Flow-through polymerase chain reactions in chip thermocyclers

The miniaturization of analytical devices by micromachining technology is destined to have a major impact on medical and bioanalytical fields. To meet the current demands for rapid DNA amplification, various instruments and innovative technologies have been introduced by several groups in recent years. The development of the devices was extended in different directions and adapted to corresponding applications. In this review the development of a variety of devices and components for performing DNA amplification as well as the comparison of batch-process thermocyclers with reaction chambers and flow-through devices for different purposes are discussed. The main attention is turned to a flow device concept for thermocycling using microfabricated elements for local heat flow management, for which simulations and considerations for further improvement regarding design, material choice and applied technology were performed. The present review article mainly discusses and compares thermocycling devices for rapid thermocycling made of silicon or of silicon and glass with a short excursion to the possibility of plastic chip devices. In order to perform polymerase chain reactions (PCRs) in the microreactors, special attention must be paid to the conditions of the internal surfaces. For microchips, surface effects are generally pronounced because the surface to volume ratio increases upon miniaturization. Solutions for solving this problem are presented. We propose an overview of layouts for batch-process thermocyclers with different parallelization of reaction chambers and also of different designs of continuous flow thermocycling chips, paying particular attention to the parameters which influence the efficiency of such chip devices. Finally we point out some recent issues for applications in the field of clinical diagnostics.     

On-chip cell culture on a microarray of extracellular matrix with surface modification of poly(dimethylsiloxane)

Microfluidic cell culture chips allow to perform assays of small-volume samples rapidly and reproducibly. Most of these chips are made of poly(dimethylsiloxane) (PDMS), which is a flexible, durable, transparent and inexpensive polymer that can be easily applied to fabrication of microstructures by photolithography and replica molding. However, not many cells are able to grow on unmodified PDMS because the cells need appropriate scaffolds on the surface. Here we report surface modification of a PDMS substrate with a microarray of extracellular matrix (ECM) for on-chip cell culture. The ECM proteins collagen and fibronectin were covalently immobilized on an 8 x 8 microarray format by micropatterned UV-induced graft polymerization through a photomask and dehydration-condensation reaction through a microfabricated stencil. Identical spots of ECMs were successfully formed and the geometry of the spots accurately corresponded to the micropattern of the photomask and stencil. We demonstrate the culture of CHO-K1 cells on the ECM microarray chip. Cells proliferated on the fibronectin spots during the 2-day culture.     

Acoustic wave based MEMS devices for biosensing applications

This paper presents a review of acoustic-wave based MEMS devices that offer a promising technology platform for the development of sensitive, portable, real-time biosensors. MEMS fabrication of acoustic wave based biosensors enables device miniaturization, power consumption reduction and integration with electronic circuits. For biological applications, the biosensors are integrated in a microfluidic system and the sensing area is coated with a biospecific layer. When a bioanalyte interacts with the sensing layer, mass and viscosity variations of the biospecific layer can be detected by monitoring changes in the acoustic wave properties such as velocity, attenuation, resonant frequency and delay time. Few types of acoustic wave devices could be integrated in microfluidic systems without significant degradation of the quality factor. The acoustic wave based MEMS devices reported in the literature as biosensors and presented in this review are film bulk acoustic wave resonators (FBAR), surface acoustic waves (SAW) resonators and SAW delay lines. Different approaches to the realization of FBARs, SAW resonators and SAW delay lines for various biochemical applications are presented. Methods of integration of the acoustic wave MEMS devices in the microfluidic systems and functionalization strategies will be also discussed.     

