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HIV-1 vaccine immunofocusing strategies may be able to induce broadly-reactive neutralizing antibodies (NAbs). Here, we engineered a panel of diverse, membrane-resident native HIV-1 trimers vulnerable to two broad targets—the V2 apex and fusion peptide (FP). Selection criteria included i) high expression and ii) infectious function, so that trimer neutralization sensitivity can be profiled in pseudovirus (PV) assays. Initially, we boosted the expression of 17 candidate trimers by truncating gp41 and introducing a gp120-gp41 SOS disulfide to prevent gp120 shedding. "Repairs" were made to fill glycan holes and eliminate other strain-specific aberrations. A new neutralization assay allowed PV infection when our standard assay was insufficient. Trimers with exposed V3 loops, a target of non-NAbs, were discarded. To try to increase V2-sensitivity, we removed clashing glycans and modified the C-strand. Notably, a D167N mutation improved V2-sensitivity in several cases. Glycopeptide analysis of JR-FL trimers revealed near complete sequon occupation and that filling the N197 glycan hole was well-tolerated. In contrast, sequon optimization and inserting/removing glycans at other positions frequently had global "ripple" effects on glycan maturation and sequon occupation throughout the gp120 outer domain and gp41. V2 MAb CH01 selectively bound to trimers with small high mannose glycans near the base of the V1 loop, thereby avoiding clashes. Knocking in a rare N49 glycan was found to perturb gp41 glycans, increasing FP NAb sensitivity—and sometimes improving expression. Finally, a biophysical analysis of VLPs revealed that i) ~25% of particles bear Env spikes, ii) spontaneous particle budding is high and only increases 4-fold upon Gag transfection, and iii) Env+ particles express ~30–40 spikes. Taken together, we identified 7 diverse trimers with a range of sensitivities to two targets to allow rigorous testing of immunofocusing vaccine concepts., Author summary Despite almost 40 years of innovation, a vaccine to induce antibodies that block HIV infection remains elusive. Challenges include the unparalleled sequence diversity of HIV’s surface spikes and its dense sugar coat that limits antibody access. A growing number of monoclonal antibodies from HIV infected donors provide vaccine blueprints, but have been difficult to induce by vaccination, due to their unusual features. However, two targets, one at the viral spike apex and another at the side of the spikes are more forgiving in their ’demands’ for unusual antibodies. Here, we made a diverse panel of HIV spikes vulnerable at these two sites to be used as vaccines to try to focus antibodies on these targets. Our selection criteria for these spikes were: i) that when expressed on particles, they are infectious, allowing us to evaluate immunogens and vaccine sera using particles made with the same trimers, ii) that spikes are easy to produce by cells in quantities sufficient for vaccine use. Ultimately, we selected 7 trimers that will allow us to explore concepts that could bring us closer to an HIV vaccine.

Extracellular vesicles (EVs) are identified as mediators of intercellular communication and cellular regulation. In the immune system, EVs play a role in antigen presentation as a part of cellular communication. To enable drug discovery and characterization of compounds that affect EV biogenesis, function, and release in immune cells, we developed and characterized a reporter cell line that allows the quantitation of EVs shed into culture media in phenotypic high-throughput screen (HTS) format. Tetraspanins CD63 and CD9 were previously reported to be enriched in EVs; hence, a construct with dual reporters consisting of CD63-Turbo-luciferase (Tluc) and CD9-Emerald green fluorescent protein (EmGFP) was engineered. This construct was transduced into the human monocytic leukemia cell line, THP-1. Cells expressing the highest EmGFP were sorted by flow cytometry as single cell, and clonal pools were expanded under antibiotic selection pressure. After four passages, the green fluorescence dimmed, and EV biogenesis was then tracked by luciferase activity in culture supernatants. The Tluc activities of EVs shed from CD63Tluc-CD9EmGFP reporter cells in the culture supernatant positively correlated with the concentrations of released EVs measured by nanoparticle tracking analysis. To examine the potential for use in HTS, we first miniaturized the assay into a robotic 384-well plate format. A 2210 commercial compound library (Maybridge) was then screened twice on separate days, for the induction of extracellular luciferase activity. The screening data showed high reproducibility on days 1 and 2 (78.6%), a wide signal window, and an excellent Z′ factor (average of 2-day screen, 0.54). One hundred eighty-seven compounds showed a response ratio that was 3SD above the negative controls in both day 1 and 2 screens and were considered as hit candidates (approximately 10%). Twenty-two out of 40 re-tested compounds were validated. These results indicate that the performance of CD63Tluc-CD9EmGFP reporter cells is reliable, reproducible, robust, and feasible for HTS of compounds that regulate EV release by the immune cells.

Extracellular vesicles (EVs) can mediate intercellular communication, including signaling between the placenta and maternal tissues. Human placental explant culture is a versatile in vitro model system to investigate placental function. We performed systematic studies to identify a defined serum-free medium that supports high trophoblast viability and metabolism, as well as release of similar populations of EVs, compared to traditional undefined conditions that contain media additives potentially contaminated with exogenous EVs. We also determined the timeframe in which trophoblast viability and functionality remained optimal. Multiplexed vesicle flow cytometry with classical EV and placenta-specific markers revealed three separate populations, small CD63+ EVs, large PLAP+ EVs, and CD63-/PLAP- EVs. The CD63+ population was higher in the first trimester and the PLAP+ population in the third trimester explants. These culture and analytical approaches will enable in vitro modeling of short-term effects of environmental perturbations associated with pregnancy complications on placental function and EV secretion.

