Comparison of fluorescence and resonance light scattering for highly sensitive microarray detection of bacterial pathogens

Highly sensitive and selective detection of butachlor based on the resonance light scattering of doped carbon quantum dots

In this work, a new method of resonance light scattering was developed for the sensitive and selective detection of butachlor. Firstly, buckwheat was used as the main carbon source to prepare a new type of doped carbon quantum dot using the hydrothermal method. A new method for the determination of butachlor was then established by the change in resonance light scattering intensity after the addition of butachlor into the doped carbon quantum dot solution. The detection effect was successfully optimized by investigating the optimum reaction conditions. Under the optimum conditions, the resonance light scattering intensity of doped carbon quantum dots was greatly enhanced at 460 nm after the addition of butachlor, and the intensity changes were linearly correlated with the butachlor concentration in the range of 1-7 μg L^-1. The detection limit was 0.136 μg L^-1, and the recoveries ranged between 98.6% and 101.8%. This method was also used for butachlor detection in environmental water.

The Surface Science of Microarray Generation-A Critical Inventory

Microarrays are powerful tools in biomedical research and have become indispensable for high-throughput multiplex analysis, especially for DNA and protein analysis. The basis for all microarray processing and fabrication is surface modification of a chip substrate and many different strategies to couple probe molecules to such substrates have been developed. We present here a critical assessment of typical biochip generation processes from a surface science point of view. While great progress has been made from a molecular biology point of view on the development of qualitative assays and impressive results have been obtained on the detection of rather low concentrations of DNA or proteins, quantitative chip-based assays are still comparably rare. We argue that lack of stable and reliable deposition chemistries has led in many cases to suboptimal quantitative reproducibility, impeded further progress in microarray development and prevented a more significant penetration of microarray technology into the diagnostic market. We suggest that surface-attached hydrogel networks might be a promising strategy to achieve highly sensitive and quantitatively reproducible microarrays.

Selective fluorescent-free detection of biomolecules on nanobiochips by wavelength dependent-enhanced dark field illumination

Individual silver nanoparticle-conjugated target protein (cTnI) molecules on gold-nanopatterned chip were selectively detected by wavelength dependent-enhanced dark field illumination. Using specific nanoparticles with unique sizes and materials, the immunotargeted nanoparticle on the chips was detected at the single-molecule level by monitoring changes in the plasmonic resonance based on wavelength dependence.

Nanoscale labels: nanoparticles and liposomes in the development of high-performance biosensors

Technology for the detection of biological species has generated considerable interest in a variety of fields including healthcare, defense, food and environmental monitoring. In a biosensor, labeled specific binding partners are used to emit a detectable signal. Owing to their unique properties, nanomaterials have been proposed as a novel label category and have led to the development of new assays and new transduction mechanisms. In this article, the role of three major types of nanoscale labels (metallic, semiconductor and liposome nanoparticles) in the development of a new generation of optical, electrochemical or gravimetric biosensors will be presented. The underlying transduction principles will be briefly explained and assay strategies relying on the use of these ‘nanolabels’ will be described. The contribution to increased assay performance and sensitivity will be highlighted. Approaches towards simple, cost efficient and sensitive assays are essential to meet the demands of a growing number of applications.

Rapid identification and high sensitive detection of cancer cells on the gold nanoparticle interface by combined contact angle and electrochemical measurements

In this study, we have proposed a novel strategy for the rapid identification and high sensitive detection of different kinds of cancer cells by means of electrochemical and contact angle measurements. A simple, unlabeled method based on the functionalized Au nanoparticles (GNPs) modified interface has been utilized to distinguish the different cancer cells, including lung cancer cells, liver cancer cells, drug sensitive leukemia K562/B.W cells and drug resistant leukemia K562/ADM cells. The relevant results indicate that under optimal conditions, this method can provide the quantitative determination of cancer cells, with a detection limit of approximately 10(3)cells mL(-1). Our observations demonstrate that the difference in the hydrophilic properties for target cellular surfaces and in the uptake efficiency of the anticancer drug daunorubicin for different cancer cells could be readily chosen as the elements of cancer identification and sensitive detection. This raises the possibility to advance the promising clinic diagnosis and monitoring of tumors with the aim of successful chemotherapy of human cancers.

