Polymer peel‐off mask for high‐resolution surface derivatization,neuron placement and guidance

We present a dry lift‐off method using a chemically resistant spin‐on plastic, polyimide, to pattern surfaces with high accuracy and resolution. Using well‐known lithographic and reactive ion etching techniques, the spin‐on polymer is patterned over a silicon dioxide surface. The plastic efficiently adheres to the silicon dioxide surface during the chemical modification and is readily lifted‐off following the derivatization process, permitting highly reliable surface derivatization. The verticality of the reactive ion etch enables sub‐micrometer features to be patterned, down to 0.8 µm. The technique is used to pattern neurons on silicon dioxide surfaces: efficient neuron placement over a 4 mm area is shown for patterns larger than 50 µm while process guidance is shown for 10 µm patterns. Biotechnol. Bioeng. 2013; 110: 2236–2241. © 2013 Wiley Periodicals, Inc.     

多孔硅Bragg反射镜适配子生物传感器检测心肌肌钙蛋白I

通过脉冲腐蚀法制备多孔硅Bragg反射镜,将心肌肌钙蛋白I（cTnI）适配子共价固定到多孔硅Bragg反射镜的孔洞中,发现适配子能与cTnI分子特异性结合。定量分析不同浓度的cTnI与适配子结合后多孔硅Bragg反射镜的反射谱峰位的红移情况。结果表明：基于多孔硅Bragg反射镜适配子生物传感器的光学检测具有良好的特异性,且具有免标记及检测时间短等优异性能。传感器的线性检测范围0．05-4nmol／L,最低检测限为0．05nmol／L。     

Slow light engineering for high Q high sensitivity photonic crystal microcavity biosensors in silicon

Current trends in photonic crystal microcavity biosensors in silicon-on-insulator (SOI), that focus on small and smaller sensors have faced a bottleneck trying to balance two contradictory requirements of resonance quality factor and sensitivity. By simultaneous control of the radiation loss and optical mode volumes, we show that both requirements can be satisfied simultaneously. Microcavity sensors are designed in which resonances show highest Q～9300 in the bio-ambient phosphate buffered saline (PBS) as well as highest sensitivity among photonic crystal biosensors. We experimentally demonstrated mass sensitivity 8.8atto-grams with sensitivity per unit area of 0.8pg/mm(2). Highest sensitivity, irrespective of the dissociation constant K(d), is demonstrated among all existing label-free optical biosensors in silicon at the concentration of 0.1μg/ml.     

纳米多孔硅阻抗生物传感器的研究

构建了1种基于多孔硅材料,无需标记的纳米生物传感器,用于对牛血清白蛋白分子进行检测。通过对多孔硅进行表面处理,形成氧化膜,将抗体固定到多孔硅氧化层表面。在磷酸盐缓冲液中,通过电化学检测系统检测加入抗原后,传感器的阻抗值的变化。磷酸缓冲液（PBS）/抗体-氧化层/硅,构成电解液/绝缘层/半导体（electro-lyte-insulator-semiconductor,EIS）结构。传感器的线性检测范围为0.01～0.27mg/mL,检测限为0.01mg/mL。     

Silicon nanopillar substrates for enhancing signal intensity in DNA microarrays

The use of ordered, high-aspect ratio nanopillar arrays on the surface of silicon-based chips to enhance signal intensity in DNA microarrays is reported. These nanopillars consisting either of a single silicon dioxide substrate or a dual silicon/silicon dioxide substrate are fabricated using deep-UV lithography followed by reactive ion etching. These pillar type arrays provide a three-dimensional high surface-density platform that increases the immobilization capacity of captured probes, enhances target accessibility and reduces background noise interference in DNA microarrays, leading to improved signal-to-noise ratios, sensitivity and specificity. Consequently, it was found that the use of such nanopillars enhanced the hybridization signals by up to seven times as compared to silicon dioxide thin film substrates. In addition, hybridization of synthetic targets to capture probes that contained a single-base variation showed that the perfect matched duplex signals on dual-substrate nanopillars can be up to 23 times higher than the mismatched duplex signals, allowing the targets to be unambiguously identified. These results suggest that the nanopillars, particularly the dual-substrate pillars, are able to enhance the hybridization signals and discrimination power in nucleic acids-based detection, providing an alternative platform for improving the performance of DNA microarrays.     