Methamphetamine (MA) is the largest drug threat across the globe, with health effects including neurotoxicity and cardiovascular disease. Recent studies have begun to link microRNAs (miRNAs) to the processes related to MA use and addiction. Our studies are the first to analyse plasma EVs and their miRNA cargo in humans actively using MA (MA‐ACT) and control participants (CTL). In this cohort we also assessed the effects of tobacco use on plasma EVs. We used vesicle flow cytometry to show that the MA‐ACT group had an increased abundance of EV tetraspanin markers (CD9, CD63, CD81), but not pro‐coagulant, platelet‐, and red blood cell‐derived EVs. We also found that of the 169 plasma EV miRNAs, eight were of interest in MA‐ACT based on multiple statistical criteria. In smokers, we identified 15 miRNAs of interest, two that overlapped with the eight MA‐ACT miRNAs. Three of the MA‐ACT miRNAs significantly correlated with clinical features of MA use and target prediction with these miRNAs identified pathways implicated in MA use, including cardiovascular disease and neuroinflammation. Together our findings indicate that MA use regulates EVs and their miRNA cargo, and support that further studies are warranted to investigate their mechanistic role in addiction, recovery, and recidivism.

ISIS 104838, a 2'-O-methoxyethyl (2'-MOE)-modified antisense oligonucleotide (ASO), causes a moderate, reproducible, dose-dependent, but selflimiting decrease in platelet (PLT) counts in monkeys and humans. To determine the etiology of PLT decrease in cynomolgus monkeys, a 12-week repeat dose toxicology study in 5 cynomolgus monkeys given subcutaneous injections of ISIS 104838 (30-60 mg/kg/week). Monkeys were also injected intravenously with 111Indium(In)-oxine-labeled PLTs to investigate PLT sequestration. In response to continued dosing, PLT counts were decreased by 50%-90% by day 30 in all monkeys. PLT decreases were accompanied by 2- to 4.5-fold increases in immunoglobulin M(IgM), which were typified by a 2- to 5-fold increase in antiplatelet factor 4 (antiPF4) IgM and antiPLT IgM, respectively. Monocyte chemotactic protein 1 increased upon dosing of ISIS 104838, concomitant with a 2- to 6-fold increase in monocyte-derived extracellular vesicles (EVs), indicating monocyte activation but not PLT activation. Despite a 2- to 3-fold increase in von Willebrand factor antigen in all monkeys following ASO administration, only 2 monkeys showed a 2- to 4-fold increase in endothelial EVs. Additionally, a ∼60 - 80%% increase in PLT sequestration in liver and spleen was also observed. Collectively, these results suggest the overall increase in total IgM, antiPLT IgM and/or antiPF4 IgM, in concert with monocyte activation contributed to increased PLT sequestration in spleen and liver, leading to decreased PLTs in peripheral blood.

The composition and function of platelet-derived Extracellular Vesicles (EVs) in health and in disease are a major topic of investigation in biomedical research. However, efforts to delineate specific molecular repertoires and roles for different types of EVs in the circulation are limited not only by the lack of flow cytometers capable of analyzing submicron- and nano-materials across the full size spectrum of plasma EVs, but also by the lack of standardized methods and reference materials that would permit inter-laboratory reproducibility for these analyses. In this review, we summarize the flow cytometry of EVs, with a focus on platelet vesicles in plasma. In addition to delineating the basic principles that govern what precautions must be considered when using flow cytometry for the analysis of platelet vesicles, we provide an overview for how to standardize, control, annotate, and report EV flow cytometry data reproducibly, while looking forward to a next generation of high sensitivity instruments for the analysis of EVs and other submicron biomaterials in the circulation.

Extracellular vesicles (EVs) are attracting attention as vehicles for inter-cellular signaling that may have value as diagnostic or therapeutic targets. EVs are released by many cell types and by different mechanisms, resulting in phenotypic heterogeneity that makes them a challenge to study. Flow cytometry is a popular tool for characterizing heterogeneous mixtures of particles such as cell types within blood, but the small size of EVs makes them difficult to measure using conventional flow cytometry. To address this limitation, a high sensitivity flow cytometer was constructed and EV measurement approaches that allowed them to enumerate and estimate the size of individual EVs, as well as measure the presence of surface markers to identify phenotypic subsets of EVs. Several fluorescent membrane probes were evaluated and it was found that the voltage sensing dye di-8-ANEPPS could produce vesicle fluorescence in proportion to vesicle surface area, allowing for accurate measurements of EV number and size. Fluorescence-labeled annexin V and anti-CD61 antibody was used to measure the abundance of these surface markers on EVs in rat plasma. It was shown that treatment of platelet rich plasma with calcium ionophore resulted in an increase in the fraction of annexin V and CD61-positive EVs. Vesicle flow cytometry using fluorescence-based detection of EVs has the potential to realize the potential of cell-derived membrane vesicles as functional biomarkers for a variety of applications.

Extracellular vesicles (EVs) are released by cells and can be found in cell culture supernatants and biofluids. EVs carry proteins, nucleic acids, and other cellular components and can deliver these to nearby or distant cells, making EVs of interest as both disease biomarkers and therapeutic targets. EVs in biofluids are heterogeneous, coming from different cell types and from different sources with the cell, which limits the usefulness of bulk EV analysis methods that report the average features of all EVs present. Single-particle measurements such as flow cytometry would be preferred, but the small size and low abundance of surface antigens challenges conventional flow cytometry approaches, leading to the development of vesicle-specific assays and experimental design. Among the key issues that have emerged are: (a) judicious choice of detection (triggering) approach; (b) appropriate control experiments to confirm the vesicular nature of the detected events and the contribution of coincidence (aka swarm detection); and (c) the importance of fluorescence calibration to allow data to be compared over time and between laboratories. We illustrate these issues in the context of fluorescence-triggered Vesicle Flow Cytometry (VFC), a general approach to the quantitative measurement of EV number, size, and surface marker expression.