The use of gold nanoparticles in diagnostics and detection

The widespread use of gold nanoparticles (GNPs) as labels in diagnostics and detection is due to a unique combination of chemical and physical properties that allow biological molecules to be detected at low concentrations. In this critical review detection methods based on GNPs are divided up and discussed based on the way in which signals are generated in response to specific target molecules. Particular attention is devoted to methods that allow target molecules to be detected with the unaided eye because these, more than any other, harness the full range of properties that make GNPs unique. Methods that are discussed include those in which specific target molecules induce a visible colour change, chromatographic methods that allow non-specialized users to perform sophisticated tests without additional equipment and methods in which trace amounts of GNPs are rendered visible to the unaided eye by catalytic deposition of a metal such as silver. The use of metal deposition as a means of enhancing the signal for optical and electrical detection is also reviewed. The other detection methods included in this review are based on interactions between GNPs and molecules located in close proximity to their surface. These include methods in which light emission from such molecules is enhanced (surface enhanced Raman scattering) or quenched (fluorescence), and methods in which the accumulation of specific target molecules induce subtle changes in the extinction spectra of GNPs that can be followed in real time with inexpensive equipment (166 references).

Comparison of detection and signal amplification methods for DNA microarrays

One of the factors limiting the use of DNA microarray technology for the detection of pathogenic organisms from clinical and environmental matrices has been inadequate assay sensitivity. To assess the effectiveness of post-hybridization secondary detection steps to enhance the sensitivity of DNA microarray-based pathogen detection, we evaluated a panel of 11 commercial and novel hybridization detection and signal amplification methods (direct labeling, indirect aminoallyl labeling, antibody, DNA dendrimers, viral particles, internally fluorescent nanoparticles, tyramide signal amplification, resonance light scattering nanoparticles and quantum dots) using a multiplex PCR and spotted long oligonucleotide microarray for Vibrio cholerae. Quantitative parameters such as sensitivity, signal intensity, background, assay complexity, time and cost were assessed and provide comparative criteria to be considered for DNA microarray experimental design. While the most important parameter is likely to vary based on the assay, when weighted equally, the findings suggest that recognition element- and dye-functionalized viral particles provide the most attractive option for microarray detection and signal amplification.

Identification of biological microparticles using ultrafast depletion spectroscopy

We show how an ultrafast pump-pump excitation induces strong fluorescence depletion in biological samples, such as bacteria-containing droplets, in contrast with fluorescent interferents, such as polycyclic aromatic compounds, despite similar spectroscopic properties. Application to the optical remote discrimination of biotic versus non-biotic particles is proposed. Further improvement is required to allow the discrimination of one pathogenic among other non-pathogenic micro-organisms. This improved selectivity may be reached with optimal coherent control experiments, as discussed in the paper.

Light scattering sensing detection of pathogens based on the molecular recognition of immunoglobulin with cell wall-associated protein A

In this contribution, we report a rapid optical detection method of pathogens using Staphylococcus aureus (S. aureus) as the model analyte based on the molecular recognition of immunoglobulin with cell wall-associated Protein A (SpA). It was found that the molecular recognition of human immunoglobulin (IgG) with protein A on the cell wall of S. aureus on glass slide sensing area could result in strong surface enhanced light scattering (SELS) signals, and the SELS intensity (deltaI) increases proportionally with the concentration of S. aureus over the range of 2.5x10(5)-1.0x10(8) CFU mL(-1) with right angle light scattering (RALS) signals detection mode. In order to identify the solid support based molecular recognition between IgG with SpA, we also employed water-soluble CdS quantum dots (CdS-QDs) as a fluorescent marker for IgG by immobilizing the IgG onto the surfaces of CdS-QDs through covalent binding in order to generate recognition probes for SpA on the cell wall of S. aureus. Consequently, the fluorescent method also showed that the detection for pathogens with solid supports is reliable based on the molecular recognition of IgG with SpA.

