Quantitative single cell analysis and sorting

Extended lag phase indicates the dormancy of biphenyl degrading Rhodococcus biphenylivorans TG9 under heat stress

Microbial remediation is a green and sustainable technology, but harsh environmental conditions could lead to microbial dormancy, such as entering a viable but non-culturable (VBNC) state. However, the evidence of VBNC is controversial and limited. In this study, heat stress (60 °C), one of the leading challenges for mesophilic degrading bacteria, was mimicked to investigate the physiological response of Rhodococcus biphenylivorans TG9. After 2 h of heat stress, the culturable TG9 cell count decreased from 10⁸ cells/mL to undetectable while the viable cell count was still 10⁵ cells/mL. The biphenyl degradation efficiency of stressed TG9 dropped by 50% compared to that of cells at logarithmic phase. During heat stress, the respiratory activity of TG9 declined dramatically while the intracellular ATP level initially increased and then decreased. Notably, the corresponding indicators recovered when restored to 30 °C. These characteristics were in consistent with bacteria entering into VBNC state. Furthermore, fluorescence activated cell sorting together with single cell as seed culture detection verified the unculturability and viability of VBNC state of TG9 cells. Also, we found that single cells in VBNC state could resuscitate and regrowth with significantly extended lag phase (LP). Our results highlight the potential of TG9 for microbial remediation and hint LP duration as an indicator for survival state of bacteria.

Detection of cancer cells and tumor margins during colorectal cancer surgery by intraoperative flow cytometry

BACKGROUND

Flow Cytometry is an analytical technique for the precise quantification of cellular phenotype. Intraoperative Flow Cytometry (iFC) utilizes flow cytometry for DNA content/ploidy and cell cycle distribution analysis during surgery for cancer cell characterization and evaluation of tumor margins. Various types of cancers, including intracranial, head and neck, breast and liver malignancies have been evaluated with iFC. In the current study we present an intraoperative Flow Cytometry protocol for colorectal cancer cell detection and potential resection margin evaluation.

MATERIALS AND METHODS

This study includes 106 colorectal cancer patients in which samples from cancer and normal colon epithelium were prospectively collected intraoperatively and comparatively assessed with iFC. Patients' demographics, tumor data and cytometry parameters were assessed.

RESULTS

We have demonstrated that a cut-off value of 10.5% for tumor-index (fraction of cells in S and G2/M cell cycle phases) predicts with ∼91% accuracy (82.2% sensitivity and 99.9% specificity) the presence of cancer cells. Evaluation of tumor margins by iFC in the subpopulation of rectal cancer patients with or without neoadjuvant therapy, revealed an accuracy of 79% and 88%, respectively.

CONCLUSION

Our data support that regarding colorectal cancer, iFC is a useful adjunct method for tumor cell identification and probably margin evaluation, which could be utilized in rectal cancer treatment in the era of organ sparing procedures.

A review of bioinformatics tools and web servers in different microarray platforms used in cancer research

Over the past decade, conventional lab work strategies have gradually shifted from being limited to a laboratory setting towards a bioinformatics era to help manage and process the vast amounts of data generated by omics technologies. The present work outlines the latest contributions of bioinformatics in analyzing microarray data and their application to cancer. We dissect different microarray platforms and their use in gene expression in cancer models. We highlight how computational advances empowered the microarray technology in gene expression analysis. The study on protein-protein interaction databases classified into primary, derived, meta-database, and prediction databases describes the strategies to curate and predict novel interaction networks in silico. In addition, we summarize the areas of bioinformatics where neural graph networks are currently being used, such as protein functions, protein interaction prediction, and in silico drug discovery and development. We also discuss the role of deep learning as a potential tool in the prognosis, diagnosis, and treatment of cancer. Integrating these resources efficiently, practically, and ethically is likely to be the most challenging task for the healthcare industry over the next decade; however, we believe that it is achievable in the long term.

