Input–output decoupling control design for switched Boolean control networks

We investigate the input–output decoupling problem of switched Boolean control networks (SBCNs) in this paper. Based on the matrix expression of Boolean functions, the dynamics of SBCNs are converted into an algebraic form via semi-tensor product of matrices first. Then, using the redundant variable separation technique, we give the necessary and sufficient conditions for the existence of three kinds of controllers to detect whether an SBCN can be input–output decomposed or not, respectively, including the open-loop controllers, the state feedback controllers, and the output feedback controllers. Meanwhile, a constructive procedure is presented to construct the open-loop controllers, as well as the state feedback controllers and output feedback controllers. Finally, an illustrative example is given to show that the new results obtained are effective.     

DNA combing on low-pressure oxygen plasma modified polysilsesquioxane substrates for single-molecule studies

Molecular combing and flow-induced stretching are the most commonly used methods to immobilize and stretch DNA molecules. While both approaches require functionalization steps for the substrate surface and the molecules, conventionally the former does not take advantage of, as the latter, the versatility of microfluidics regarding robustness, buffer exchange capability, and molecule manipulation using external forces for single molecule studies. Here, we demonstrate a simple one-step combing process involving only low-pressure oxygen (O₂) plasma modified polysilsesquioxane (PSQ) polymer layer to facilitate both room temperature microfluidic device bonding and immobilization of stretched single DNA molecules without molecular functionalization step. Atomic force microscopy and Kelvin probe force microscopy experiments revealed a significant increase in surface roughness and surface potential on low-pressure O₂ plasma treated PSQ, in contrast to that with high-pressure O₂ plasma treatment, which are proposed to be responsible for enabling effective DNA immobilization. We further demonstrate the use of our platform to observe DNA-RNA polymerase complexes and cancer drug cisplatin induced DNA condensation using wide-field fluorescence imaging.     

基于对称函数产生器的对称函数实现

为直接利用现有逻辑器件实现多输出对称函数,通过对２线－４线译码器的逻辑功能和二变量基本对称函数的定义的比较,提出２线－４－线译码器可用作二变量基本对称函数产生器。由于任意ｎ变量的基本对称函数均可通过二变量基本对称函数产生器的树型扩展得到实现,因此,任意ｎ变量的对称函数可以用２线－４线译码器予以实现。文中分别就变量数为奇数和偶数的情况进行了讨论。本文提出的对称函数综合方法在实现多输出对称函数时可获得     

Microfluidic platform for the study of intercellular communication via soluble factor-cell and cell-cell paracrine signaling

Diffusion of autocrine and paracrine signaling molecules allows cells to communicate in the absence of physical contact. This chemical-based, long-range communication serves crucial roles in tissue function, activation of the immune system, and other physiological functions. Despite its importance, few in vitro methods to study cell-cell signaling through paracrine factors are available today. Here, we report the design and validation of a microfluidic platform that enables (i) soluble molecule-cell and/or (ii) cell-cell paracrine signaling. In the microfluidic platform, multiple cell populations can be introduced into parallel channels. The channels are separated by arrays of posts allowing diffusion of paracrine molecules between cell populations. A computational analysis was performed to aid design of the microfluidic platform. Specifically, it revealed that channel spacing affects both spatial and temporal distribution of signaling molecules, while the initial concentration of the signaling molecule mainly affects the concentration of the signaling molecules excreted by the cells. To validate the microfluidic platform, a model system composed of the signaling molecule lipopolysaccharide, mouse macrophages, and engineered human embryonic kidney cells was introduced into the platform. Upon diffusion from the first channel to the second channel, lipopolysaccharide activates the macrophages which begin to produce TNF-α. The TNF-α diffuses from the second channel to the third channel to stimulate the kidney cells, which express green fluorescent protein (GFP) in response. By increasing the initial lipopolysaccharide concentration an increase in fluorescent response was recorded, demonstrating the ability to quantify intercellular communication between 3D cellular constructs using the microfluidic platform reported here. Overall, these studies provide a detailed analysis on how concentration of the initial signaling molecules, spatiotemporal dynamics, and inter-channel spacing affect intercellular communication.     