Progress of new label-free techniques for biosensors: a review

The detection techniques used in biosensors can be broadly classified into label-based and label-free. Label-based detection relies on the specific properties of labels for detecting a particular target. In contrast, label-free detection is suitable for the target molecules that are not labeled or the screening of analytes which are not easy to tag. Also, more types of label-free biosensors have emerged with developments in biotechnology. The latest developed techniques in label-free biosensors, such as field-effect transistors-based biosensors including carbon nanotube field-effect transistor biosensors, graphene field-effect transistor biosensors and silicon nanowire field-effect transistor biosensors, magnetoelastic biosensors, optical-based biosensors, surface stress-based biosensors and other type of biosensors based on the nanotechnology are discussed. The sensing principles, configurations, sensing performance, applications, advantages and restriction of different label-free based biosensors are considered and discussed in this review. Most concepts included in this survey could certainly be applied to the development of this kind of biosensor in the future.     

Adsorption of avidin on microfabricated surfaces for protein biochip applications

The adsorption of the protein avidin from hen egg white on patterns of silicon dioxide and platinum surfaces on a microchip and the use of fluorescent microscopy to detect binding of biotin are described. A silicon dioxide microchip was formed using plasma-enhanced chemical vapor deposition while platinum was deposited using radiofrequency sputtering. After cleaning using a plasma arc, the chips were placed into solutions containing avidin or bovine serum albumin. The avidin was adsorbed onto the microchips from phosphate-buffered saline (PBS) or from PBS to which ammonium sulfate had been added. Avidin was also adsorbed onto bovine serum albumin (BSA)-coated surfaces of oxide and platinum. Fluorescence microscopy was used to confirm adsorption of labeled protein, or the binding of fluorescently labeled biotin onto previously adsorbed, unlabeled avidin. When labeled biotin in PBS was presented to avidin adsorbed onto a BSA-coated microchip, the fluorescence signal was significantly higher than for avidin adsorbed onto the biochip alone. The results show that a simple, low-cost adsorption process can deposit active protein onto a chip in an approach that has potential application in the development of protein biochips for the detection of biological species.     

Potent inhibition of ribonuclease A by oligo(vinylsulfonic acid)

Ribonuclease A (RNase A) can make multiple contacts with an RNA substrate. In particular, the enzymatic active site and adjacent subsites bind sequential phosphoryl groups in the RNA backbone through Coulombic interactions. Here, oligomers of vinylsulfonic acid (OVS) are shown to be potent inhibitors of RNase A that exploit these interactions. Inhibition is competitive with substrate and has Ki = 11 pm in assays at low salt concentration. The effect of salt concentration on inhibition indicates that nearly eight favorable Coulombic interactions occur in the RNase A.OVS complex. The phosphonic acid and sulfuric acid analogs of OVS are also potent inhibitors although slightly less effective. OVS is also shown to be a contaminant of MES and other buffers that contain sulfonylethyl groups. Oligomers greater than nine units in length can be isolated from commercial MES buffer. Inhibition by contaminating OVS is responsible for the apparent decrease in catalytic activity that has been observed in assays of RNase A at low salt concentration. Thus, OVS is both a useful inhibitor of RNase A and a potential bane to chemists and biochemists who use ethanesulfonic acid buffers.     

Acid growth effects in maize roots: Evidence for a link between auxin-economy and proton extrusion in the control of root growth