Identification of human pathogens isolated from blood using microarray hybridisation and signal pattern recognition

Background

Pathogen identification in clinical routine is based on the cultivation of microbes with subsequent morphological and physiological characterisation lasting at least 24 hours. However, early and accurate identification is a crucial requisite for fast and optimally targeted antimicrobial treatment. Molecular biology based techniques allow fast identification, however discrimination of very closely related species remains still difficult.

Results

A molecular approach is presented for the rapid identification of pathogens combining PCR amplification with microarray detection. The DNA chip comprises oligonucleotide capture probes for 25 different pathogens including Gram positive cocci, the most frequently encountered genera of Enterobacteriaceae, non-fermenter and clinical relevant Candida species. The observed detection limits varied from 10 cells (e.g. E. coli) to 10⁵ cells (S. aureus) per mL artificially spiked blood. Thus the current low sensitivity for some species still represents a barrier for clinical application. Successful discrimination of closely related species was achieved by a signal pattern recognition approach based on the k-nearest-neighbour method. A prototype software providing this statistical evaluation was developed, allowing correct identification in 100 % of the cases at the genus and in 96.7 % at the species level (n = 241).

Conclusion

The newly developed molecular assay can be carried out within 6 hours in a research laboratory from pathogen isolation to species identification. From our results we conclude that DNA microarrays can be a useful tool for rapid identification of closely related pathogens particularly when the protocols are adapted to the special clinical scenarios.

Unravelling microbial communities with DNA-microarrays: challenges and future directions

High-throughput technologies are urgently needed for monitoring the formidable biodiversity and functional capabilities of microorganisms in the environment. Ten years ago, DNA microarrays, miniaturized platforms for highly parallel hybridization reactions, found their way into environmental microbiology and raised great expectations among researchers in the field. In this article, we briefly summarize the state-of-the-art of microarray approaches in microbial ecology research and discuss in more detail crucial problems and promising solutions. Finally, we outline scenarios for an innovative combination of microarrays with other molecular tools for structure-function analysis of complex microbial communities.

Genome content determination in methicillin-resistant Staphylococcus aureus

Staphylococcus aureus is a major pathogen responsible for both nosocomial and community-acquired infections. While the first S. aureus isolates displaying resistance to methicillin were reported in the early 1960s, endemic strains of methicillin-resistant S. aureus (MRSA) carrying multiple resistance determinants only became a worldwide nosocomial problem in the early 1980s, carrying a threefold attributable cost and a threefold excess length of hospital stay when compared with methicillin-susceptible S. aureus bacteremia. Recent efforts in the field of high-throughput sequencing resulted in the release of several MRSA genome sequences enabling the development of massively parallel tools to study clinical isolates of MRSA at the organism scale. Microarrays covering whole genomes and high-throughput sequencing devices are the two main techniques currently utilizable for whole-genome characterization. These tools not only provide information for the development of genotyping assays but also allow evaluation of potential virulence of the strains, by enumerating genetic-encoded resistance markers and toxin content. This appears particularly attractive for understanding the epidemiology of MRSA and the relationship between genome content on one side and virulence potential or epidemicity on the other side. In addition, sequence information is mandatory for the development of molecular tests allowing the rapid identification, genotyping and characterization of clinical isolates.

Nanoparticles for multiplex diagnostics and imaging

The drive to understand biology and medicine at the molecular level with accurate quantitation demands much of current high-throughput analysis systems. Nanomaterials and nanotechnology combined with modern instrumentation have the potential to address this emerging challenge. Using a variety of nanomaterials for multiplex diagnostics and imaging applications will offer sensitive, rapid and cost-effective solutions for the modern clinical laboratory. New nanomaterials have been developed with optical-encoding capabilities for selective tagging of a wide range of medically important targets, including bacteria, cancer cells and individual molecules, such as proteins and DNA, in a single assay. We envision further development in this field will provide numerous advanced tools with increased sensitivity and improved multiplexing capability, for unique applications in molecular biology, genomics and drug discovery.