Touch Imprint Intraoperative Flow Cytometry as a Complementary Tool for Detailed Assessment of Resection Margins and Tumor Biology in Liver Surgery for Primary and Metastatic Liver Neoplasms

Liver resection is the main treatment for primary and metastatic liver tumors in order to achieve long-term survival with good quality of life. The ultimate goal of surgical oncology is to achieve complete tumor removal with adequate clear surgical margins. Flow cytometry is a powerful analytical technique with applications such as phenotypic analysis and quantification of DNA content. Intraoperative flow cytometry (iFC) is the application of flow cytometry for DNA content/ploidy and cell cycle distribution analysis during surgery for tumor cell analysis and margin evaluation. It has been used for cell analysis of intracranial tumors and recently of head and neck carcinomas and breast carcinomas, as well as for tumor margin evaluation. Herein, we present a novel touch imprint iFC protocol for the detailed assessment of tumor margins during excision of malignant hepatic lesions. The protocol aims to offer information on surgical margins after removal of malignant liver tumors based on DNA content of cancer cells and to corroborate the results of iFC with that of histopathological analysis. Based on the established role of iFC in other types of malignancies, our specialized protocol has the potential, through characterization of cells in liver transection surface post hepatectomy, to offer significant information on the type of resection and tumor biology. This information can be used to effectively guide intra- and postoperative patient management.

Large-scale investigation of single cell activities and response dynamics in a microarray chip with a microfluidics-fabricated microporous membrane

Microengineering technology involving microfabrication, micropatterning and microfluidics enables promising advances in single cell manipulation and analysis. Herein, we describe a parallel, large-scale, and temporal investigation of diverse single cell activities and response dynamics using a facile-assembled microwell array chip with a microfluidics-molded microporous membrane. We demonstrated that the versatility with respect to geometrical homogeneity and diversity of microporous membrane fabrication, as well as the stability, repeatability, and reproducibility rely on the well-improved molding. Serial and practical operations including controllable single cell trapping, array-like culture or chemical stimulation, and temporal monitoring can be smoothly completed in the chip. We confirmed that the microwell array chip allowed an efficient construction of a single cell array. Using the cell array, on-chip detection of single cell behaviours under various culture and drug therapy conditions to explore phenotypic heterogeneity was achieved in massive and dynamic manners. These achievements provide a facile and reliable methodology for fabricating microporous membranes with precise control and for developing universal microplatforms to perform robust manipulation and versatile analysis of single cells. This work also offers an insight into the development of easy to fabricate/use and market-oriented microsystems for single cell research, pharmaceutical development, and high-throughput screening.

The Past, Present and Future of Flow Cytometry in Central Nervous System Malignancies

Central nervous system malignancies (CNSMs) are categorized among the most aggressive and deadly types of cancer. The low median survival in patients with CNSMs is partly explained by the objective difficulties of brain surgeries as well as by the acquired chemoresistance of CNSM cells. Flow Cytometry is an analytical technique with the ability to quantify cell phenotype and to categorize cell populations on the basis of their characteristics. In the current review, we summarize the Flow Cytometry methodologies that have been used to study different phenotypic aspects of CNSMs. These include DNA content analysis for the determination of malignancy status and phenotypic characterization, as well as the methodologies used during the development of novel therapeutic agents. We conclude with the historical and current utility of Flow Cytometry in the field, and we propose how we can exploit current and possible future methodologies in the battle against this dreadful type of malignancy.

Multiplexed Nanobiosensors: Current Trends in Early Diagnostics

The ever-growing demand for fast, cheap, and reliable diagnostic tools for personalised medicine is encouraging scientists to improve existing technology platforms and to create new methods for the detection and quantification of biomarkers of clinical significance. Simultaneous detection of multiple analytes allows more accurate assessment of changes in biomarker expression and offers the possibility of disease diagnosis at the earliest stages. The concept of multiplexing, where multiple analytes can be detected in a single sample, can be tackled using several types of nanomaterial-based biosensors. Quantum dots are widely used photoluminescent nanoparticles and represent one of the most frequent choices for different multiplex systems. However, nanoparticles that incorporate gold, silver, and rare earth metals with their unique optical properties are an emerging perspective in the multiplexing field. In this review, we summarise progress in various nanoparticle applications for multiplexed biomarkers.