We examined the extracellular vesicle (EV) and RNA composition of pooled normal cerebrospinal fluid (CSF) samples and CSF from five major neurological disorders: Alzheimer’s disease (AD), Parkinson’s disease (PD), low-grade glioma (LGG), glioblastoma multiforme (GBM), and subarachnoid haemorrhage (SAH), representing neurodegenerative disease, cancer, and severe acute brain injury. We evaluated: (I) size and quantity of EVs by nanoparticle tracking analysis (NTA) and vesicle flow cytometry (VFC), (II) RNA yield and purity using four RNA isolation kits, (III) replication of RNA yields within and between laboratories, and (IV) composition of total and EV RNAs by reverse transcription–quantitative polymerase chain reaction (RT-qPCR) and RNA sequencing (RNASeq). The CSF contained ~106 EVs/μL by NTA and VFC. Brain tumour and SAH CSF contained more EVs and RNA relative to normal, AD, and PD. RT-qPCR and RNASeq identified disease-related populations of microRNAs and messenger RNAs (mRNAs) relative to normal CSF, in both total and EV fractions. This work presents relevant measures selected to inform the design of subsequent replicative CSF studies. The range of neurological diseases highlights variations in total and EV RNA content due to disease or collection site, revealing critical considerations guiding the selection of appropriate approaches and controls for CSF studies.

Systemic inflammation co-activates coagulation, which unchecked culminates in a lethal syndrome of multi-organ microvascular thrombosis known as disseminated intravascular coagulation (DIC). We studied an endotoxin-induced inflammatory state in rats to identify biomarkers of hemostatic imbalance favoring hypercoagulability. Intraperitoneal injection of LPS at 15 mg/kg body weight resulted in peripheral leukopenia and widespread neutrophilic sequestration characteristic of an acute systemic inflammatory response. Early indicators of hemostatic pathway activation developed within 4 hours, including increased circulating concentrations of procoagulant extracellular vesicles (EVs), EVs expressing endothelial cell and platelet membrane markers, and high concentration of soluble intercellular adhesion molecule-1 (sICAM-1), plasminogen activator inhibitor-1 (PAI-1), and D-dimers. Inflammation persisted throughout the 48-hour observation period; however, increases were found in a subset of serum microRNA (miRNA) that coincided with gradual resolution of hemostatic protein abnormalities and reduction in EV counts. Dose-adjusted LPS treatment in rats provides a time-course model to develop biomarker profiles reflecting procoagulant imbalance and rebalance under inflammatory conditions.

Extracellular vesicles (EVs) have emerged as a promising biomarker platform for glioblastoma patients. However, the optimal method for quantitative assessment of EVs in clinical bio-fluid remains a point of contention. Multiple high-resolution platforms for quantitative EV analysis have emerged, including methods grounded in diffraction measurement of Brownian motion (NTA), tunable resistive pulse sensing (TRPS), vesicle flow cytometry (VFC), and transmission electron microscopy (TEM). Here we compared quantitative EV assessment using cerebrospinal fluids derived from glioblastoma patients using these methods. For EVs 150 nm in diameter), NTA consistently detected lower number of EVs relative to TRPS. These results unveil the strength and pitfalls of each quantitative method alone for assessing EVs derived from clinical cerebrospinal fluids and suggest that thoughtful synthesis of multi-platform quantitation will be required to guide meaningful clinical investigations.

There is a long standing interest in measuring complete emission spectra from individual cells in flow cytometry. We have developed flow cytometry instruments and analysis approaches to enable this to be done routinely and robustly. Our spectral flow cytometers use a holographic grating to disperse light from single cells onto a CCD for high speed, wavelength-resolved detection. Customized software allows the single cell spectral data to be displayed and analyzed to produce new spectra-derived parameters. We show that familiar reference and calibration beads can be employed to quantitatively assess instrument performance. We use microspheres stained with six different quantum dots to compare a virtual bandpass filter approach with classic least squares (CLS) spectral unmixing, and then use antibody capture beads and CLS unmixing to demonstrate immunophenotyping of peripheral blood mononuclear cells using spectral flow cytometry. Finally, we characterize and evaluate several near infrared (NIR) emitting fluorophores for use in spectral flow cytometry. Spectral flow cytometry offers a number of attractive features for single cell analysis, including a simplified optical path, high spectral resolution, and streamlined approaches to quantitative multiparameter measurements. The availability of robust instrumentation, software, and analysis approaches will facilitate the development of spectral flow cytometry applications.

The yeast two-hybrid (Y2H) assay is a widely used method to study protein-protein interactions, a major objective in postgenome research. Despite the tremendous utility of the Y2H assay, several issues including accuracy, speed, automation, and cost-effectiveness limit its application in high-throughput analysis. We have created an improved Y2H assay reporter system by integrating the codon-optimized yeast enhanced green fluorescent protein (yEGFP) gene into the ADE2 locus of the AH109 yeast strain and evaluated reporter expression using the strong and weak triggers via flow cytometry. We also performed flow cytometry-based Y2H assays in liquid cultures as well as in a cDNA library screening. We have shown that yEGFP, but not EGFP, is a sensitive Y2H reporter for flow cytometric detection. We also show that this yEGFP-based Y2H could be easily adapted to high-throughput format without conventional agar plating. Moreover, our data demonstrate that this system can be used for cDNA library screening. We have developed sensitive and efficient flow cytometry-based Y2H assay system that is well suited for large-scale protein-protein interaction identification and characterization. When compared with the conventional plate and filter membrane-based nutrient and colorimetric analysis, our flow cytometric assay offers convenient, quantitative, and faster reporter analysis compatible with existing liquid handling robots.