Comparison of amplification methods for transcriptomic analyses of low abundance prokaryotic RNA sources

Microarrays have established as instrumental for bacterial detection, identification, and genotyping as well as for transcriptomic studies. For gene expression analyses using limited numbers of bacteria (derived from in vivo or ex vivo origin, for example), RNA amplification is often required prior to labeling and hybridization onto microarrays. Evaluation of the fidelity of the amplification methods is crucial for the robustness and reproducibility of microarray results. We report here the first utilization of random primers and the highly processive Phi29 phage polymerase to amplify material for transcription profiling analyses. We compared two commercial amplification methods (GenomiPhi and MessageAmp kits) with direct reverse-transcription as the reference method, focusing on the robustness of mRNA quantification using either microarrays or quantitative RT-PCR. Both amplification methods using either poly-A tailing followed by in vitro transcription, or direct strand displacement polymerase, showed appreciable linearity. Strand displacement technique was particularly affordable compared to in vitro transcription-based (IVT) amplification methods and consisted in a single tube reaction leading to high amplification yields. Real-time measurements using low-, medium-, and highly expressed genes revealed that this simple method provided linear amplification with equivalent results in terms of relative messenger abundance as those obtained by conventional direct reverse-transcription.

Diagnostic applications of microarrays

Microarrays were designed to monitor the expression of many genes in parallel, providing substantially more information than Northern blots or reverse transcription polymerase chain reaction analysing one or few genes at a time. The large sequencing projects provided the content for detailed expression studies under a variety of stimuli and conditions. The human genome project identified around 30 000 human genes. Estimated number of protein products is, however, 10-30 times higher, mainly due to the alternative splicing and post-translational modifications. The identification of gene functions requires both genomic and proteomic approaches, including protein microarrays, and numerous current microarray projects focus on deciphering gene expression patterns under a variety of conditions. Establishing the key genes and gene products for particular conditions opens the way for diagnostic applications using multiparameter, high-throughput assays. This format can also accommodate existing blood screening assays, potentially providing a single testing platform. This review considers the progress in diagnostic microarrays in a wider context of in vitro diagnostics field.

A new immune resonance scattering spectral assay for trace fibrinogen with gold nanoparticle label

Gold nanoparticles in size of 9.0 nm was prepared by the trisodium citrate and used to label goat anti-human fibrinogen. In the pH 6.2 buffer solution and in the presence of polyethylene glycol (PEG), the immune reaction between gold-labeled goat anti-human fibrinogen and fibrinogen took place and the labeled gold nanoparticles were released from the goat anti-human fibrinogen, and the released gold particles aggregated which leaded the resonance scattering intensity at 560 nm (I560 nm) to enhance greatly. The I560 nm is proportional to the fibrinogen concentration in the range from 0.027 to 1.07 microg mL(-1). The detection limit is 1.14 ng mL(-1). This simple assay was applied to determination of fibrinogen in human plasma, with satisfactory results.

Rapid bacterial identification using evanescent-waveguide oligonucleotide microarray classification

Bacterial identification relies primarily on culture-based methodologies and requires 48-72 h to deliver results. We developed and used i) a bioinformatics strategy to select oligonucleotide signature probes, ii) a rapid procedure for RNA labelling and hybridization, iii) an evanescent-waveguide oligoarray with exquisite signal/noise performance, and iv) informatics methods for microarray data analysis. Unique 19-mer signature oligonucleotides were selected in the 5'-end of 16s rDNA genes of human pathogenic bacteria. Oligonucleotides spotted onto a Ta(2)O(5)-coated microarray surface were incubated with chemically labelled total bacterial RNA. Rapid hybridization and stringent washings were performed before scanning and analyzing the slide. In the present paper, the eight most abundant bacterial pathogens representing >54% of positive blood cultures were selected. Hierarchical clustering analysis of hybridization data revealed characteristic patterns, even for closely related species. We then evaluated artificial intelligence-based approaches that outperformed conventional threshold-based identification schemes on cognate probes. At this stage, the complete procedure applied to spiked blood cultures was completed in less than 6 h. In conclusion, when coupled to optimal signal detection strategy, microarrays provide bacterial identification within a few hours post-sampling, allowing targeted antimicrobial prescription.