Structural behavior of nanometric carbohydrate films transduced by a resonant technique

New optical nanoresonance effects enabled us to study the effect of ions on nanometric carbohydrate thin layers on chips. Immobilization was done via spin coating of the derivatized carbohydrate polymer at a metallized chip surface forming ultrathin films (about 50-300 nm thick) followed by photochemical cross-linking. Deposition of metal-nanoclusters, synthesized by chemical means and sputter coating on top of the polymer, induced an optical resonance effect, which transduced changes of polymer structure quantitatively into an optical signal that can be observed directly as resonance shift of a narrow optical peak. The response of the sensor chip even visible to the eye was quantified spectroscopically in the visible and ir range of the spectrum. The lifetime of thin film was good, and thus application as a sensor was limited only by the mechanical stability of the reactive matrix, but not by photobleaching or molecular leakage. Due to the inherent hydrophilic nature of the alginate polymer, the response time of this new sensor is governed by simple aqueous diffusion of the ionic calcium for up to 300 nm completed within less than one second. Monitoring of calcium fluctuations in a high background of magnesium and even serum was demonstrated with a dynamic range optimal for physiological measurements and a linear response up to 5 mM. Surface and alignment of polymer chain were influenced by the nanostructure of the supporting metal film-contrary to alginic acid, chitosan was deposited well aligned to the nanocrystals of the support.     

Gravimetric biosensors based on acoustic waves in thin polymer films

Most gravimetric biosensors use thin piezoelectric quartz crystals, either as resonating crystals (quartz crystal microbalance, QCM), or as bulk/surface acoustic wave (SAW) devices. In the majority of these the mass response is inversely proportional to the crystal thickness which, at a limit of about 150 microns, gives inadequate sensitivity. A new system is described in which acoustic waves are launched in very thin (10 microns) tensioned polymer films to produce an oscillatory device. A theoretical equation for this system is almost identical to the well-known Sauerbrey equation used in the QCM method. Because the polymer films are so thin, a 30-fold increase in sensitivity is predicted and verified by adding known surface masses. Temperature sensitivity is a problem so a separate control sensor and careful temperature regulation are necessary. Preliminary results showing the real time binding of protein (IgG), a step towards immunosensor development, and the use of mass enhancing particles are presented. Inexpensive materials are used so disposable gravimetric biosensors may become feasible.     

Bacteria detection using disposable optical leaky waveguide sensors

Novel disposable absorbing material clad leaky waveguide sensor devices (LWD) have been developed for the detection of pathogenic particles such as bacteria. These chips are tailored to give the maximum extension of the evanescent field at the sensor surface in order to place the entire volume of the bacteria captured by immobilized antibodies on the chip surface within this field. This in turn increases the interaction of the light with the bacteria's bulk volume. Disposable LWD chips were fabricated at room temperature and without the use of expensive fabrication equipment. These LWDs have been characterised by detecting refractive index (RI) changes, scattering and fluorescence from bacterial spores at the sensor surface when illuminated at the coupling angle. The detection limit of Bacillus subtilis var. niger (BG) bacterial spores was 10(4) spores/ml and the illumination intensity of the spores was found to be three times greater than the illumination intensity generated using the surface plasmon resonance (SPR).     

五种SPR传感芯片的再生制备及其应用

基于表面等离子体共振技术(surface plasmon resonance, SPR)的生物传感器,能够实时监测生物分子间的相互作用,且无需标记,已被广泛应用于蛋白质组学、药物研发、临床诊断、食品安全和环境监测等领域,并且显示出广阔的应用前景。传感芯片是Biacore系列仪器的核心部件,目前芯片只能从Biacore公司购买,价格昂贵,导致很多仪器利用率低下,资源处于闲置状态。阐述了用于Biacore系列仪器的五种传感芯片（J1,C1,CM5,SA和NTA芯片）的再生制备方法,并列举了应用实例,制备方法操作简单,成本低廉。通过多年的改进与优化,制备的芯片能够达到Biacore芯片同等品质。此方法的推广,将有助于推动表面等离子共振技术在各个领域的广泛应用。     

An interleukin-6 ZnO/SiO(2)/Si surface acoustic wave biosensor

A novel high sensitivity ZnO/SiO(2)/Si Love mode surface acoustic wave (SAW) biosensor for the detection of interleukin-6 (IL-6), is reported. The biosensors operating at 747.7MHz and 1.586GHz were functionalized by immobilizing the monoclonal IL-6 antibody onto the ZnO biosensor surface both through direct surface adsorption and through covalent binding on gluteraldehyde. The morphology of the IL-6 antibody-protein complex was studied using scanning electron microscopy (SEM), and the mass of the IL-6 protein immobilized on the surface was measured from the frequency shift of the SAW resonator biosensor. The biosensor was shown to have extended linearity, which was observed to improve with higher sensor frequency and for IL-6 immobilization through the monoclonal antibody. Preliminary results of biosensor measurements of low levels of IL-6 in normal human serum are reported. The biosensor can be fully integrated with CMOS Si chips and developed as a portable real time detection system for the interleukin family of proteins in human serum.     