Long-range and superfast trapping of DNA molecules in an ac electrokinetic funnel

In this work we report a microfluidic platform capable of trapping and concentrating a trace amount of DNA molecules efficiently. Our strategy invokes nonlinear electro-osmotic flow induced by charge polarization under high-frequency ac fields. With the asymmetric quadrupole electrode design, a unique converging flow structure can be created for generating focusing effects on DNA molecules. This focusing in turn transforms into a robust funnel that can collect DNA molecules distantly from the bulk and pack them into a compact cone with the aid of short-range dipole-induced self-attraction and dielectrophoresis. Our results reveal that not only can DNA molecules be concentrated within just a few seconds, but also they can be focused into threads of 1 mm in length, demonstrating the superfast and long-range trapping capability of this funnel. In addition, pico M DNA solutions can be concentrated with several decades of enhancement without any continuous feeding. Alternating concentration and release of DNA molecules is also illustrated, which has potentials in concentrating and transporting biomolecules in a continuous fashion using microdevices.     

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.     

The role of acoustofluidics in targeted drug delivery

With the fast development of acoustic systems in clinical and therapeutic applications, acoustically driven microbubbles have gained a prominent role as powerful tools to carry, transfer, direct, and target drug molecules in cells, tissues, and tumors in the expanding fields of targeted drug delivery and gene therapy. The aim of the present study is to establish a biocompatible acoustic microfluidic system and to demonstrate the generation of an acoustic field and its effects on microbubbles and biological cells in the microfluidic system. The acoustic field creates non-linear oscillations of the microbubble-clusters, which results in generation of shear stress on cells in such microsystems. This effectively helps in delivering extracellular probes in living cells by sonoporation. The sonoporation is investigated under the combined effects of acoustic stress and hydrodynamic stress during targeted drug and gene delivery.     

Gold nanoparticle-assisted single base-pair mismatch discrimination on a microfluidic microarray device

Two simple gold nanoparticle (GNP)-based DNA analysis methods using a microfluidic device are presented. In the first method, probe DNA molecules are immobilized on the surface of a self-assembled submonolayer of GNPs. The hybridization efficiency of the target oligonulceotides was improved due to nanoscale spacing between probe molecules. In the second method, target DNA molecules, oligonulceotides or polymerase chain reaction (PCR) amplicons, are first bound to GNPs and then hybridized to the immobilized probe DNA on a glass slide. With the aid of GNPs, we have successfully discriminated, at room temperature, between two PCR amplicons (derived from closely related fungal pathogens, Botrytis cinerea and Botrytis squamosa) with one base-pair difference. DNA analysis on the microfluidic chip avoids the use of large sample volumes, and only a small amount of oligonucelotides (8 fmol) or PCR products (3 ng), was needed in the experiment. The whole procedure was accomplished at room temperature in 1 h, and apparatus for high temperature stringency was not required.     

Parallel combinatorial chemical synthesis using single-layer poly(dimethylsiloxane) microfluidic devices

Improving methods for high-throughput combinatorial chemistry has emerged as a major area of research because of the importance of rapidly synthesizing large numbers of chemical compounds for drug discovery and other applications. In this investigation, a novel microfluidic chip for performing parallel combinatorial chemical synthesis was developed. Unlike past microfluidic systems designed for parallel combinatorial chemistry, the chip is a single-layer device made of poly(dimethylsiloxane) that is extremely easy and inexpensive to fabricate. Using the chip, a 2×2 combinatorial series of amide-formation reactions was performed. The results of this combinatorial synthesis indicate that the new device is an effective platform for running parallel organic syntheses at significantly higher throughput than with past methodologies. Additionally, a design algorithm for scaling up the 2×2 combinatorial synthesis chip to address more complex cases was developed.     