BACKGROUND Polymorphisms in the TNF-alpha promoter region have recently been shown to be associated with susceptibility to cervical cancer. Some polymorphisms have been reported to influence transcription for this cytokine. Altered local levels in the cervix may influence an individual's immune response, thereby affecting persistence of human papillomavirus (HPV) 16 infection, a primary etiological factor for cervical cancer. METHODS AND RESULTS The association of 11 TNF-alpha single-nucleotide polymorphisms (SNPs) with susceptibility to HPV16-associated cervical cancer was investigated. Sequencing of the TNF-alpha promoter region confirmed 10 SNPs, and 1 previously unreported SNP (161 bp upstream of the transcriptional start site) was discovered. Microsphere-array flow cytometry-based genotyping was performed on 787 samples from Hispanic and non-Hispanic white women (241 from randomly selected control subjects, 205 from HPV16-positive control subjects, and 341 from HPV16-positive subjects with cervical cancer). The genotype distribution of 3 SNPs (-572, -857, and -863) was significantly different between case subjects and control subjects. Analysis of haplotypes, which were computationally inferred from genotype data, also revealed statistically significant differences in haplotype distribution between case subjects and control subjects. CONCLUSIONS We report new associations between several TNF-alpha SNPs and susceptibility to cervical cancer that support the involvement of the TNF- alpha promoter region in development of cervical cancer.

Background General methods for accurate determination of microsphere surface protein loading are needed for applications from protein arrays to molecular assembly studies. Current methods include bulk absorption measurements of stained microspheres or use of known fluorescently tagged binding partners, which limit sensitivity and general applicability, respectively. Methods Microspheres bearing covalently coupled proteins were stained with 3-(4-carboxybenzoyl)quinoline-2-carboxaldehyde (CBQCA) using different incubation times and dye concentrations to determine optimal staining conditions. The CBQCA fluorescence of microspheres (measured by flow cytometry) bearing known amounts of protein were used to generate standard curves of CBQCA fluorescence response versus the amount of microsphere surface protein. CBQCA was also used to stain noncovalent protein interactions. Results Maximal labeling was attained within 1 h with 1 mM CBQCA. Linear fluorescence response occurred between 8 × 104 and 1 × 106 proteins/microsphere. CBQCA staining did not disturb noncovalent protein interactions. Conclusions We have developed methods using CBQCA and flow cytometry to quickly and simply quantify the amount of protein on the surface of a microsphere. Importantly, this approach could be extended to other formats (e.g., chips). Further, because it does not disturb noncovalent protein–protein interactions, it may be possible to use this approach to detect protein interactions without the use of purified prestained probes. Published 2005 Wiley-Liss, Inc.

A rapid and sensitive multiplexed, microsphere-based immunoassay was developed for simultaneous typing and subtyping of the influenza virus by flow cytometry. Influenza virus type- and/or subtype-specific monoclonal antibodies (capture antibodies) were covalently coupled to size- or color-coded microspheres. The antibody-coupled microspheres were used to capture the influenza viruses in the sample, and the bound viruses were then detected and quantified with a cocktail of fluorochrome-conjugated, influenza virus-specific polyclonal antibodies (reporter antibodies) using flow cytometry. By utilizing appropriate size- or color-coded microspheres, the multiplexed immunoassay can be readily formatted into a duplexed assay for influenza virus typing (A vs. B) or a four-plexed assay for simultaneous typing and subtyping (A vs. B and H1 vs. H3).

Background Enhanced green fluorescent protein (EGFP) is used extensively to assess gene expression on cells; however, quantification of this expression by flow cytometry has been limited by the unavailability of calibration standards. Thus, we characterized the response of an experimental set of EGFP calibration standards to environmental changes and then quantitate the expression of EGFP, in molecules of equivalent soluble fluorochrome (MESF) units, of a transfected Molt-4 T cell line by flow cytometry. Methods Characterization of the EGFP standards: EGFP standards were equilibrated in suspension solutions having a pH range of 5.0–9.0, temperatures of 37–80°C, and osmolalities of 100–600 mOsm/kg. Quantification of EGFP on cells: For transfections, Molt-4 T cells were incubated with two different concentrations (0.2 μg and 0.4 μg) of pEGFP-N2 vector and the EGFP expression was quantified after 48 h by flow cytometry using the EGFP standards and by the cytofluor technique using a standard curve of known EGFP solutions. Results The fluorescence intensity of the EGFP standards increased from pH 5.0 to 9.0 and remained relatively constant from 37°C to 65°C, and from 100 to 600 mOsm/kg. After transfection, the expression of the populations with high and low EGFP expression averaged 8,098 ± 584 MESF and 3,808 ± 375 MESF respectively. No significant differences were observed after comparing the MESF values obtained by flow cytometry and the values obtained by Cytofluor technique (high: 8,791 ± 492 MESF; low: 4,082 ± 398 MESF). Conclusions Our data demonstrate the feasibility of using calibration standards to quantify EGFP expression on cells. Our results emphasize the importance of monitoring the effects of environmental changes in the fluorescence intensity of both standards and samples when quantifying the expression of EGFP on living cells. © 2004 Wiley-Liss, Inc.