Use of Sodium Lauroyl Sarcosinate in a High-Sensitivity Protein Assay by Resonance Light Scattering Technique

A simple and high-sensitivity method has been developed for the determination of proteins in aqueous solutions by resonance light scattering (RLS) technique. At pH 3.4 and ionic strength 1.2 × 10-3, the weak RLS intensity of sodium lauroyl sarcosinate was greatly enhanced by the addition of proteins with the maximum peak located at 391 nm. Under the optimum conditions, the enhanced RLS intensities were in proportion to the concentrations of proteins in the range of 0.04 to 2.1 μg/mL for lysozyme, 0.0025 to 1.2 μg/mL for bovine serum albumin, 0.0075 to 0.9 μg/mL for human serum albumin, 0.02 to 1.4 μg/mL for γ-globulin, 0.02 to 0.8 μg/mL for egg albumin, and 0.01 to 0.6 μg/mL for hemoglobin. Low detection limits ranging from 0.8 ng/mL to 4.3 ng/mL depending on the kind of proteins that have been achieved. The protein concentrations in synthetic samples and real biochemical samples were determined with satisfactory results. This method presented here is not only sensitive and simple but also reliable and suitable for practical bioassay applications.

An Optical Biosensor for Rapid and Label-Free Detection of Cells

We report a broadly applicable optical method for rapid and label-free detection of as few as 45 cells. In this method, bacterial cells are detected by measuring the amount of laser light transmitted through a small glass well functionalized with antibodies which specifically recognize and capture the cells. The described approach is simple, rapid, economical, and promising for portable and high-throughput detection of a wide variety of pathogenic and infectious cells.

[6] Scanning Microarrays: Current Methods and Future Directions

The microarray platform is a powerful tool for conducting large-scale, high-throughput gene expression experiments. However, careful attention to detail throughout the five major steps in the microarray process--design, printing, hybridization, scanning, and analysis--must be used to ensure that reliable and accurate conclusions are obtained from data. The act of scanning the array has received the least attention of all parts of the microarray process, despite it being a critical quality-limiting component. This chapter specifically addresses the effects of scan parameters and limitations of the scanning technology divided into two categories: instrumentation effects (those that arise from the scanning instrumentation itself) and user-controller parameters (those that an operator chooses) for the most common microarray platform--the two-color cDNA microarray printed on a glass substrate. Significant research efforts have gone into developing microarray analysis techniques, but the field is ripe for research to characterize the variability and errors introduced by the scanning process itself, the scanner instrumentation, and the user. Implications of these errors for large-scale, multiple slide and multiple laboratory experiments are discussed. Wise choices for scanning parameters and consideration of instrument specifics will ultimately increase data reliability and reduce the need for complex preprocessing mechanisms prior to the extraction of expression information. In addition, emerging technologies such as surface plasmon imaging, resonance light scattering, and hyperspectral imaging are presented briefly as promising, complementary techniques to traditional scanning methods.

Development of a nanoparticle-labeled microfluidic immunoassay for detection of pathogenic microorganisms

The light-scattering properties of submicroscopic metal particles ranging from 40 to 120 nm in diameter have recently been investigated. These particles scatter incident white light to generate monochromatic light, which can be seen either by the naked eye or by dark-field microscopy. The nanoparticles are well suited for detection in microchannel-based immunoassays. The goal of the present study was to detect Helicobacter pylori- and Escherichia coli O157:H7-specific antigens with biotinylated polyclonal antibodies. Gold particles (diameter, 80 nm) functionalized with a secondary antibiotin antibody were then used as the readout. A dark-field stereomicroscope was used for particle visualization in poly(dimethylsiloxane) microchannels. A colorimetric quantification scheme was developed for the detection of the visual color changes resulting from immune reactions in the microchannels. The microchannel immunoassays reliably detected H. pylori and E. coli O157:H7 antigens in quantities on the order of 10 ng, which provides a sensitivity of detection comparable to those of conventional dot blot assays. In addition, the nanoparticles within the microchannels can be stored for at least 8 months without a loss of signal intensity. This strategy provides a means for the detection of nanoparticles in microchannels without the use of sophisticated equipment. In addition, the approach has the potential for use for further miniaturization of immunoassays and can be used for long-term archiving of immunoassays.

