Quantitative studies of carbohydrate-protein interaction using functionalized bacterial spores in solution and on chips

Carbohydrate-protein interaction is one of the most important molecular events deemed critical for numerous biological processes. Therefore, understanding this interaction is essential. In this study, we used bacterial spore display techniques to present multiple copies of streptavidin on the surface of spores to explore carbohydrate-protein interaction in solution and on chips. By applying bacterial spores displaying streptavidin, we developed a new method which allows sensitive, versatile, and passive detection of carbohydrate-protein interactions with a 10-fold increase in sensitivity. The linear relationship of interactions between carbohydrates and labeled concanavalin A (con A) in solution and on functionalized bacterial spore chips has also been confirmed. To the best of our knowledge, this is the first example of development and characterization of binding behavior in carbohydrateprotein interactions using bacterial spore-displayed streptavidin. We believe this strategy may enable new high-throughput screening of carbohydrate interactions as well as establish a basis for monitoring inhibitors of carbohydrate-binding proteins when developing new drugs.     

Microbial inactivation for safe and rapid diagnostics of infectious samples

The high risk associated with biological threat agents dictates that any suspicious sample be handled under strict surety and safety controls and processed under high-level containment in specialized laboratories. This study attempted to find a rapid, reliable, and simple method for the complete inactivation of a wide range of pathogens, including spores, vegetative bacteria, and viruses, while preserving microbial nucleic acid fragments suitable for PCRs and proteinaceous epitopes for detection by immunoassays. Formaldehyde, hydrogen peroxide, and guanidium thiocyanate did not completely inactivate high titers of bacterial spores or viruses after 30 min at 21°C. Glutaraldehyde and sodium hypochlorite showed high microbicidal activity but obliterated the PCR or enzyme-linked immunosorbent assay (ELISA) detection of bacterial spores or viruses. High-level inactivation (more than 6 log(10)) of bacterial spores (Bacillus atrophaeus), vegetative bacteria (Pseudomonas aeruginosa), an RNA virus (the alphavirus Pixuna virus), or a DNA virus (the orthopoxvirus vaccinia virus) was attained within 30 min at 21°C by treatment with either peracetic acid or cupric ascorbate with minimal hindrance of subsequent PCR tests and immunoassays. The data described here should provide the basis for quickly rendering field samples noninfectious for further analysis under lower-level containment and considerably lower cost.     

高脱氮活性海洋着色菌YL28生物膜特性

【背景】细菌生物膜在废水处理领域显示出良好的前景,但目前应用于海水养殖水体处理的菌株主要源自淡水菌株,存在难以适应海水高盐环境的问题。源自红树林的海洋着色菌(Marichromatiumgracile)YL28应用于海水养殖水体处理,不仅具有高效除氮能力,而且趋光贴壁能力很强。【目的】阐明海洋着色菌(Marichromatium gracile) YL28的生物膜形成特性和规律,以期为海水养殖水体生物膜反应系统的开发和应用提供参考。【方法】以生物膜和游离菌体生物量、脱氢酶活性、生物膜多糖含量和蛋白含量、无机三态氮去除活性为测定指标,在光照厌氧环境中研究海洋着色菌YL28菌株的生物膜形成规律、生物活性和脱氮效果。【结果】随着时间延长,4 000 lx光照时游离菌体生物量逐渐升高,但在稳定期前快速降低,而成膜生物量经过延滞期后逐渐升高并趋于稳定,表明培养过程中游离菌体能趋光贴壁生长并形成生物膜。在0-5 000 lx光照范围内培养4 d,低光照强度(500 lx)时成膜率(71.21%)最高,1 000-4 000 lx光照强度下成膜率虽然不是最高(54.64%-68.66%),但适宜菌体成膜,膜生物量干重达到0.60-0.80 mg/cm2。除了5 000 lx光照对成膜菌体脱氢酶活性有不利影响外,成膜菌体和游离菌体脱氢酶活性随光照强度升高而升高,而且没有明显差异。生物膜的形成会导致光反应器内部光照受限,但反应器内部游离菌体的脱氢酶活性并没有降低,由此表明,培养液中的菌体主要在生物膜及其界面生长并游离扩散至培养液中。随光照强度(1 000-5 000 lx)和培养时间(4-10 d)的变化,胞外复合物(Extracellularpolymericsubstances,EPS)中蛋白含量变异较大,多糖含量变化较小;随时间延长,蛋白含量升高,其中3 000 lx时蛋白含量最高;4 000 lx时生物膜菌体与游离菌体脱氮活性相比,单位质量菌体的氨氮和亚硝氮去除活性未受到明显影响,而硝氮去除活性有所降低。【结论】海洋着色菌YL28具有良好的生物膜形成能力,其成膜过程主要是菌体趋光贴壁生长成膜,成膜菌体具有良好的脱氮活性,这为利用生物膜系统消除海水养殖水体氮污染奠定了基础。     