We have developed a rapid, duplexed microsphere-based immunoassay for the characterization of influenza virus types that has the potential to overcome many of the limitations of current detection methods. The assay uses microspheres of two sizes, each coupled to an influenza type A- or type B-specific monoclonal antibody (MAb), to capture influenza viruses in the sample. A cocktail of fluorescently labeled, influenza-specific polyclonal antibodies then binds the captured viruses. The sandwich complexes are measured using a multiparameter flow cytometer. The assay can distinguish between influenza types A and B in a single reaction with good reproducibility and high sensitivity. Detection sensitivity is much higher than that of commercially available influenza diagnosis quick kits: the FLU OIA (Thermo Biostar) kit and the Directigen Flu A+B kit (Becton Dickinson). The multiplexing capabilities of the current assay, which are not possible with enzyme-linked immunosorbent assay (ELISA) and the commercially available kits, reduce sample handling and consume fewer costly reagents. This assay represents a more efficient and sensitive method of characterizing influenza types. With inclusion of influenza subtype-specific antibodies as capture antibodies, this microsphere-based immunoassay can be expanded to differentiate among influenza types and subtypes in a single reaction to improve world-wide influenza surveillance.

Cholera toxin entry into mammalian cells is mediated by binding of the pentameric B subunit (CTB) to ganglioside GM(1) in the cell membrane. We used flow cytometry to quantitatively measure in real time the interactions of fluorescently labeled pentameric cholera toxin B-subunit (FITC-CTB) with its ganglioside receptor on microsphere-supported phospholipid membranes. A model that describes the multiple steps of this mode of recognition was developed to guide our flow cytometric experiments and extract relevant equilibrium and kinetic rate constants. In contrast to previous studies, our approach takes into account receptor cross-linking, an important feature for multivalent interactions. From equilibrium measurements, we determined an equilibrium binding constant for a single subunit of FITC-CTB binding monovalently to GM(1) presented in bilayers of approximately 8 x 10(7) M(-1) while that for binding to soluble GM(1)-pentasaccharide was found to be approximately 4 x 10(6) M(-1). From kinetic measurements, we determined the rate constant for dissociation of a single site of FITC-CTB from microsphere-supported bilayers to be (3.21 +/- 0.03) x 10(-3) s(-1), and the rate of association of a site on FITC-CTB in solution to a GM(1) in the bilayer to be (2.8 +/- 0.4) x 10(4) M(-1) s(-1). These values yield a lower estimate for the equilibrium binding constant of approximately 1 x 10(7) M(-1). We determined the equilibrium surface cross-linking constant [(1.1 +/- 0.1) x 10(-12) cm(2)] and from this value and the value for the rate constant for dissociation derived a value of approximately 3.5 x 10(-15) cm(2) s(-1) for the forward rate constant for cross-linking. We also compared the interaction of the receptor binding B-subunit with that of the whole toxin (A- and B-subunits). Our results show that the whole toxin binds with approximately 100-fold higher avidity than the pentameric B-subunit alone which is most likely due to the additional interaction of the A(2)-subunit with the membrane surface. Interaction of cholera toxin B-subunit and whole cholera toxin with gangliosides other than GM(1) revealed specific binding only to GD1(b) and asialo-GM(1). These interactions, however, are marked by low avidity and require high receptor concentrations to be observed.

The marriage between immunology and cytometry is one of the most stable and productive in the recent history of science. A rapid search in PubMed shows that, as of July 2017, using “flow cytometry immunology” as a search term yields more than 68 000 articles, the first of which, interestingly, is not about lymphocytes. It might be stated that, after a short engagement, the exchange of the wedding rings between immunology and cytometry officially occurred when the idea to link fluorochromes to monoclonal antibodies came about. After this, recognizing different types of cells became relatively easy and feasible not only by using a simple fluorescence microscope, but also by a complex and sometimes esoteric instrument, the flow cytometer that is able to count hundreds of cells in a single second, and can provide repetitive results in a tireless manner. Given this, the possibility to analyse immune phenotypes in a variety of clinical conditions has changed the use of the flow cytometer, which was incidentally invented in the late 1960s to measure cellular DNA by using intercalating dyes, such as ethidium bromide. The epidemics of HIV/AIDS in the 1980s then gave a dramatic impulse to the technology of counting specific cells, since it became clear that the quantification of the number of peripheral blood CD4+ T cells was crucial to follow the course of the infection, and eventually for monitoring the therapy. As a consequence, the development of flow cytometers that had to be easy-to-use in all clinical laboratories helped to widely disseminate this technology. Nowadays, it is rare to find an immunological paper or read a conference abstract in which the authors did not use flow cytometry as the main tool to dissect the immune system and identify its fine and complex functions. Of note, recent developments have created the sophisticated technology of mass cytometry, which is able to simultaneously identify dozens of molecules at the single cell level and allows us to better understand the complexity and beauty of the immune system.

Nanotechnology has been extensively explored for cancer diagnostics. However, the specificity of current methods to identify simultaneously several cancer biomarkers is limited due to color overlapping of bio-conjugated nanoparticles. Here, we present a technique to increase both the molecular and spectral specificity of cancer diagnosis by using tunable silver-gold nanorods with narrow surface-enhanced Raman scattering (SERS) and high photothermal contrast. The silver-gold nanorods were functionalized with four Raman-active molecules and four antibodies specific to breast cancer markers and with leukocyte-specific CD45 marker. More than two orders of magnitude of SERS signal enhancement was observed from these hybrid nanosystems compared to conventional gold nanorods. Using an antibody rainbow cocktail, we demonstrated highly specific detection of single breast cancer cells in unprocessed human blood. By integrating multiplex targeting, multicolor coding, and multimodal detection, our approach has the potential to improve multispectral imaging of individual tumor cells in complex biological environments.

High-content screening (HCS, also known as high-content analysis, or HCA) is an approach to cell biology that combines automated imaging and quantitative data analysis in a high-throughput format suitable for large-scale applications such as drug discovery and systems biology. At present, HCS is primarily a fluorescence imaging method, typically measuring only a few fluorochoromes at one time. Fluorescence multiplexing at slightly higher levels is possible, but limitations in available fluorophores and instrument design make high-level multiplexing with fluorescence very challenging. The narrow spectral features of Raman scattering and the great signal enhancements exhibited by nanoparticle surface-enhanced Raman scattering (SERS) make it a potentially attractive complement to fluorescence probes from highly multiplexed HCS. In this chapter, we compare fluorescence and SERS probes, spectral imaging applications, and prospects for combining these two optical detection modalities for highly multiplexed HCS.