DNA-based microarray studies in visceral leishmaniasis: identification of biomarkers for diagnostic, prognostic and drug target for treatment

Visceral leishmaniasis (VL) is one of the major infectious diseases affecting the poorest regions of the world. Current therapy is not very much satisfactory. The alarming rise of drug resistance and the unavailability of an effective vaccine against VL urges research towards identifying new targets or biomarkers for its effective treatment. New technology developments offer some fresh hope in its diagnosis, treatment, and control. DNA microarray approach is now broadly used in parasitology research to facilitate the thoughtful of mechanisms of disease and identification of drug targets and biomarkers for diagnostic and therapeutic development. An electronic search on "VL" and "Microarray" was conducted in Medline and Scopus and papers published in the English mentioning use of DNA microarray on VL were selected and read to write this paper review. Functional analysis and interpretation of microarray results remain very challenging due to the inherent nature of experimental workflows, access, cost, and complexity of data obtained. We have explained and emphasized the use of curate knowledge of microarray in the case of VL for the identification of therapeutic target and biomarker and their selection/implementation in clinical use.

Extracting lipid vesicles from plasma membranes via self-assembly of clathrin-inspired scaffolding nanoparticles

Single-cell analysis is a new and rapidly expanding field, the goal of which is obtaining fresh information from individual cells to understand the regulatory mechanisms of cell development and diseases. Conventional approaches generally rely on the cell lysis which, however, is destructive to cells and against multiple sampling from the living cell. Here, we propose and design a scaffolding nanoparticle (NP) system that enables us to sample cytoplasmic contents without rupturing the cellular membrane, by mimicking the unusual features of clathrin. Our simulation results reveal the design principles, following which scaffolding NPs can extract lipid vesicles from plasma membranes, with both the pathway and the mechanism resembling the clathrin-mediated endocytosis, i.e. multiple NPs deposit at the membrane, assembling into cage-like structures to deform the membrane into a vesicle shape. As important design parameters, the interaction between different NPs should be properly stronger than that between each NP and the membrane to ensure the cage formation, and optimal NP concentration and the membrane surface tension are also requisite for extracting lipid vesicles. Our results provide useful guidelines for design of bio-inspired scaffolding NPs as an intelligent machine for practical use in but not limited to the single-cell analysis.

Computer Tools to Analyze Microarray Data

Microarrays are broadly used in genomic analyses and find several applications in biology and medicine, providing a significant amount of data from a single experiment. Different kinds of microarrays are available which are identifiable by characteristics such as the type of probes, the surface used as support, and the method used for target detection. Although microarrays have been applied in many biological areas, their management, and investigation require advanced computational tools to speed up data analysis and at the same time make the interpretation of the results easier. To better deal with microarray datasets of large size, the development of analysis tools that are simple to use as well as able to produce accurate predictions, and of comprehensible models is essential. The tools have to provide an exhaustive collection of information to discriminate and identify SNPs, which are associated with the activity of particular genes affecting biological functions (e.g., a particular drug response), or involved in the development of complex diseases. The object of this chapter is to provide a review of software tools that are easy to use even for nonexperts of the domain, and that are able to efficiently deal with microarray data.

Microarray Technologies in Fungal Diagnostics

Microarray technologies have been a major research tool in the last decades. In addition they have been introduced into several fields of diagnostics including diagnostics of infectious diseases. Microarrays are highly parallelized assay systems that initially were developed for multiparametric nucleic acid detection. From there on they rapidly developed towards a tool for the detection of all kind of biological compounds (DNA, RNA, proteins, cells, nucleic acids, carbohydrates, etc.) or their modifications (methylation, phosphorylation, etc.). The combination of closed-tube systems and lab on chip devices with microarrays further enabled a higher automation degree with a reduced contamination risk. Microarray-based diagnostic applications currently complement and may in the future replace classical methods in clinical microbiology like blood cultures, resistance determination, microscopic and metabolic analyses as well as biochemical or immunohistochemical assays. In addition, novel diagnostic markers appear, like noncoding RNAs and miRNAs providing additional room for novel nucleic acid based biomarkers. Here I focus an microarray technologies in diagnostics and as research tools, based on nucleic acid-based arrays.