Evaluation of a microwire sensor functionalized to detect Escherichia coli bacterial cells

A functionalized microwire sensor based on dielectrophoresis (DEP) and antigen-antibody reaction was initially developed for sensitive and selective detection of E. coli O157:H7. The dynamics of gold-tungsten microwires were manipulated using an automated X-Y-Z stage and the sensing process included antibody immobilization and bacterial detection, and cell quantification. Antibodies were first immobilized on surface of the microwire to improve sensing specificity, and then coupled with DEP for capture of E. coli cells in a mixture of E. coli cells and non-conductive polystyrene beads. Afterward, fluorescein-conjugated secondary antibodies were applied to the wire for quantification of captured bacteria. Field Emission Scanning Electron Microscope (FESEM) figures and fluorescence intensities of bacteria on the wire validated the sensing mechanism. The entire immobilization and detection procedure could be completed within 30 min with simple operations. Performance of the microwire sensor was not significantly affected when conducted in orange juice. In addition, the detection limit of this sensor was about 5 bacterial cells per microwire in 1000 CFU/mL bacterial suspensions when the electric field generated at 3 MHz and 20 peak to peak voltage (V(pp)), and only targeted E. coli cells were concentrated and captured.     

Ultrasonic deposition of cells on a surface

Bacteria in water have been driven to a glass surface by an ultrasonic standing wave. On an antibody coated surface capture of Bacillus subtilis var niger (BG) spores (6.6 x 10(6) ml(-1)) was increased more than 200-fold over above the efficiency in the absence of ultrasound. In microfluidic (non-turbulent) systems detection of particles by sensors operating at a surface is diffusion limited. This results in very low detection abilities particularly for particles with diameters greater than 1 microm. Ultrasound is used here to drive bacterial spores to a wall and overcome this limitation. The results confirm: (1) pressure nodes can be formed close to the water-glass interface when the glass thickness is near half the ultrasonic wavelength; (2) the antibody used was able to capture spores in the presence of an ultrasonic standing wave.     

Magnetic scanometric DNA microarray detection of methyl tertiary butyl ether degrading bacteria for environmental monitoring

A magnetoresistive biosensing platform based on a single magnetic tunnel junction (MTJ) scanning probe and DNA microarrays labeled with magnetic particles has been developed to provide an inexpensive, sensitive and reliable detection of DNA. The biosensing platform was demonstrated on a DNA microarray assay for quantifying bacteria capable of degrading methyl tertiary butyl ether (MTBE), where concentrations as low as 10 pM were detectable. Synthetic probe bacterial DNA was immobilized on a microarray glass slide surface, hybridized with the 48 base pair long biotinylated target DNA and subsequently incubated with streptavidin-coated 2.8 μm diameter magnetic particles. The biosensing platform then makes use of a micron-sized MTJ sensor that was raster scanned across a 3 mm by 5 mm glass slide area to capture the stray magnetic field from the tagged DNA and extract two dimensional magnetic field images of the microarray. The magnetic field output is then averaged over each 100 μm diameter DNA array spot to extract the magnetic spot intensity, analogous to the fluorescence spot intensity used in conventional optical scanners. The magnetic scanning result is compared with results from a commercial laser scanner and particle coverage optical counting to demonstrate the dynamic range and linear sensitivity of the biosensing platform as a potentially inexpensive, sensitive and portable alternative for DNA microarray detection for field applications.     

Rapid detection of Bacillus anthracis using monoclonal antibody functionalized QCM sensor