The applications of flow cytometry are being extended beyond cells into molecular interactions and genomic analyses. The authors explain how instrumentation and reagent development are combining to improve flow cytometric throughput by orders of magnitude beyond that possible just a few years ago, such that the combination of sensitivity, throughput and versatility makes flow cytometry an analytical platform with applications at all stages of drug discovery.

Membrane destabilization is an essential step in the process of membrane fusion. In many cell types, exocytotic fusion may occur sporadically at microscopically localized sites on the surface of the cell, making it difficult to study the chemical and physical features of the membrane (or membranes) that promote fusion. In the sperm cell, exocytosis occurs synchronously at a distinct region on the sperm head. This localization of function makes the sperm cell a useful model to investigate the structural features of the bilayers that control membrane fusion. During sperm maturation, the anterior head membranes undergo a well-defined series of chemical, physical, and functional changes that are necessary to produce a fertile gamete. These changes include the addition of highly unsaturated phosphatidylcholine, a decrease in general membrane stability, and an increase in the ability to respond to physiological and pharmacological inducers of exocytosis. Concomitant addition of cholesterol and an actively maintained asymmetric transmembrane phospholipid distribution modulate these effects to stabilize the membrane of the mature sperm for storage. The environment of the female tract provides conditions that promote efflux of cholesterol from the sperm plasma membrane as well as the loss of membrane asymmetry. The cholesterol-poor, lipid-symmetric plasma membrane has a destabilized inner leaflet that facilitates membrane fusion upon binding of the sperm to the appropriate egg coat receptors. We summarize these features in a mechanistic model in which the sperm membrane contains destabilizing components to confer fusogenic potential as well as stabilizing components organized to maximize membrane integrity. This combination prevents premature fusion in the male tract. After deposition in the female tract and removal of the stabilizing components, followed by reorganization of the fusogenic components, the membrane becomes poised to fuse upon receipt of the final biological stimulus.

Interest in measuring the complete fluorescence spectra of individual cells in flow can be traced to the earliest days of flow cytometry. Recent advances in detectors, optics, and computation have made it possible to make full spectral measurements in the sub-millisecond time frame in which flow cytometry measurements typically occur. This opens up new possibilities for applying spectroscopy to the analysis of individual cells. This unit reviews historical and contemporary approaches to spectral flow cytometry, as well as instrument design, calibration, and data analysis for spectral flow cytometry applications.

Background Plasmodium berghei rodent malaria is a well-known model for the investigation of anti-malarial drug efficacy in vivo. However, the availability of drug in vitro assays in P. berghei is reduced when compared with the spectrum of techniques existing for Plasmodium falciparum. New alternatives to the current manual or automated methods described for P. berghei are attractive. The present study reports a new ELISA drug in vitro assay for P. berghei using two monoclonal antibodies against the parasite lactate dehydrogenase (pLDH). Methods This procedure includes a short-in vitro culture, the purification of schizonts and the further generation of synchronized mice infections. Early stages of the parasite are then incubated against different concentrations of anti-malarial drugs using micro-plates. The novelty of this procedure in P. berghei relies on the quantification of the drug activity derived from the amount of pLDH estimated by an ELISA assay using two monoclonal antibodies: 14C1 and 19G7. The IC50s obtained through the ELISA assay were compared with those from the micro-test. Results The initial parameters of the synchronized samples used in the in vitro assays were a parasitaemia of 0.5% and haematocrit of 1%, with an incubation period of 22 hours at 36.5°C. pLDH detection using a 14C1 coating at 10 μg/ml and 19G7 at 2.5 × 10-3 μg/ml provided good readouts of optical densities with low background in negative controls and specific detection levels for all parasite stages. IC50s values derived from the ELISA assay for artesunate, chloroquine, amodiaquine and quinine were: 15, 7, 2, and 144 nM, respectively. When artesunate and chloroquine IC50s were evaluated using the micro-test similar values were obtained. Conclusion This ELISA-based in vitro drug assay is easy to implement, fast, and avoids the use radioisotopes or expensive equipment. The utility of this simple assay for screening anti-malarial drug activity against P. berghei in vitro is demonstrated.

Carbohydrate-protein interactions are involved in many crucial biological processes, from protein stability, to immune response, to pathogen infection. A fast and reliable method to determine carbohydrate binding affinity and specificity was developed as an alternative to ELISA and glycan microarray screening.Optically distinct neutravidin-coated microspheres were functionalized with biotinylated carbohydrates, to create a glycan array in suspension format. A range of fluorescently labeled carbohydrate binding agents including lectins, toxins, and viruses were incubated with the glycan suspension array. In addition to characterizing carbohydrate binding preference, simultaneous strain typing of influenza virus was performed using additional multiplex microspheres conjugated to antibodies specific for influenza A subtypes. Inactivated virus was incubated with the microspheres, detected using fluorescence-labeled anti-influenza virus antibodies, and measured by flow cytometry.Biotinylated carbohydrates were successfully captured by neutravidin conjugated microspheres as observed by specific binding of fluorescently labeled lectins SNA-I and MAA and Cholera toxin B (CTB) subunit. Antibodies were also conjugated to microspheres allowing for multiplex analysis of influenza virus sub-type and receptor specificity of human influenza A subtype H1N1 and avian influenza A subtype H5N1. Each subtype of influenza virus bound only to those microspheres displaying carbohydrates with its specific receptor and anti-influenza A antibody. These results have been confirmed previously by other methods, including hemagglutination and glycan microarray.This approach provides improved control over carbohydrate surface density, increased throughput for the analysis of many samples and conditions, reduced sample volumes, and better quantification.