Antigen arrays for profiling autoantibody repertoires

Autoantibodies are a key component for the diagnosis, prognosis and monitoring of various diseases. In order to discover novel autoantibody targets, highly multiplexed assays based on antigen arrays hold a great potential and provide possibilities to analyze hundreds of body fluid samples for their reactivity pattern against thousands of antigens in parallel. Here, we provide an overview of the available technologies for producing antigen arrays, highlight some of the technical and methodological considerations and discuss their applications as discovery tools. Together with recent studies utilizing antigen arrays, we give an overview on how the different types of antigen arrays have and will continue to deliver novel insights into autoimmune diseases among several others.

Nanoscale bio-platforms for living cell interrogation: current status and future perspectives

The living cell is a complex entity that dynamically responds to both intracellular and extracellular environments. Extensive efforts have been devoted to the understanding intracellular functions orchestrated with mRNAs and proteins in investigation of the fate of a single-cell, including proliferation, apoptosis, motility, differentiation and mutations. The rapid development of modern cellular analysis techniques (e.g. PCR, western blotting, immunochemistry, etc.) offers new opportunities in quantitative analysis of RNA/protein expression up to a single cell level. The recent entries of nanoscale platforms that include kinds of methodologies with high spatial and temporal resolution have been widely employed to probe the living cells. In this tutorial review paper, we give insight into background introduction and technical innovation of currently reported nanoscale platforms for living cell interrogation. These highlighted technologies are documented in details within four categories, including nano-biosensors for label-free detection of living cells, nanodevices for living cell probing by intracellular marker delivery, high-throughput platforms towards clinical current, and the progress of microscopic imaging platforms for cell/tissue tracking in vitro and in vivo. Perspectives for system improvement were also discussed to solve the limitations remains in current techniques, for the purpose of clinical use in future.

Chronic effects of the ionic liquid [C4mim][Cl] towards the microalga Scenedesmus quadricauda

Chronic effects of the ionic liquid [C4mim][Cl] (mp 73 °C) towards the microalga, Scenedesmus quadricauda were studied by flow cytometry, monitoring multiple endpoints of cell density, esterase activity, membrane integrity, reactive oxygen species and chlorophyll fluorescence. Toxicity was clearly in evidence, and although increased esterase activity indicated hormesis during initial exposure to [C4mim][Cl], inhibition of both esterase activity and chlorophyll fluorescence became apparent after 3 days. Cell density was also decreased by culturing with [C4mim][Cl], but this effect was clearly concentration-dependent and only became significant during the second half of the experiment. In contrast, [C4mim][Cl] had only a modest effect on reactive oxygen species (ROS) and caused little damage to cell membranes.

Flow cytometric microsphere-based immunoassay as a novel non-radiometric method for the detection of glutamic acid decarboxylase autoantibodies in type 1 diabetes mellitus

The first measurable sign of arising autoimmunity in type 1 diabetes mellitus is the detection of autoantibodies against beta-cell antigens, such as glutamic acid decarboxylase (GAD65). GAD65 autoantibodies (GADA) are usually measured by the Radioligand Binding Assay (RBA). The aim of this work was to develop protocols of flow cytometric microsphere-based immunoassays (FloCMIA) which involved glutamic acid decarboxylase fused to thioredoxin (TrxGAD65) adsorbed on polystyrene microspheres. Detection of bound GADA was accomplished by the use of anti-human IgG-Alexa Fluor 488 (protocol A), anti-human IgG-biotin and streptavidin-dichlorotriazinyl aminofluorescein (DTAF) (protocol B) or TrxGAD65-biotin and streptavidin-DTAF (protocol C). Serum samples obtained from 46 patients assayed for routine autoantibodies at Servicios Tecnológicos de Alto Nivel (STAN-CONICET) were analyzed by RBA, ELISA and three alternative FloCMIA designs. Protocol C exhibited the highest specificity (97.8%) and sensitivity (97.4%) and a wide dynamic range (1.00-134.40 SDs). Samples obtained from 40 new-onset diabetic patients were also analyzed to further evaluate the performance of protocol C. The latter protocol showed a sensitivity of 58.6% and a prevalence of 47.5%. Two patients resulted positive only by FloCMIA protocol C and its SDs were higher than those of RBA and ELISA, showing a significantly wide dynamic range. In conclusion, FloCMIA proved to be highly sensitive and specific, requiring a low sample volume; it is environmentally adequate, innovative and represents a cost-effective alternative to traditional GADA determination by RBA and/or ELISA, making it applicable to most medium-complexity laboratories.