The role of proton excretion in the growth of apical segments of maize roots has been examined. Growth is stimulated by acidic buffers and inhibited by neutral buffers. Organic buffers such as 2[N-morpholino] ethane sulphonic acid (MES) — 2-amino-2-(hydroxymethyl)propane-1,3 diol (Tris) are more effective than phosphate buffers in inhibiting growth. Fusicoccin(FC)-induced growth is also inhibited by neutral buffers. The antiauxins 4-chlorophenoxyisobutyric acid (PCIB) and 2-(naphthylmethylthio) propionic acid (NMSP) promote growth and H⁺-excretion over short time periods; this growth is also inhibited by neutral buffers. We conclude that growth of maize roots requires proton extrusion and that regulation of root growth by indol-3yl-acetic acid (IAA) may be mediated by control of this proton extrusion.Abbreviations IAA indol-3yl-acetic acid - ABA abscisic acid - FC fusicoccin - PCIB 4-chlorophenoxy-isobutyric acid - MES 2(N-morpholino)ethane sulphonic acid - Tris 2-amino-2-(hydroxymethyl) propane-1,3-diol - NMSP 2-(naphthylmethylthio)propionic acid     

Top-Down Nanofabrication and Characterization of 20 nm Silicon Nanowires for Biosensing Applications

A top-down nanofabrication approach is used to develop silicon nanowires from silicon-on-insulator (SOI) wafers and involves direct-write electron beam lithography (EBL), inductively coupled plasma-reactive ion etching (ICP-RIE) and a size reduction process. To achieve nanometer scale size, the crucial factors contributing to the EBL and size reduction processes are highlighted. The resulting silicon nanowires, which are 20 nm in width and 30 nm in height (with a triangular shape) and have a straight structure over the length of 400 μm, are fabricated precisely at the designed location on the device. The device is applied in biomolecule detection based on the changes in drain current (I_ds), electrical resistance and conductance of the silicon nanowires upon hybridization to complementary target deoxyribonucleic acid (DNA). In this context, the scaled-down device exhibited superior performances in terms of good specificity and high sensitivity, with a limit of detection (LOD) of 10 fM, enables for efficient label-free, direct and higher-accuracy DNA molecules detection. Thus, this silicon nanowire can be used as an improved transducer and serves as novel biosensor for future biomedical diagnostic applications.     

Quantitative proteomics reveals key pathways in the symbiotic interface and the likely extracellular property of soybean symbiosome

An effective symbiosis between legumes and rhizobia relies largely on diverse proteins at the plantrhizobium interface for material transportation and signal transduction during symbiotic nitrogen fixation.Here, we report a comprehensive proteome atlas of the soybean symbiosome membrane(SM), peribacteroid space(PBS), and root microsomal fraction(RMF) using state-of-the-art label-free quantitative proteomic technology. In total, 1759 soybean proteins with diverse functions are detected in the SM,...     

Control of pH and its Effect on Ammonium Utilization by Nitrate Reductase Deficient Plants,Cells, and Protoplasts of Nicotiana tabacum

Nitrate reductase deficient plants of Nicotiana tabacum were unable to utilize ammonium efficiently unless the medium was buffered against excessive acidity accumulation. In addition to succinate, calcium carbonate, MES and phosphate buffers allowed plants to utilize ammonium efficiently. Similar observations were made regarding callus derived from stem tissue of these plants. Plants could be grown in compost, in a physiological state suitable for protoplast isolation, when watered with nutrient solutions containing NH₄NO₃ and MES buffer. Protoplast division and proliferation to the stage of plant regeneration was possible using Murashige and Skoog (1962) basal medium buffered with succinate, calcium carbonate or MES but not phosphate.     

Optimisation of a silicon/silicon dioxide substrate for a fluorescence DNA microarray

This paper presents a comprehensive theory and experimental characterisation of the modulation of the fluorescence intensity by the construction of optical interferences on oxidised silicon substrates used for DNA microarrays. The model predicts a 90-fold variation of the fluorescence signal depending on the oxide thickness. For a Cy3 dye, the signal is maximal for a 90 nm oxide thickness corresponding to a 7.5-fold enhancement with respect to a standard glass substrate. For experimental validation of the model, we have prepared Si/SiO2 substrates with different parallel steps of decreasing oxide thicknesses on the same sample using a buffered oxide etch (BOE) etching process after thermal oxidation. The SiO2 surface has been functionalized by a silane monolayer before in situ synthesis of L185 oligonucleotide probes. After hybridisation with complementary targets, the variations of the fluorescence intensity versus oxide thickness are in very good accordance with the theoretical model. The experimental comparison against a glass substrate shows a 10-fold enhancement of the detection sensitivity. Our results demonstrate that a Si/SiO2 substrate is an attractive alternative to standard glass slides for the realisation of fluorescence DNA microarrays whenever detection sensitivity is an important issue.     