Evaluation of two- and three-dimensional streptavidin binding platforms for surface plasmon resonance spectroscopy studies of DNA hybridization and protein-DNA binding

Surface plasmon resonance (SPR) spectroscopy has been used to study DNA assembly, DNA hybridization, and protein-DNA interactions on two streptavidin (SA) sensor chips. On one chip, SA molecules are immobilized on a biotin-exposed surface, forming an ordered two-dimensional (2D) SA monolayer. The other chip, BIAcore's SA chip, contains SA molecules immobilized within a three-dimensional (3D) carboxylated dextran matrix. Compared to the 2D chip, the 3D SA matrix allows for a slower immobilization rate of biotinylated DNA due to diffusion limitation in the dextran matrix, but with twice the amount of the immobilized DNA due to the greater number of reactive sites, which in turn enables a higher sensitivity for DNA hybridization detection. Interestingly, having a greater DNA probe dispersion in the 3D matrix does not induce a higher DNA hybridization efficiency. In a study of protein binding to immobilized DNA (estrogen receptor to estrogen response elements), aiming at assessing the DNA sequence dependent protein binding behavior, the 2D and 3D chips produce different binding characteristics. On the 2D chip, the protein binding exhibits a better selectivity to the specific sequences, regardless of binding stringency (e.g. salt concentration), whereas on the 3D chip, the liquid handling system needs to be optimized in order to minimize transport limitations and to detect small affinity differences. Through this study we demonstrate that the physicochemical structure of SPR chips affects the apparent binding behaviors of biomolecules. When interpreting SPR binding curves and selecting a sensor chip, these effects should be taken into account.     

Swimming Using Surface Acoustic Waves

Microactuation of free standing objects in fluids is currently dominated by the rotary propeller, giving rise to a range of potential applications in the military, aeronautic and biomedical fields. Previously, surface acoustic waves (SAWs) have been shown to be of increasing interest in the field of microfluidics, where the refraction of a SAW into a drop of fluid creates a convective flow, a phenomenon generally known as SAW streaming. We now show how SAWs, generated at microelectronic devices, can be used as an efficient method of propulsion actuated by localised fluid streaming. The direction of the force arising from such streaming is optimal when the devices are maintained at the Rayleigh angle. The technique provides propulsion without any moving parts, and, due to the inherent design of the SAW transducer, enables simple control of the direction of travel.     

Self-assembling protein arrays on DNA chips by auto-labeling fusion proteins with a single DNA address

The high-throughput deposition of recombinant proteins on chips, beads or biosensor devices would be greatly facilitated by the implementation of self-assembly concepts. DNA-directed immobilization via conjugation of proteins to an oligonucleotide would be preeminently suited for this purpose. Here, we present a unique method to attach a single DNA address to proteins in one step during the purification from the E. coli lysate by fusion to human O6-alkylguanine-DNA-alkyltransferase (SNAP-tag) and the Avitag. Use of the conjugates in converting a DNA chip into a protein chip by self assembly is demonstrated.     

聚合物微流控芯片消毒灭菌技术研究进展

聚合物微流控芯片成本低、易加工,目前在医药、生物检测和化学合成等领域得到了普遍应用。以热塑性聚合物聚甲基丙烯酸甲酯(polymethylmethacrylate,PMMA)和热固型聚合物聚二甲基硅氧烷(polydimethy lsiloxane,PDMS)为基材的高分子聚合物材料因具有较好的生物相容性和光学透明性,已逐渐成为聚合物微流控芯片加工的主导材料,被广泛应用于生物医药类微流控芯片的制备。鉴于该类芯片应用场景的特殊性,需在使用前进行消毒灭菌处理以避免微生物干扰。目前,针对PMMA和PDMS的消毒灭菌方法包括高压蒸汽灭菌、紫外线灭菌、电子束、60Co γ射线辐射灭菌、超临界二氧化碳灭菌、乙醇消毒、环氧乙烷灭菌、过氧化氢低温等离子体灭菌、绿原酸消毒、清洗剂消毒。本文从基本原理、消毒灭菌方法、应用场景等方面,回顾和总结了相关技术在PMMA和PDMS基体微流控芯片中的实现方法,并在芯片材质、适用范围等方面分析了所适用的消毒灭菌方法,为以聚合物为基材的生物医药类微流控芯片的消毒灭菌提供有益参考。     