ELISA in the multiplex era: potentials and pitfalls

Multiplex immunoassays confer several advantages over widely adopted singleplex immunoassays including increased efficiency at a reduced expense, greater output per sample volume ratios and higher throughput predicating more resolute, detailed diagnostics and facilitating personalised medicine. Nonetheless, to date, relatively few protein multiplex immunoassays have been validated for in vitro diagnostics in clinical/point-of-care settings. This review article will outline the challenges, which must be ameliorated prior to the widespread integration of multiplex immunoassays in clinical settings: (i) biomarker validation; (ii) standardisation of immunoassay design and quality control (calibration and quantification); (iii) availability, stability, specificity and cross-reactivity of reagents; (iv) assay automation and the use of validated algorithms for transformation of raw data into diagnostic results. A compendium of multiplex immunoassays applicable to in vitro diagnostics and a summary of the diagnostic products currently available commercially are included, along with an analysis of the relative states of development for each format (namely planar slide based, suspension and planar/microtitre plate based) with respect to the aforementioned issues.

Plasmonic micro-beads for fluorescence enhanced, multiplexed protein detection with flow cytometry

The fluorescence enhancement of small molecule fluorophores was achieved on micro-beads through gold nano-island coating, enabling the detection of low-abundant protein biomarkers.

An electrochemical surface plasmon resonance imaging system targeting cell analysis

This paper presents an electrochemical-surface plasmon resonance imaging (EC-SPRI) system, enabling the characterization of optical and electrical properties of cells, simultaneously. The developed surface plasmon resonance (SPR) imaging system was capable of imaging micro cavities with a dimension of 10 μm × 10 μm and differentiated glycerol solutions with a group of refractive indices (RIs). Furthermore, the EC-SPRI system was used to image A549 cells, suggesting corresponding RI and morphology changes during the cell death process. In the end, electrochemical and SPR methods were used in combination, recording oxidation peaks of A549 cells in the cyclic voltage curves and SPR response unit increase, simultaneously.

Microarray in parasitic infections

Modern biology and genomic sciences are rooted in parasitic disease research. Genome sequencing efforts have provided a wealth of new biological information that promises to have a major impact on our understanding of parasites. Microarrays provide one of the major high-throughput platforms by which this information can be exploited in the laboratory. Many excellent reviews and technique articles have recently been published on applying microarrays to organisms for which fully annotated genomes are at hand. However, many parasitologists work on organisms whose genomes have been only partially sequenced. This review is mainly focused on how to use microarray in these situations.

Utility, reliability and reproducibility of immunoassay multiplex kits

Multiplex technologies are becoming increasingly important in biomarker studies as they enable patterns of biomolecules to be examined, which provide a more comprehensive depiction of disease than individual biomarkers. They are crucial in deciphering these patterns, but it is essential that they are endorsed for reliability, reproducibility and precision. Here we outline the theoretical basis of a variety of multiplex technologies: Bead-based multiplex immunoassays (i.e. Cytometric Bead Arrays, Luminex™ and Bio-Plex Pro™), microtitre plate-based arrays (i.e. Mesoscale Discovery (MSD) and Quantsys BioSciences QPlex), Slide-based Arrays (i.e. FastQuant™) and reverse phase protein arrays. Their utility, reliability and reproducibility are discussed.

Detection of single tumor cell resistance with aptamer biochip

In this study, a novel RNA aptamer biochip was developed for tumor cell capture and detection of single cell resistance. This biochip consists of a polydimethylsiloxane (PDMS) cover containing a channel for introducing cells and sustaining their activity and microelectrode matrix on a silicon dioxide layer. Epidermal growth factor receptor (EGFR) aptamers which specifically identify and isolate tumor cells were attached in the gap between two electrodes. After cell biochip incubation, surplus tumor cells were removed, and those dwelling on the intervals were further analyzed. When resistance measurement was completed, these cells were flushed away via controlled flow acceleration, and were collected for further analysis. The results demonstrate the convenience and efficiency of using anti-EGFR aptamer biochips for the detection of single cell resistance. This novel aptamer biochip may be used for the isolation of circulating tumor cells from peripheral blood and cell counting, or be assembled with other lab-on-a-chip components for follow-up gene and protein analysis.