Coating efficiency of a 1 -acid glycoprotein in competitive enzyme immunosorbent assays with antigen immobilized on the solid phase

Coating efficiency of rat and human serum a 1 -acid glycoprotein (a 1 -AGP) was investigated for competitive enzyme immunosorbent assays with antigen immobilized on the solid phase by using different pHs and buffers. Blocking materials and pH of coating buffer had a marked influence on the amount of a 1 -AGP that binds to plate. Usually, carbonate buffer is used at pH 9.6 or 9.0, but phosphate buffered saline (PBS) at pH 7.2 can be used for an effective coating. At pH 7.2, coating of a 1 -AGP in Tris buffered saline was five - tenfold as effective as in PBS and phosphate buffer. Blocking of uncoated surface with casein was ten - twenty times as effective as with fetal bovine serum albumin for coating of a 1 -AGP.     

Baroresistant buffer mixtures for biochemical analyses

Hydrostatic pressure is a useful tool in the study of varied fields such as protein aggregation, association, folding, ligand binding, and allostery. Application of pressure can have a significant effect on the pK(a) values of buffers commonly used for biochemical analysis. Consequently, cationic buffers, rather than neutral ones, are generally used to minimize pH effects; however, even with these buffers, the change in pH over 3 kbar may be consequential in highly pH-sensitive biochemical systems. Using fluorescence-based assays, we have systematically examined the effects of pressure on various buffers in the neutral pH range. We show that many commonly used cationic and Good's buffers increase in pH with pressure on the order of 0.1 to 0.3 pH units/kbar, in agreement with other published values. Carboxylates and phosphate decrease in pH to a similar extent. Buffer mixtures, composed of both cationic and carboxylate or phosphate components, are shown to be an order of magnitude less pressure sensitive than the individual component buffers. Using various relative concentrations of Tris and either phosphate, tricarballylate (1,2,3-propanetricarboxylate), or CDA (1,1-cyclohexane diacetate) at pH values between 7 and 8 yields baroresistant buffer mixtures. Buffer mixtures can be optimized for a specific pH, and a list of mixtures is presented for general laboratory use.     

Label-free virus detection using silicon photonic microring resonators

Viruses represent a continual threat to humans through a number of mechanisms, which include disease, bioterrorism, and destruction of both plant and animal food resources. Many contemporary techniques used for the detection of viruses and viral infections suffer from limitations such as the need for extensive sample preparation or the lengthy window between infection and measurable immune response, for serological methods. In order to develop a method that is fast, cost-effective, and features reduced sample preparation compared to many other virus detection methods, we report the application of silicon photonic microring resonators for the direct, label-free detection of intact viruses in both purified samples as well as in a complex, real-world analytical matrix. As a model system, we demonstrate the quantitative detection of Bean pod mottle virus, a pathogen of great agricultural importance, with a limit of detection of 10 ng/mL. By simply grinding a small amount of leaf sample in buffer with a mortar and pestle, infected leaves can be identified over a healthy control with a total analysis time of less than 45 min. Given the inherent scalability and multiplexing capability of the semiconductor-based technology, we feel that silicon photonic microring resonators are well-positioned as a promising analytical tool for a number of viral detection applications.     

Biochemical stability and molecular dynamic characterization of Aspergillus fumigatus cystathionine γ-lyase in response to various reaction effectors