Modeling and validation of autoinducer-mediated bacterial gene expression in microfluidic environments

Biosensors exploiting communication within genetically engineered bacteria are becoming increasingly important for monitoring environmental changes. Currently, there are a variety of mathematical models for understanding and predicting how genetically engineered bacteria respond to molecular stimuli in these environments, but as sensors have miniaturized towards microfluidics and are subjected to complex time-varying inputs, the shortcomings of these models have become apparent. The effects of microfluidic environments such as low oxygen concentration, increased biofilm encapsulation, diffusion limited molecular distribution, and higher population densities strongly affect rate constants for gene expression not accounted for in previous models. We report a mathematical model that accurately predicts the biological response of the autoinducer N-acyl homoserine lactone-mediated green fluorescent protein expression in reporter bacteria in microfluidic environments by accommodating these rate constants. This generalized mass action model considers a chain of biomolecular events from input autoinducer chemical to fluorescent protein expression through a series of six chemical species. We have validated this model against experimental data from our own apparatus as well as prior published experimental results. Results indicate accurate prediction of dynamics (e.g., 14% peak time error from a pulse input) and with reduced mean-squared error with pulse or step inputs for a range of concentrations (10 μM–30 μM). This model can help advance the design of genetically engineered bacteria sensors and molecular communication devices.     

Microfluidic based high throughput synthesis of lipid-polymer hybrid nanoparticles with tunable diameters

Core-shell hybrid nanoparticles (NPs) for drug delivery have attracted numerous attentions due to their enhanced therapeutic efficacy and good biocompatibility. In this work, we fabricate a two-stage microfluidic chip to implement a high-throughput, one-step, and size-tunable synthesis of mono-disperse lipid-poly (lactic-co-glycolic acid) NPs. The size of hybrid NPs is tunable by varying the flow rates inside the two-stage microfluidic chip. To elucidate the mechanism of size-controllable generation of hybrid NPs, we observe the flow field in the microchannel with confocal microscope and perform the simulation by a numerical model. Both the experimental and numerical results indicate an enhanced mixing effect at high flow rate, thus resulting in the assembly of small and mono-disperse hybrid NPs. In vitro experiments show that the large hybrid NPs are more likely to be aggregated in serum and exhibit a lower cellular uptake efficacy than the small ones. This microfluidic chip shows great promise as a robust platform for optimization of nano drug delivery system.     

基于或-符合展开系数图的布尔差分计算

分析了逻辑函数在部分变量取反时的或-符合展开系数图(即dj图)和降维或-符合展开系数图(即降维dj图),在此基础上提出了用dj图和降维dj图计算逻辑函数的一阶布尔差分和二阶布尔差分的图形方法。实例表明,该图形方法有直观、简单等特点。它能给出逻辑函数布尔差分的最简或/符合式。     

Sustained release of hydrophobic drugs by the microfluidic assembly of multistage microgel/poly (lactic-co-glycolic acid) nanoparticle composites

The poor solubility of many newly discovered drugs has resulted in numerous challenges for the time-controlled release of therapeutics. In this study, an advanced drug delivery platform to encapsulate and deliver hydrophobic drugs, consisting of poly (lactic-co-glycolic acid) (PLGA) nanoparticles incorporated within poly (ethylene glycol) (PEG) microgels, was developed. PLGA nanoparticles were used as the hydrophobic drug carrier, while the PEG matrix functioned to slow down the drug release. Encapsulation of the hydrophobic agents was characterized by fluorescence detection of the hydrophobic dye Nile Red within the microgels. In addition, the microcomposites prepared via the droplet-based microfluidic technology showed size tunability and a monodisperse size distribution, along with improved release kinetics of the loaded cargo compared with bare PLGA nanoparticles. This composite system has potential as a universal delivery platform for a variety of hydrophobic molecules.     

On demand nanoliter-scale microfluidic droplet generation,injection, and mixing using a passive microfluidic device