Since the anthrax spore bioterrorism attacks in America in 2001, the early detection of Bacillus anthracis spores and vegetative cells has gained significant interest. At present, many polyclonal antibody-based quartz crystal microbalance (QCM) sensors have been developed to detect B. anthracis simulates. To achieve a simultaneous rapid detection of B. anthracis spores and vegetative cells, this paper presents a biosensor that utilizes an anti-B. anthracis monoclonal antibody designated to 8G3 (mAb 8G3, IgG) functionalized QCM sensor. Having compared four kinds of antibody immobilizations on Au surface, an optimized mAb 8G3 was immobilized onto the Au electrode with protein A on a mixed self-assembled monolayer (SAM) of 11-mercaptoundecanoic acid (11-MUA) and 6-mercaptohexan-1-ol (6-MHO) as adhesive layer. The detection of B. anthracis was investigated under three conditions: dip-and-dry, static addition and flow through procedure. The results indicated that the sensor yielded a distinct response to B. anthracis spores or vegetative cells but had no significant response to Bacillus thuringiensis species. The functionalized sensor recognized B. anthracis spores and vegetative cells specifically from its homophylic ones, and the limit of detection (LOD) reached 10(3)CFU or spores/ml of B. anthracis in less than 30 min. Cyclic voltammogram (CV) and scanning electronic microscopy (SEM) were performed to characterize the surface of the sensor in variable steps during the modification and after the detection. The mAb functionalized QCM biosensor will be helpful in the fabrication of a similar biosensor that may be available in anti-bioterrorism in the future.     

Surface plasmon resonance assay for real-time monitoring of somatic coliphages in wastewaters

The surface plasmon resonance (SPR) technique is a well-established method for the measurement of molecules binding to surfaces and the quantification of binding constants between surface-immobilized proteins and proteins in solution. In this paper we describe an extension of the methodology to study bacteriophage-bacterium interactions. A two-channel microfluidic SPR sensor device was used to detect the presence of somatic coliphages, a group of bacteriophages that have been proposed as fecal pollution indicators in water, using their host, Escherichia coli WG5, as a target for their selective detection. The bacterium, E. coli WG5, was immobilized on gold sensor chips using avidin-biotin and bacteriophages extracted from wastewater added. The initial binding of the bacteriophage was observed at high concentrations, and a separate, time-delayed cell lysis event also was observed, which was sensitive to bacteriophage at low concentrations. As few as 1 PFU/ml of bacteriophage injected into the chamber could be detected after a phage incubation period of 120 min, which equates to an approximate limit of detection of around 10(2) PFU/ml. The bacteriophage-bacterium interaction appeared to cause a structural change in the surface-bound bacteria, possibly due to collapse of the cell, which was observed as an increase in mass density on the sensor chip. These results suggest that this methodology could be employed for future biosensor technologies and for quantification of the bacteriophage concentration.     

Glycoconjugates for the recognition of Bacillus spores

Carbohydrates act as ligands in many biological processes, including the folding and secretion of proteins, cell-cell recognition, adhesion, and sporulation in the Bacillus genus. Fluorescent-labeled disaccharide glycoconjugates have been applied to evaluate binding to bacterial spores assuming that the spore surface is covered with carbohydrates. This study has shown that specific recognition of bacterial spores is based on interactions between disaccharide glycoconjugates acting as ligands and monosaccharide units expressed on the exterior of bacterial spores. Using fluorophore-assisted carbohydrate electrophoresis (FACE), carbohydrates that are expressed on the exterior of the spores were enumerated. The findings have an impact on how to improve ligand selection, essential for sensor development. In addition, the findings provide new information for inhibition of bacterial spores, and in general, demonstrate how carbohydrates function as recognition signals in nature.     

Development of instrumentation to allow the detection of microorganisms using light scattering in combination with surface plasmon resonance

This paper describes work carried out to develop a biosensor which allows two separate detection principles to operate simultaneously at the same surface. A prototype device was constructed that provided Kretschmann-configuration surface plasmon resonance (SPR) measurement of refractive index (RI) changes using an 820 nm LED light source, whilst a 635 nm diode laser was used to produce light scattering signals from bacterial spores. Both effects occurred at a gold-coated surface. The RI changes were measured conventionally from the side of the gold layer nearer to the light sources. The scattered light was imaged from the opposite face which was in contact with the aqueous sample. Specific detection of bacterial spores through the light scattering mode using antibody capture was investigated. The flow dynamics and interactions with the surface of individual spores were observed. A comparison with SPR for detection using the same antibody/antigen pair was made. Spore suspensions that were readily detectable by light scattering at 10(7) ml(-1) did not provide significant responses by SPR. The potential for future developments is discussed.     