Cystathionine γ-lyase (CGL) is a key enzyme in the methionine–cysteine cycle in all living organisms forming cysteine, α-ketobutyrate and ammonia via homocysteine and cystathionine intermediates. Although, human and plant CGLs have been extensively studied at the molecular and mechanistic levels, there has been little work on the molecular and catalytic properties of fungal CGL. Herein, we studied in detail for the first time the molecular and catalytic stability of Aspergillus fumigatus CGL, since conformational instability, inactivation and structural antigenicity are the main limitations of the PLP-dependent enzymes on various therapeutic uses. We examined these properties in response to buffer compositions, stabilizing and destabilizing agents using Differential Scanning Fluorometery (DSF), steady state and gel-based fluorescence of the intrinsic hydrophobic core, stability of internal aldimine linkage and catalytic properties. The activity of the recombinant A. fumigatus CGL was 13.8 U/mg. The melting temperature (T_m) of CGL in potassium phosphate buffer (pH 7.0–8.0) was 73.3 °C, with ∼3 °C upshifting in MES and sodium phosphate buffers (pH 7.0). The conformational thermal stability was increased in potassium phosphate, sodium phosphate and MES buffers, in contrast to Tris–HCl, HEPES (pH 7.0) and CAPS (pH 9.0–10.0). The thermal stability and activity of CGL was slightly increased in the presence of trehalose and glycerol that might be due to hydration of the enzyme backbone, unlike the denaturing effect of GdmCl and urea. Modification of surface CGL glutamic and aspartic acids had no significant effect on the enzyme conformational and catalytic stability. Molecular modeling and dynamics simulations unveil the high conformational stability of the overall scaffold of CGL with high flexibility at the non-structural regions. CGL structure has eight buried Trp residues, which are reoriented to the enzyme surface and get exposed to the solvent under perturbation of destabilizers. Furthermore, electrostatic calculations of selected snapshots of CGL 3D structure under different experimental conditions showed a remarkable differences on the polarity of the enzyme surface.     

A quantitative study of detection mechanism of a label-free impedance biosensor using ultrananocrystalline diamond microelectrode array

It is well recognized that label-free biosensors are the only class of sensors that can rapidly detect antigens in real-time and provide remote environmental monitoring and point-of-care diagnosis that is low-cost, specific, and sensitive. Electrical impedance spectroscopy (EIS) based label-free biosensors have been used to detect a wide variety of antigens including bacteria, viruses, DNA, and proteins due to the simplicity of their detection technique. However, their commercial development has been hindered due to difficulty in interpreting the change in impedance upon antigen binding and poor signal reproducibility as a result of surface fouling and non-specific binding. In this study, we develop a circuit model to adequately describe the physical changes at bio functionalized surface and provide an understanding of the detection mechanism based on electron exchange between electrolyte and surface through pores surrounding antibody-antigen. The model was successfully applied to extract quantitative information about the bio surface at different stages of surface functionalization. Further, we demonstrate boron-doped ultrananocrystalline diamond (UNCD) microelectrode array (3 × 3 format, 200 μm diameter) improves signal reproducibility significantly and increases sensitivity by four orders of magnitude. This study marks the first demonstration of UNCD array based biosensor that can reliably detect a model Escherichia coli K12 bacterium using EIS, positioning this technology for rapid adoption in point-of-use applications.     

Real-time quantitation of viral replication and inhibitor potency using a label-free optical biosensor

Real-time detection of viral replication inside cells remains a challenge to researchers. The Epic^® System is a high-throughput, label-free optical detection platform capable of measuring molecular interaction in a biochemical assay, as well as integrated cellular response from measurement of cellular dynamic mass redistribution (DMR) in a cell-based assay. DMR has previously been used to measure cell signaling upon receptor stimulation. In this report, we present the first example of Epic^® measurement of viral replication-induced cellular response and demonstrate that this system is extremely powerful not only for the sensitive and quantitative detection of viral replication inside cells but also for screening of viral inhibitors. By comparing with conventional assays used for the measurement of viral replication, we show that the Epic^® response has many advantages including sensitivity, high throughput, real-time quantification and label-free detection. We propose that the Epic^® system for measurement of integrated cellular response will be an excellent method for elucidating steps in viral replication as well as for the high-throughput screening of inhibitors of rhinovirus and other viruses.     

Quantitative Microplate Assay for Real-Time Nuclease Kinetics

Utilizing the phenomenon of nucleases exposing oligonucleotide phosphate backbones to phosphatases we present a novel quantitative method for kinetics of nuclease catalysis. Inorganic phosphate released from nuclease products by phosphatases could be quantified in real-time by a fluorescent sensor of inorganic phosphate. Two different nucleases were employed, showing the versatility of this assay for multiple turnover label-free nuclease studies.