Zinc stabilizes somatic cell membranes and DNA, inhibits respiration, is present in high concentrations in the male reproductive tract, and may stabilize sperm during storage and ejaculation. Zinc removal from sperm may be necessary to prepare sperm for fertilization (capacitation). Incubation with Zn 2+ chelators, e.g., D-penicillamine, can capacitate hamster sperm (Andrews and Bavister, Gamete Res 1989; 23:159-70). In the present study, the Zn2+-specific fluorochrome N-(6-methoxy-8-quinolyl)-p-toluenesulfonamide (TSQ) and the vital stain propidium iodide were used to assess the zinc content of live hamster sperm with flow cytometry before and after capacitation. Capacitation was monitored with a salt-stored zona pellucida penetration assay or the occurrence of spontaneous or induced (with lysophosphatidylcholine) acrosome reactions. The effect of added zinc on sperm capacitation was also evaluated. Image Analysis was used to determine the subcellular location of zinc (TSQ fluorescence) and atomic absorption to determine whether the total zinc content of sperm changes during capacitation. Sperm incubated under non-capacitating conditions had high TSQ fluorescence and could not penetrate zonae pellucidae. Sperm incubated under capacitating conditions (plus BSA or D-penicillamine) were zinc-depleted (low fluorescence) and penetrated 90% or 78% of zonae, respectively. Image analysis showed a significant reduction in zinc in the acrosomal region during capacitation with BSA, but this did not correlate with the occurrence of spontaneous acrosome reactions. The atomic absorption data showed that the total zinc content of sperm was reduced by 44% or 40% when sperm were incubated under capacitating conditions (BSA or D-penicillamine, respectively). Zona pellucida penetration was completely inhibited when zinc was present throughout the capacitation period but not when it was added at the end of incubation. These data indicate that removal of zinc from hamster sperm is correlated with capacitation and may play a key regulatory role in this process.

The effects of dilauroylphosphatidylcholine (PC12) on ram epididymal sperm motility, acrosome reaction (AR) induction, plasma membrane permeability, mitochondrial function, and sperm penetration into zona-free hamster eggs were determined. PC12 (50 microM) induced cell motility in caput and cauda sperm, as measured by subjective estimation and automated motility analysis. Motion parameters of treated caput sperm approached those of control ejaculated sperm. Flow cytometric analysis revealed that membrane permeability to propidium iodide and mitochondrial uptake of rhodamine 123 changed during epididymal transit. PC12 induced the AR in sperm from all epididymal regions relative to control incubated sperm (caput 17% vs. control 8%; corpus 29% vs. control 13%; proximal cauda 48% vs. control 4%; distal cauda 51% vs. control 9%). After PC12 treatment, egg penetration by sperm was increased for sperm from the corpus (corpus 7% vs. control 0%) and cauda (proximal 48% vs. control 0%; distal 51% vs. control 0%), but not for caput sperm (caput 0% vs. control 0%). These studies establish that some sperm in each region of the epididymis possess the capacity for movement and the AR. Caput sperm, however, were unique in that they could not penetrate eggs. Additional maturational changes must occur in the caput and/or corpus epididymidis before penetration capacity can be expressed.

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. Keywords: flow cytometry, proteomic, genomic, quantitation, molecular

This unit describes an extrinsic staining protocol using the amine-reactive CBQCA dye to measure the amount of protein on the surface of a microsphere. This approach is novel in that it allows microspheres bearing proteins without known binding partners to be accurately quantified on a flow cytometer. Keywords: flow cytometry; surface chemistry; protein; microspheres

In this article, I have given an overview of the application of microparticle-based flow cytometry to high resolution molecular analysis. The applications described range from kinetic analysis of interaction mechanisms to highly sensitive and parallel screening assays. Some of these types of applications are now widely used, supported by commercial kits and reagents. Others are being integrated into high throughput screening environments for disease marker and drug discovery. Current research in new optical encoding schemes for microparticles, new detection schemes for fluorescence and other optical signals, and microparticle fabrication and surface chemistries promise to lead to even more flexible and robust assay systems for molecular analysis

The role of nitric oxide (NO) in the genesis of cerebral malaria is controversial. Most investigators propose that the unfortunate consequence of the high concentrations of NO produced to kill the parasite is the development of cerebral malaria. Here we have tested this high NO bioavailability hypothesis in the setting of experimental cerebral malaria (ECM), but find instead that low NO bioavailability contributes to the genesis of ECM. Specifically, mice deficient in vascular NO synthase showed parasitemia and mortality similar to that observed in control mice. Exogenous NO did not affect parasitemia but provided marked protection against ECM; in fact, mice treated with exogenous NO were clinically indistinguishable from uninfected mice at a stage when control infected mice were moribund. Administration of exogenous NO restored NO-mediated signaling in the brain, decreased proinflammatory biomarkers in the blood, and markedly reduced vascular leak and petechial hemorrhage into the brain. Low NO bioavailability in the vasculature during ECM was caused in part by an increase in NO-scavenging free hemoglobin in the blood, by hypoargininemia, and by low blood and erythrocyte nitrite concentrations. Exogenous NO inactivated NO-scavenging free hemoglobin in the plasma and restored nitrite to concentrations observed in uninfected mice. We therefore conclude that low rather than high NO bioavailability contributes to the genesis of ECM.