We here present and characterize a programmable nanoliter scale droplet-on-demand device that can be used separately or readily integrated into low cost single layer rapid prototyping microfluidic systems for a wide range of user applications. The passive microfluidic device allows external (off-the-shelf) electronically controlled pinch valves to program the delivery of nanoliter scale aqueous droplets from up to 9 different inputs to a central outlet channel. The inputs can be either continuous aqueous fluid streams or microliter scale aqueous plugs embedded in a carrier fluid, in which case the number of effective input solutions that can be employed in an experiment is no longer strongly constrained (100 s–1000 s). Both nanoliter droplet sequencing output and nanoliter-scale droplet mixing are reported with this device. Optimization of the geometry and pressure relationships in the device was achieved in several hardware iterations with the support of open source microfluidic simulation software and equivalent circuit models. The requisite modular control of pressure relationships within the device is accomplished using hydrodynamic barriers and matched resistance channels with three different channel heights, custom parallel reversible microfluidic I/O connections, low dead-volume pinch valves, and a simply adjustable array of external screw valves. Programmable sequences of droplet mixes or chains of droplets can be achieved with the device at low Hz frequencies, limited by device elasticity, and could be further enhanced by valve integration. The chip has already found use in the characterization of droplet bunching during export and the synthesis of a DNA library.     

A prototypic microfluidic platform generating stepwise concentration gradients for real-time study of cell apoptosis

This work describes the development of a prototypic microfluidic platform for the generation of stepwise concentration gradients of drugs. A sensitive apoptotic analysis method is integrated into this microfluidic system for studying apoptosis of HeLa cells under the influence of anticancer drug, etoposide, with various concentrations in parallel; it measures the yellow fluorescent protein∕cyan fluorescent protein fluorescence resonance energy transfer (FRET) signal that responds to the activation of caspase-3, an indicator of cell apoptosis. Sets of microfluidic valves on the chip generate stepwise concentration gradient of etoposide in various cell-culture microchambers. The FRET signals from multiple chambers are simultaneously monitored under a fluorescent microscope for long-time observation and the on-chip results are compared with those from 96-well plate study and the methylthiazolyldiphenyl-tetrazolium bromide (MTT) assay. The microfluidic platform shows several advantages including high-throughput capacity, low drug consumption, and high sensitivity.     

DNA-library assembly programmed by on-demand nano-liter droplets from a custom microfluidic chip

Nanoscale synthetic biology can benefit from programmable nanoliter-scale processing of DNA in microfluidic chips if they are interfaced effectively to biochemical arrays such as microwell plates. Whereas active microvalve chips require complex fabrication and operation, we show here how a passive and readily fabricated microchip can be employed for customizable nanoliter scale pipetting and reaction control involving DNA. This recently developed passive microfluidic device, supporting nanoliter scale combinatorial droplet generation and mixing, is here used to generate a DNA test library with one member per droplet exported to addressed locations on microwell plates. Standard DNA assembly techniques, such as Gibson assembly, compatible with isothermal on-chip operation, are employed and checked using off-chip PCR and assembly PCR. The control of output droplet sequences and mixing performance was verified using dyes and fluorescently labeled DNA solutions, both on-chip and in external capillary channels. Gel electrophoresis of products and DNA sequencing were employed to further verify controlled combination and functional enzymatic assembly. The scalability of the results to larger DNA libraries is also addressed by combinatorial input expansion using sequential injection plugs from a multiwell plate. Hence, the paper establishes a proof of principle of the production of functional combinatorial mixtures at the nanoliter scale for one sequence per well DNA libraries.     

拟南芥GH3基因家族启动子序列分析

GH3 基因家族是植物生长素早期响应基因家族之一.拟南芥 10个GH3 基因启动子序列分析表明:GH3 基因的转录起始位点一般在起始密码子上游65~145bp之内,TATA box大多分布在(-24)~(-40)bp区域.MDB和MatInspector分析显示,AtGH3 s基因的上游调控区域普遍存在组织和器官特异性表达元件、激素响应元件以及环境响应元件,表明GH3 基因的表达受到多因素调控;同时,基因芯片数据显示AuxREs对生长素的响应非常重要,但也可能存在其他的生长素响应元件.     

布尔逻辑检索和自然语言检索对比研究

采用4种检索方式（无过滤布尔逻辑、过滤布尔逻辑、无过滤自然语言和过滤自然语言）对7个常见数据库ASP、GS、JSTOR、LexisNexis、ProQuest Central、PubMed、Scopus和Web of Science检索测试,最后分析了在目前技术环境下,布尔逻辑和自然语言检索相比,哪种方式更加有效。