一种葡聚糖芯片的再生方法、表征及其应用*

表面等离子体共振（surface plasmon resonance, SPR）生物传感器,作为一种适时快捷,无需标记的生物分子相互作用研究工具,已广泛应用于生物化学分析与研究。羧甲基化葡聚糖修饰的CM5传感芯片是Biacore 系列仪器应用最为普遍的核心部件,目前CM5芯片主要从法玛西亚公司购买,价格昂贵,且一旦共价交联的受体分子失活,就不能重复利用。阐述了一种简便、低成本、用于SPR生物传感器的葡聚糖修饰金膜芯片的再生方法及其表征和应用。用此方法再生的芯片能被循环伏安法和原子力显微镜很好地表征,并成功地用于抗前列腺特异性抗原(prostate-specific antigen,PSA)固定和PSA检测, 同时测定了PSA与其抗体之间的动力学和亲和常数。     

A genetic algorithm-Bayesian network approach for the analysis of metabolomics and spectroscopic data: application to the rapid identification of Bacillus spores and classification of Bacillus species

Background  

The rapid identification of Bacillus spores and bacterial identification are paramount because of their implications in food poisoning, pathogenesis and their use as potential biowarfare agents. Many automated analytical techniques such as Curie-point pyrolysis mass spectrometry (Py-MS) have been used to identify bacterial spores giving use to large amounts of analytical data. This high number of features makes interpretation of the data extremely difficult We analysed Py-MS data from 36 different strains of aerobic endospore-forming bacteria encompassing seven different species. These bacteria were grown axenically on nutrient agar and vegetative biomass and spores were analyzed by Curie-point Py-MS.     

Differential photoinhibition of bacterial and archaeal ammonia oxidation

Inhibition by light potentially influences the distribution of ammonia oxidizers in aquatic environments and is one explanation for nitrite maxima near the base of the euphotic zone of oceanic waters. Previous studies of photoinhibition have been restricted to bacterial ammonia oxidizers, rather than archaeal ammonia oxidizers, which dominate in marine environments. To compare the photoinhibition of bacterial and archaeal ammonia oxidizers, specific growth rates of two ammonia-oxidizing archaea (Nitrosopumilus maritimus and Nitrosotalea devanaterra) and bacteria (Nitrosomonas europaea and Nitrosospira multiformis) were determined at different light intensities under continuous illumination and light/dark cycles. All strains were inhibited by continuous illumination at the highest intensity (500 μE m(-2) s(-1)). At lower light intensities, archaeal growth was much more photosensitive than bacterial growth, with greater inhibition at 60 μE m(-2) s(-1) than at 15 μE m(-2) s(-1), where bacteria were unaffected. Archaeal ammonia oxidizers were also more sensitive to cycles of 8-h light/16-h darkness at two light intensities (60 and 15 μE m(-2) s(-1)) and, unlike bacterial strains, showed no evidence of recovery during dark phases. The findings provide evidence for niche differentiation in aquatic environments and reduce support for photoinhibition as an explanation of nitrite maxima in the ocean.     

Rapid and sensitive biosensor for Salmonella

The rapid and sensitive detection of Salmonella typhymurium based on the use of a polyclonal antibody immobilized by the Langmuir-Blodgett method on the surface of a quartz crystal acoustic wave device was demonstrated. The binding of bacteria to the surface changed the crystal resonance parameters; these were quantified by the output voltage of the sensor instrumentation. The sensor had a lower detection limit of a few hundred cells/ml, and a response time of < 100 s over the range of 10(2)-10(10) cells/ml. The sensor response was linear between bacterial concentrations of 10(2)-10(7) cells/ml, with a sensitivity of 18 mV/decade. The binding of bacteria was specific with two binding sites needed to bind a single cell. The sensors preserve approximately 75% of their sensitivity over a period of 32 days.     

Low-level detection of a bacillus anthracis simulant using Love-wave biosensors on 36 degrees YX LiTaO3

We present an acoustic Love-wave biosensor for detection of the Bacillus anthracis simulant, Bacillus thuringiensis at or below inhalational infectious levels. The present work is an experimental study of 36 degrees YX cut LiTaO3 based Love-wave devices for detection of pathogenic spores in aqueous conditions. Given that the detection limit (D1) of Love-wave-based sensors is a strong function of the overlying waveguide, two waveguide materials have been investigated, which are polyimide and polystyrene. To determine the mass sensitivity of Love-wave sensor, bovine serum albumin (BSA) protein was injected into the Love-wave test cell while recording the magnitude and phase shift across each sensor. Polyimide had the lowest mass detection limit with an estimated value of 1.0-2.0 ng/cm2, as compared to polystyrene where D1 = 2.0 ng/cm2. Suitable chemistries were used to orient antibodies on the Love-wave sensor using protein G. The thickness of each biofilm was measured using ellipsometry from which the surface concentrations were calculated. The monoclonal antibody BD8 with a high degree of selectivity for anthrax spores was used to capture the non-pathogenic simulant B. thuringiensis B8 spores. Bacillus subtilis spores were used as a negative control to determine whether significant non-specific binding would occur. Spore aliquots were prepared using an optical counting method, which permitted removal of background particles for consistent sample preparation. This work demonstrates that Love-wave biosensors are promising for low-level detection for whole-cell biological pathogens.     