Enhancing Results of Microarray Hybridizations Through Microagitation

Protein and DNA microarrays have become a standard tool in proteomics/genomics research. In order to guarantee fast and reproducible hybridization results, the diffusion limit must be overcome. Surface acoustic wave (SAW) micro-agitation chips efficiently agitate the smallest sample volumes (down to 10 μL and below) without introducing any dead volume. The advantages are reduced reaction time, increased signal-to-noise ratio, improved homogeneity across the microarray, and better slide-to-slide reproducibility. The SAW micromixer chips are the heart of the Advalytix ArrayBooster, which is compatible with all microarrays based on the microscope slide format.     

Chemiluminescence micro-flow-injection analysis on a chip.

Chemiluminescence microflow-injection analysis (microFIA) systems on a chip have been developed. The technology of laser ablation was used to fabricate the microchannels on the polymethyl methacrylate (PMMA) chip. The three sampling structure, including double-tee sampling structure, microvalve sampling structure and injection pump with accurate time control, were used. The microcolumn for specific molecular recognition, including molecularly imprinted polymer, enzyme and bacteria, were used to enhance selectivity. These microFIA systems have been applied to clinical analysis, assessment of food safety, in vivo and real-time determination of drugs, and pharmacokinetics studies.     

Evanescent resonator chips: a universal platform with superior sensitivity for fluorescence-based microarrays

In the present paper, we introduce for the first time a novel generation of a universal fluorescence transducer, the so-called evanescent resonator (ER) platform. The device comprises a transparent substrate and a thin dielectric surface layer containing sub-micron corrugated structures. The ER chip exhibits an inherent physical signal amplification due to confinement of excitation energy in the thin surface layer. Energy confinement is based on interference effects created by the abnormal reflection geometry and leads to efficient excitation of surface-bound fluorophores in the evanescent field of the chip. The evanescent resonator platform has the potential to increase the fluorescence yield of labelled biomolecules to more than 100-fold when compared with conventional microarray chips. The new ER device has been developed for analysis of nucleic acids from different species. However, it can be used with all kinds of biomolecular affinity systems. The platform combines superior sensitivity with exceptional reproducibility and ease of use. The chips are compatible with commercially available laser scanners, confocal microscopes, and portable or miniaturised CCD read-out equipment.     

Microfluidics for in vivo imaging of neuronal and behavioral activity in Caenorhabditis elegans

The nematode C. elegans is an excellent model organism for studying behavior at the neuronal level. Because of the organism's small size, it is challenging to deliver stimuli to C. elegans and monitor neuronal activity in a controlled environment. To address this problem, we developed two microfluidic chips, the 'behavior' chip and the 'olfactory' chip for imaging of neuronal and behavioral responses in C. elegans. We used the behavior chip to correlate the activity of AVA command interneurons with the worm locomotion pattern. We used the olfactory chip to record responses from ASH sensory neurons exposed to high-osmotic-strength stimulus. Observation of neuronal responses in these devices revealed previously unknown properties of AVA and ASH neurons. The use of these chips can be extended to correlate the activity of sensory neurons, interneurons and motor neurons with the worm's behavior.     