Spintronic platforms for biomedical applications

Since the fundamental discovery of the giant magnetoresistance many spintronic devices have been developed and implemented in our daily life (e.g. information storage and automotive industry). Lately, advances in the sensors technology (higher sensitivity, smaller size) have potentiated other applications, namely in the biological area, leading to the emergence of novel biomedical platforms. In particular the investigation of spintronics and its application to the development of magnetoresistive (MR) biomolecular and biomedical platforms are giving rise to a new class of biomedical diagnostic devices, suitable for bench top bioassays as well as point-of-care and point-of-use devices. Herein, integrated spintronic biochip platforms for diagnostic and cytometric applications, hybrid systems incorporating magnetoresistive sensors applied to neuroelectronic studies and biomedical imaging, namely magneto-encephalography and magneto-cardiography, are reviewed. Also lab-on-a-chip MR-based platforms to perform biological studies at the single molecule level are discussed. Overall the potential and main characteristics of such MR-based biomedical devices, comparing to the existing technologies while giving particular examples of targeted applications, are addressed.

Cell separations by flow cytometry

Flow cytometry has become a standard method for separating individual subsets of cells from a heterogeneous population. Multilaser, multicolour cell sorters are increasingly common and have become more complex in recent years increasing the number of applications available. However, a cell sorting experiment is only as good as the input sample, and the preparation of this is extremely important. This chapter describes the methods used to prepare samples for flow cytometry and how they can be adapted and optimised according to cell type.

Cytometric microsphere array for subtyping avian influenza virus

Avian influenza is a highly contagious disease, and different subtypes of avian influenza virus (AIV) have different levels of pathogenicity. A microsphere-based fluorescent assay was initially established for subtyping AIV. DNA fragments were amplified with biotinylated primers. AIV subtype-specific DNA probes with an amino-linker at the 5' end were covalently bound with carboxy-modified encoded beads. The modified beads and the denatured DNA fragments were mixed together for hybridization. Then, quantum dots-streptavidin (QDs-streptavidin) was added to conjugated biotinylated PCR products. The reaction products were screened by flow cytometry. AIV strains (such as H5N1 and H9N2) could be determined and subtyped according to their combination of encoded beads and fluorescent QDs. The method's combined sensitivity of the nucleic acids of H5N1 and H9N2 avian influenza virus at a threshold of 74 pg and 1 pg could be detected. This is a powerful method for detecting many pathogens or many types of a pathogen simultaneously.

A fluorescent microsphere-based method for assay of multiple analytes in plasma

Measurement of multiple analytes can provide increased sensitivity and specificity for the detection and management of disease. The enzyme-linked immunosorbent assay (ELISA) is currently the "gold standard" for protein quantification; however, individual assays for each analyte must be performed, placing demand on sample volume. On the contrary, multiplex assays using microsphere-based technologies allow for multiple analytes to be simultaneously assayed within a single sample. Here, we present a protocol for the preparation and development of a multiple-analyte assay in human plasma using the BioPlex 200 platform (Bio-Rad), which incorporates xMAP technology (Luminex).

Optical biosensors to analyze novel biomarkers in oncology

Many cancer types are characterized by poor survival and unpredictable therapy response. Easy-to-perform molecular analyses may help patient stratification and treatment tailoring. Several integrated devices have been proposed to overcome current analysis equipment limitations. They offer improved sensitivity and easy availability of parallel detection. Particularly, unlabelled optical biosensors combine the manifold advantages of integrated sensors (e.g. easy handling, portability and low-volume requirement) with detection of target molecules in their original form. Here, we review integrated optical biosensor current features, and discuss their possible application to the detection of protein variants from body fluids, with particular regard to histone modifications. Indeed, histone post-translational modifications are a set of epigenetic markers frequently deregulated in cancer. Available technology does not allow a comprehensive analysis of all histone modifications in a single patient. Thus, label-free optical biosensors may pave the way to the discovery and detection of a novel class of biomarkers in oncology.