Integration of a surface acoustic wave biosensor in a microfluidic polymer chip

SAW devices based on horizontally polarized surface shear waves (HPSSW) enable label-free, sensitive and cost-effective detection of biomolecules in real time. It is known that small sampling volumes with low inner surface areas and minimal mechanical stress arising from sealing elements of miniaturized sampling chambers are important in this field. Here, we present a new approach to integrate SAW devices with sampling chamber. The sensor device is encapsulated within a polymer chip containing fluid channel and contact points for fluidic and electric connections. The chip volume is only 0.9 microl. The polymeric encapsulation was performed tailor-made by Rapid Micro Product Development 3Dimensional Chip-Size-Packaging (RMPD 3D-CSP), a 3D photopolymerisation process. The polymer housing serves as tight and durable package for HPSSW biosensors and allows the use of the complete chips as disposables. Preliminary experiments with these microfluidic chips are shown to characterise the performance for their future applications as generic bioanalytical micro devices.     

A comparison of protocols for the optimisation of detection of bacteria using a surface acoustic wave (SAW) biosensor

A dual channel surface acoustic wave (SAW) device has been used as a biosensor to detect two different microorganisms, Legionella and Escherichia coli, simultaneously. A series of experiments was conducted to optimise the use of the SAW for bacterial detection using a novel protocol of coating bacteria on the sensor surface prior to addition of the antibody. Results were compared with an experiment in which a conventional protocol was utilised, where antibody was coated on the sensor surface prior to exposure to bacteria. The concentration of bacteria that attached to the surface of the SAW device was related to the antibody that specifically bound to it and therefore to frequency in a dose dependent fashion. Unlike conventional microbiological techniques quantitative results can be obtained for Legionella and E. coli down to 10(6) cells per ml within 3 h. In addition E. coli was detected down to 10(5) cells per ml in a modified protocol using sheep IgG as a blocking agent.     

Feasibility of using real-time optical methods for detecting the presence of viable bacteria aerosols at low concentrations in clean room environments

An experimental investigation was carried out to determine the agreement between two methods of viable bacteria aerosol detection. Various amounts of Bacillus globigii (BG) spores were aerosolized in 1-s bursts into a HEPA-filtered air stream and sampled simultaneously with a fluorescence aerosol particle sensor (FLAPS) and a slit to agar biological air sampler. The slit sampler incorporated 150-mm malt extract culture plates, which were incubated at 37°C for at least 12 h before culturable BG particles were counted in terms of colony-forming units (CFU). A relationship between CFU and optically detected viable bacteria particles was determined as culturable particle concentrations decreased. Through further analytical procedures, the FLAPS showed a limit of detection (LOD) of 4.2 bacterial particle/2.5 l of sampled air or 1.7 × 10³ m⁻³. This real-time bacteria aerosol monitor could be used to detect burst contamination events during a surgical procedure. The technology may be used for developing a dose–response relationship between bacterial particle exposure and infection, a tool potentially helpful in determining patient risk.     

Microarray of recombinant antibodies using a streptavidin sensor surface self-assembled onto a gold layer

We have developed a sensitive method for the detection of recombinant antibody-antigen interactions in a microarray format. The biochip sensor platform used in this study is based on an oriented streptavidin monolayer that provides a biological interface with well-defined surface architecture that dramatically reduces nonspecific binding interactions. All the antibody or antigen probes were biotinylated and coupled onto streptavidin-coated biochip surfaces (1 microL total volume). The detection limits for the immobilized probes on the microarray surface were 0.5 microgram/mL (200 fmol/spot) for the peptide antigen and 0.1 microgram/mL (3 fmol/spot) for the recombinant antibodies. Optimal concentrations for the detection of the Cy5-labeled protein target were in the range of 20 micrograms/mL. Protein microchips were used to measure antibody-antigen kinetics, to find optimal temperature conditions, and to establish the shelf life of recombinant antibodies immobilized on the streptavidin surface. For recombinant antibody fragments with a kDa of 10-100 nM, we have established an easy and direct immunoassay. In addition, we developed an indirect method for antibody detection with no need for expensive and time-consuming antibody purifications and modifications. Such a method was shown to be useful for large-scale screening of recombinant antibody fragments directly after their functional expression in bacteria. Our data demonstrate that recombinant antibody fragments are suitable components in the construction of antibody chips.