Electrotaxis Studies of Lung Cancer Cells using a Multichannel Dual-electric-field Microfluidic Chip

The behavior of directional cell migration under a direct current electric-field (dcEF) is referred to as electrotaxis. The significant role of physiological dcEF in guiding cell movement during embryo development, cell differentiation, and wound healing has been demonstrated in many studies. By applying microfluidic chips to an electrotaxis assay, the investigation process is shortened and experimental errors are minimized. In recent years, microfluidic devices made of polymeric substances (e.g., polymethylmethacrylate, PMMA, or acrylic) or polydimethylsiloxane (PDMS) have been widely used in studying the responses of cells to electrical stimulation. However, unlike the numerous steps required to fabricate a PDMS device, the simple and rapid construction of the acrylic microfluidic chip makes it suitable for both device prototyping and production. Yet none of the reported devices facilitate the efficient study of the simultaneous chemical and dcEF effects on cells. In this report, we describe our design and fabrication of an acrylic-based multichannel dual-electric-field (MDF) chip to investigate the concurrent effect of chemical and electrical stimulation on lung cancer cells. The MDF chip provides eight combinations of electrical/chemical stimulations in a single test. The chip not only greatly shortens the required experimental time but also increases accuracy in electrotaxis studies.     

Accuracy of genotype imputation in Nelore cattle

Background

Genotype imputation from low-density (LD) to high-density single nucleotide polymorphism (SNP) chips is an important step before applying genomic selection, since denser chips tend to provide more reliable genomic predictions. Imputation methods rely partially on linkage disequilibrium between markers to infer unobserved genotypes. Bos indicus cattle (e.g. Nelore breed) are characterized, in general, by lower levels of linkage disequilibrium between genetic markers at short distances, compared to taurine breeds. Thus, it is important to evaluate the accuracy of imputation to better define which imputation method and chip are most appropriate for genomic applications in indicine breeds.

Methods

Accuracy of genotype imputation in Nelore cattle was evaluated using different LD chips, imputation software and sets of animals. Twelve commercial and customized LD chips with densities ranging from 7 K to 75 K were tested. Customized LD chips were virtually designed taking into account minor allele frequency, linkage disequilibrium and distance between markers. Software programs FImpute and BEAGLE were applied to impute genotypes. From 995 bulls and 1247 cows that were genotyped with the Illumina® BovineHD chip (HD), 793 sires composed the reference set, and the remaining 202 younger sires and all the cows composed two separate validation sets for which genotypes were masked except for the SNPs of the LD chip that were to be tested.

Results

Imputation accuracy increased with the SNP density of the LD chip. However, the gain in accuracy with LD chips with more than 15 K SNPs was relatively small because accuracy was already high at this density. Commercial and customized LD chips with equivalent densities presented similar results. FImpute outperformed BEAGLE for all LD chips and validation sets. Regardless of the imputation software used, accuracy tended to increase as the relatedness between imputed and reference animals increased, especially for the 7 K chip.

Conclusions

If the Illumina® BovineHD is considered as the target chip for genomic applications in the Nelore breed, cost-effectiveness can be improved by genotyping part of the animals with a chip containing around 15 K useful SNPs and imputing their high-density missing genotypes with FImpute.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-014-0069-1) contains supplementary material, which is available to authorized users.     

Influence of intermediate aminodextran layers on the signal response of surface acoustic wave biosensors

Surface acoustic wave (SAW) devices based on horizontally polarized surface shear waves enable direct and label-free detection of proteins in real time. Binding reactions on the sensor surface are detected by determining changes in surface wave velocity caused mainly by mass adsorption or change of viscoelasticity in the sensing layer. Intermediate hydrogel layers have been proven to be useful to immobilize capture molecules or ligands corresponding to the analyte. However, the SAW signal response strongly depends on the morphology of the hydrogel due to different relative changes of its acoustomechanical parameters such as viscoelasticity and density. In this work five aminodextrans (AMD) and one diamino polyethylene glycol (DA-PEG) were used as intermediate hydrogel layers. Sensors with immobilized streptavidin and samples containing biotinylated bovine serum albumin were used to exemplify affinity assays based on immobilized capture molecules for protein detection. The effects of the three-dimensional AMDs and the two-dimensional (2D) DA-PEG on the SAW signal response were investigated. The signal height decreased with increasing molar mass and increasing amount of immobilized AMD. Consequently, thin hydrogel layers are ideal to obtain optimum signal responses in this type of assay, whereas it is not necessarily a 2D hydrogel that gives the best results.