Biosensors in microfluidic chips

A biosensor is a sensing device that incorporates a biological sensing element and a transducer to produce electrochemical, optical, mass, or other signals in proportion to quantitative information about the analytes in the given samples. The microfluidic chip is an attractive miniaturized platform with valuable advantages, e.g., low cost analysis requiring low reagent consumption, reduced sample volume, and shortened processing time. Combination of biosensors and microfluidic chips enhances analytical capability so as to widen the scope of possible applications. This review provides an overview of recent research activities in the field of biosensors integrated on microfluidic chips, focusing on the working principles, characteristics, and applicability of the biosensors. Theoretical background and applications in chemical, biological, and clinical analysis are summarized and discussed.

Utilization of microparticles in next-generation assays for microflow cytometers

Micron-sized particles have primarily been used in microfabricated flow cytometers for calibration purposes and proof-of-concept experiments. With increasing frequency, microparticles are serving as a platform for assays measured in these small analytical devices. Light scattering has been used to measure the agglomeration of antibody-coated particles in the presence of an antigen. Impedance detection is another technology being integrated into microflow cytometers for microparticle-based assays. Fluorescence is the most popular detection method in flow cytometry, enabling highly sensitive multiplexed assays. Finally, magnetic particles have also been used to measure antigen levels using a magnetophoretic micro-device. We review the progress of microparticle-based assays in microflow cytometry in terms of the advantages and limitations of each approach.

Emerging molecular assays for detection and characterization of respiratory viruses

This article describes several emerging molecular assays that have potential applications in the diagnosis and monitoring of respiratory viral infections. These techniques include direct nucleic acid detection by quantum dots, loop-mediated isothermal amplification, multiplex ligation-dependent probe amplification, amplification using arbitrary primers, target-enriched multiplexing amplification, pyrosequencing, padlock probes, solid and suspension microarrays, and mass spectrometry. Several of these systems already are commercially available to provide multiplex amplification and high-throughput detection and identification of a panel of respiratory viral pathogens. Further validation and implementation of such emerging molecular assays in routine clinical virology services will enhance the rapid diagnosis of respiratory viral infections and improve patient care.

Basic concepts of microarrays and potential applications in clinical microbiology

The introduction of in vitro nucleic acid amplification techniques, led by real-time PCR, into the clinical microbiology laboratory has transformed the laboratory detection of viruses and select bacterial pathogens. However, the progression of the molecular diagnostic revolution currently relies on the ability to efficiently and accurately offer multiplex detection and characterization for a variety of infectious disease pathogens. Microarray analysis has the capability to offer robust multiplex detection but has just started to enter the diagnostic microbiology laboratory. Multiple microarray platforms exist, including printed double-stranded DNA and oligonucleotide arrays, in situ-synthesized arrays, high-density bead arrays, electronic microarrays, and suspension bead arrays. One aim of this paper is to review microarray technology, highlighting technical differences between them and each platform's advantages and disadvantages. Although the use of microarrays to generate gene expression data has become routine, applications pertinent to clinical microbiology continue to rapidly expand. This review highlights uses of microarray technology that impact diagnostic microbiology, including the detection and identification of pathogens, determination of antimicrobial resistance, epidemiological strain typing, and analysis of microbial infections using host genomic expression and polymorphism profiles.

An efficient method for enumerating oral spirochetes using flow cytometry

Spirochetes, such as Treponema denticola, are thin walled, helical, motile bacteria. They are notoriously difficult to enumerate due to their thinness and the difficulties associated with culturing them. Here we have developed a modified oral bacterial growth medium (OBGM) that significantly improves the cultivation of T. denticola compared with a previously published growth medium. Three methods for the enumeration of T. denticola, semi-solid growth medium colony-forming unit (CFU) counts, DNA analysis and flow cytometry, are described and compared. Enumeration of T. denticola using the semi-solid agar method resulted in a positive linear relationship with absorbance of the culture (R(2)=0.9423). However, the semi-solid agar method was found to consistently underestimate (by 50 fold) the T. denticola cell density compared to previously published data. DNA analysis of T. denticola cultures reliably and consistently resulted in a positive linear relationship with absorbance (R(2)=0.9360), giving a calculated cell density of 6.9 x 10(8)cells/mL at an absorbance of 0.2 at 650 nm. Flow cytometry was also found to result in a positive linear relationship with absorbance (R(2)=0.9874), giving a calculated cell density of 6.6 x 10(8)cells/mL at an absorbance of 0.2 at 650 nm. In comparing all of these enumeration methods, the flow cytometry method was found to have distinct advantages, as it is accurate, rapid, and could distinguish between live and dead bacteria. Thus flow cytometry is a recommended means for the rapid and reliable enumeration of viable spirochetes from culture.

