alternative structural evolution processes, namely, a node-based adaptive strategy and a resetting switching law. We illustrate our results with numerical simulation.     

Size-dependent trajectories of DNA macromolecules due to insulative dielectrophoresis in submicrometer-deep fluidic channels

In this paper, we demonstrate for the first time that insulative dielectrophoresis can induce size-dependent trajectories of DNA macromolecules. We experimentally use λ (48.5 kbp) and T4GT7 (165.6 kbp) DNA molecules flowing continuously around a sharp corner inside fluidic channels with a depth of 0.4 μm. Numerical simulation of the electrokinetic force distribution inside the channels is in qualitative agreement with our experimentally observed trajectories. We discuss a possible physical mechanism for the DNA polarization and dielectrophoresis inside confining channels, based on the observed dielectrophoresis responses due to different DNA sizes and various electric fields applied between the inlet and the outlet. The proposed physical mechanism indicates that further extensive investigations, both theoretically and experimentally, would be very useful to better elucidate the forces involved at DNA dielectrophoresis. When applied for size-based sorting of DNA molecules, our sorting method offers two major advantages compared to earlier attempts with insulative dielectrophoresis: Its continuous operation allows for high-throughput analysis, and it only requires electric field strengths as low as ∼10 V∕cm.     

转型时期企业生存发展环境进化与企业成长战略演变

文章从企业与环境互动演化的角度,探讨了我国企业在经济转型过程中的成长经验与成长战略,确认了企业与环境良性互动,企业根据环境的变化,由机会捕捉型成长向素质、能力型成长转型的典型成长战略演化路线。文章的结论对企业制定成长战略和对各级政府制定相关区域发展战略有参考价值。     

Fluctuations of DNA mobility in nanofluidic entropic traps

We studied the mobility of DNA molecules driven by an electric field through a nanofluidic device containing a periodic array of deep and shallow regions termed entropic traps. The mobility of a group of DNA molecules was measured by fluorescent video microscopy. Since the depth of a shallow region is smaller than the DNA equilibrium size, DNA molecules are trapped for a characteristic time and must compress themselves to traverse the boundary between deep and shallow regions. Consistent with previous experimental results, we observed a nonlinear relationship between the mobility and electric field strength, and that longer DNA molecules have larger mobility. In repeated measurements under seemingly identical conditions, we measured fluctuations in the mobility significantly larger than expected from statistical variation. The variation was more pronounced for lower electric field strengths where the trapping time is considerable relative to the drift time. To determine the origin of these fluctuations, we investigated the dependence of the mobility on several variables: DNA concentration, ionic strength of the solvent, fluorescent dye staining ratio, electroosmotic flow, and electric field strength. The mobility fluctuations were moderately enhanced in conditions of reduced ionic strength and electroosmotic flow.     

Focusing and trapping of DNA molecules by head-on ac electrokinetic streaming through join asymmetric polarization

In this work, invoking join asymmetric ac polarization using double half-quadrupole electrodes in a symmetric arrangement, we demonstrate a head-on ac electro-osmotic streaming capable of focusing and trapping DNA molecules efficiently. This is manifested by the observation that picomolar DNA molecules can be trapped into a large crosslike spot with at least an order of magnitude concentration enhancement within just half a minute. We identify that the phenomenon is a combined result of the formation of two prefocused DNA jets flowing toward each other, dipole-induced attraction between focused DNA molecules, and dielectrophoretic trap on the spot. With an additional horizontal pumping, we observe that the trap can transform into a peculiar pitchfork streaming capable of continuous collection and long-distance transport of concentrated DNA molecules. We also show that the same electrode design can be used to direct assembly of submicrometer particles. This newly designed microfluidic platform not only has potentials in enhancing detection sensitivity and facilitating functional assembly for on-chip analysis but also provides an added advantage of transporting target molecules in a focused and continuous manner.     

Simulation guided design of a microfluidic device for electrophoretic stretching of DNA

We have used Brownian dynamics-finite element method (BD-FEM) to guide the optimization of a microfluidic device designed to stretch DNA for gene mapping. The original design was proposed in our previous study [C. C. Hsieh and T. H. Lin, Biomicrofluidics 5(4), 044106 (2011)] for demonstrating a new pre-conditioning strategy to facilitate DNA stretching through a microcontraction using electrophoresis. In this study, we examine the efficiency of the original device for stretching DNA with different sizes ranging from 48.5 kbp (λ-DNA) to 166 kbp (T4-DNA). The efficiency of the device is found to deteriorate with increasing DNA molecular weight. The cause of the efficiency loss is determined by BD-FEM, and a modified design is proposed by drawing an analogy between an electric field and a potential flow. The modified device does not only regain the efficiency for stretching large DNA but also outperforms the original device for stretching small DNA.