Nanotechnology in clinical laboratory diagnostics

Nanotechnology-the creation and utilization of materials, devices, and systems through the control of matter on the nanometer-has been applied to molecular diagnostics. This article reviews nanobiotechnologies that are clinically relevant and have the potential to be incorporated in clinical laboratory diagnosis. Nanotechnologies enable the diagnosis at single cell and molecule level and some of these can be incorporated in the current molecular diagnostics such as biochips. Nanoparticles, such as gold nanoparticles and quantum dots, are the most widely used but various other nanotechnologies for manipulation at nanoscale as well as nanobiosensors are reviewed. These technologies will extend the limits of current molecular diagnostics and enable point-of-care diagnosis as well as the development of personalized medicine. Although the potential diagnostic applications are unlimited, most important current applications are foreseen in the areas of biomarker research, cancer diagnosis and detection of infectious microorganisms.

Gene expression analysis of Escherichia coli grown in miniaturized bioreactor platforms for high-throughput analysis of growth and genomic data

Combining high-throughput growth physiology and global gene expression data analysis is of significant value for integrating metabolism and genomics. We compared global gene expression using 500 ng of total RNA from Escherichia coli cultures grown in rich or defined minimal media in a miniaturized 50-microl bioreactor. The microbioreactor was fabricated out of poly(dimethylsiloxane) (PDMS) and glass and equipped to provide on-line, optical measurements. cDNA labeling for microarray hybridizations was performed with the GeniconRLS system. From these experiments, we found that the expression of 232 genes increased significantly in cells grown in minimum medium, including genes involved in amino acid biosynthesis and central metabolism. The expression of 275 genes was significantly elevated in cells grown in rich medium, including genes involved in the translational and motility apparatuses. In general, these changes in gene expression levels were similar to those observed in 1,000-fold larger cultures. The increasing rate at which complete genomic sequences of microorganisms are becoming available offers an unprecedented opportunity for investigating these organisms. Our results from microscale cultures using just 500 ng of total RNA indicate that high-throughput integration of growth physiology and genomics will be possible with novel biochemical platforms and improved detection technologies.

Development of a nanoparticle-labeled microfluidic immunoassay for detection of pathogenic microorganisms

The light-scattering properties of submicroscopic metal particles ranging from 40 to 120 nm in diameter have recently been investigated. These particles scatter incident white light to generate monochromatic light, which can be seen either by the naked eye or by dark-field microscopy. The nanoparticles are well suited for detection in microchannel-based immunoassays. The goal of the present study was to detect Helicobacter pylori- and Escherichia coli O157:H7-specific antigens with biotinylated polyclonal antibodies. Gold particles (diameter, 80 nm) functionalized with a secondary antibiotin antibody were then used as the readout. A dark-field stereomicroscope was used for particle visualization in poly(dimethylsiloxane) microchannels. A colorimetric quantification scheme was developed for the detection of the visual color changes resulting from immune reactions in the microchannels. The microchannel immunoassays reliably detected H. pylori and E. coli O157:H7 antigens in quantities on the order of 10 ng, which provides a sensitivity of detection comparable to those of conventional dot blot assays. In addition, the nanoparticles within the microchannels can be stored for at least 8 months without a loss of signal intensity. This strategy provides a means for the detection of nanoparticles in microchannels without the use of sophisticated equipment. In addition, the approach has the potential for use for further miniaturization of immunoassays and can be used for long-term archiving of immunoassays.

Direct detection of Staphylococcus aureus mRNA using a flow through microarray

The direct detection of mRNAs from bacterial cultures on a DNA array without amplification and labelling would greatly extend the range of applications suitable for microarray analysis. Here we describe the direct detection of 23S rRNA and seven mRNA species from total Staphylococcus aureus RNA prepared using commercially available RNA purification columns followed by fluorescent detection on a flow through microarray. RNA hybridisation was detected using paired secondary labelled probes directly 5' and 3' to immobilised 60 mers. In this way, we were able to detect the effect of 30-min exposure to antimicrobials on mRNA levels within 3 h after column purification of total RNA without the need for enzymatic manipulation. Specifically the expression of mecA was confirmed in a highly resistant strain and induction of katA and ile-tRNA synthetase genes after exposure to mupirocin could be detected.