Scrapheap challenge and the single cell

The prevailing approach to cellular molecular analyte investigations employs lysis. Using analogies with automobiles, we explain how current practise ridicules cellular individuality and meaningful variation. Single cell analysis and micro total analysis system (microTAS) prospects are discussed.

Reagents and instruments for multiplexed analysis using microparticles

Multiplexed molecular analysis by means of flow cytometry using optically encoded microspheres is a rapidly expanding application that has its roots in the earliest days of flow cytometry. The approach is driven by increasing demand for analytical methods to measure large numbers of biomolecules quantitatively and sensitively in small volumes of sample. Encoded microspheres and flow cytometry have been employed for a wide range of multiplexed molecular analysis, and detailed protocols for many of these have been developed. The goal of this unit is to provide an overview of the concepts, instruments, and reagents that enable these assays.

Detection of humoral response in patients with glioblastoma receiving EGFRvIII-KLH vaccines

The epidermal growth factor receptor variant III (EGFRvIII) is a consistent tumor-specific mutation that is widely expressed in glioblastoma multiforme (GBM) and other neoplasms. As such it represents a truly tumor-specific target for antitumor immunotherapy. Although endogenous humoral responses to EGFRvIII have been reported in patients with EGFRvIII-expressing breast cancer, it is not known whether de novo responses can be generated or endogenous responses enhanced with an EGFRvIII-specific vaccine. To assess this in clinical trials, we have developed and validated an immunoassay to measure and isolate anti-EGFRvIII and anti-KLH antibodies from the serum of patients vaccinated with an EGFRvIII-specific peptide (PEPvIII) conjugated to keyhole limpet hemocyanin (KLH). Using magnetic beads with immobilized antigen we captured and detected anti-EGFRvIII and anti-KLH antibodies in serum from patients before and after vaccinations. Using this assay, we found that significant levels of antibody for tumor-specific antigen EGFRvIII (>4 microg/mL) and KLH could be induced after vaccination with PEPvIII-KLH.

Chemical cytometry on microfluidic chips

Chemical cytometry, referring to the analysis of the chemical contents in individual cells, has been in intensive study since Kennedy's first work that was published in Science. The early researches relied on fine-tip capillaries to capture the cells and do the analyses, which were lab- and time-intensive and required high skills of operation. The emergence of microfluidics has greatly spurred this research field and a great number of research papers have been published in the last decades. Highly integrated microfluidic chips have been developed to capture multiple single cells, lyse them, perform chemical reactions in enclosed microchambers, separate contents by CE and detect chemical species in individual cells. This review focuses on the development of relevant components and their integration for on-chip chemical cytometry.

Quantitative intracellular molecular profiling using a one-dimensional flow system

We report on the development of one-dimensional microfluidic bead arrays for rapid and quantitative molecular profiling of human cancer cells. This new bioanalytical platform integrates the rapid binding kinetics of suspension bead carriers, the multiplexing and encoding capabilities of gene/protein chips, and the liquid handling advantages of microfluidic devices. Using antibody-conjugated beads in a two-site "sandwich" format, we demonstrate that the proteomic contents of as few as 56 human lung epithelial cancer cells can be determined with high sensitivity and specificity. The results indicate that each cell contains approximately 6 x 10(5) copies of the tumor suppressor protein P53. We have further examined the expression changes of P53, c-Myc, and beta-Actin as a function of anticancer drug treatment and have validated these changes by using Western blotting. This ability to quantitatively analyze normal and diseased cells raises new possibilities in studying cancer heterogeneity and circulating tumor cells.