Background: Proteases regulate many biological pathways in humans and are components of several bacterial toxins. Protease studies and development of protease inhibitors do not follow a single established methodology and are mostly protease specific. Methods: We have created recombinant fusion proteins consisting of a biotinylated attachment sequence linked to a GFP via a protease cleavage site to develop a multiplexable microsphere-based protease assay system. Using the proteases lethal factor and factor Xa, we performed kinetic experiments to determine optimal conditions for inhibitor screens and detect known inhibitors using the HyperCyt® flow cytometry system. Results: We have demonstrated specific cleavage of lethal factor and factor Xa substrates, optimized screening conditions for these substrates, shown specific inhibition of the proteases, and demonstrated high throughput detection of these inhibitors. Conclusions: The assay developed here is adaptable to any site-specific protease, compatible with high throughput flow cytometry systems, and multiplexable. Coupled with flow cytometry, which provides continuous time resolution and intrinsic resolution of free vs. bound fluorophores, this assay will be useful for high throughput screening of protease inhibitors in general and could simplify assays designed to determine protease mechanism. © 2006 International Society for Analytical Cytology

A unifying hypothesis for the genesis of cerebral malaria proposes that parasite antigens (released by replication in blood, surface molecules on parasitized erythrocytes, or merozoites) activate platelets that, in turn, contribute to the activation of the inflammatory response and increased levels of endothelial cell adhesion molecules (eCAMs). Increased levels of eCAMs result in further parasitized-erythrocyte sequestration and marked local inflammation that might disrupt the brain microvasculature, which cannot be repaired by the hemostasis system because of its procoagulant state. Disruption of the brain microvasculature can result in vascular leak and/or hemorrhaging into the brain; similar processes can occur in other vascular beds, including the lung. The blockage of functional capillaries by parasitized and/or unparasitized erythrocytes with decreased deformability or rosettes is also a key interaction between hemostasis and mechanical obstruction leading to pathogenesis. The events resulting in the development of cerebral malaria complications are multi-factorial, encompassing a dynamic interaction between three processes, thereby explaining the complexity of this deadly syndrome.

Microsphere-based immunoassay by flow cytometry has gained popularity lately in protein detection and infectious disease diagnosis due to its capacity for multiplexed analysis and simple assay format. Here, we demonstrated the power of microsphere-based immunoassay for high-sensitivity detection and accurate differentiation of influenza viruses. The effects of sample volume and bead number on the assay sensitivity of viral antigen detection were studied. Compared to enzyme-linked immunosorbent assays, flow-based bead assays provided approximately 10-fold lower detection limit for viral particle detection and performed similarly for recombinant viral hemagglutinin protein detection. A four-plexed assay for influenza virus typing and influenza B virus sublineage characterization was developed to demonstrate the potential for multiplexed viral antigen detection and differentiation.

Experimental malarial thrombocytopenia can reach life-threatening levels and is believed to be due to Abs targeting platelets for destruction by the reticuloendothelial system. However, we report that Abs account for at most 15% of platelet destruction as Plasmodium berghei-infected B cell-deficient mice exhibited profound thrombocytopenia (83%) as did C57BL/6 controls (98%). Further, no significant increase in Abs bound to intact platelets was observed during infection. P. berghei infection can enhance the activity of anti-platelet Abs as indicated by a significantly (p < 0.005) increased thrombocytopenia on day 4 of infection in mice that were administered a low dose anti-CD41 mAb compared with rat IgG1-injected controls. RAG1−/− and CD4- plus CD8-deficient mice were markedly protected from thrombocytopenia (p < 0.005) and malarial pathogenesis. CD8- or TCRγδ-deficient mice were not protected from thrombocytopenia and CD4-deficient mice were modestly protected. RAG1−/− mice exhibited significantly (p < 0.05) lower levels of plasma TNF, IFN-γ, and IL-12 during infection. IFNγ−/− and IL-12−/− mice exhibited increased survival but similar thrombocytopenia to C57BL/6 controls. Collectively, these data indicate that thrombocytopenia is necessary but not sufficient for malarial pathogenesis and Abs are not the major contributors to malarial thrombocytopenia. Rather, we propose that both CD4+ and CD8+ T cell populations play key roles in malarial thrombocytopenia; a complex bidirectional interaction between cell-mediated immunity and platelets exists during experimental severe malaria that regulates both responses.

The many proteins and nucleic acids encoded in the genome predominantly perform their functions as macromolecular assemblies. In fact, modern biomedical research often targets the interactions of individual molecules of these assemblies, usually by disrupting or enhancing specific contacts, to provide treatment for many different diseases. Therefore, efficient pharmaceutical design requires knowledge of how macromolecular assemblies are built and function. To achieve this goal, sensitive and quantitative tools are essential. This chapter will discuss the use of flow cytometry as a general platform for sensitive measurement and quantification of molecular assemblies. First, this chapter will introduce general methods for analysis of molecular interactions along with a comparison of flow cytometry with these methods. Second, an overview of current flow cytometry instrumentation, assay technologies, and applications in molecular assembly analysis will be given. Third, the implementation of the above approaches in molecular assembly will be discussed. Finally, potential future directions of flow cytometry in molecular assembly analysis will be explored. At present, the analysis of macromolecular assemblies is performed by a wide variety of techniques that are chosen for the target molecules under study (proteins, DNA, lipids, etc.), the type of measurement required (kinetic or equilibrium), and whether the assembly of interest needs to be studied in vivo or in vitro. This continuum of techniques can be divided into the heterogeneous assays, which require a separation step to resolve products from reactants, and homogeneous assays, which can measure interactions without a separation step. Heterogeneous assays, in general, use radioisotopes, which are not perturbing; offer excellent sensitivity; and provide accurate quantification. The products are quantified after a separation step such as gel filtration, gel electrophoresis, or centrifugation. Rapid quench methods can provide subsecond kinetic resolution; however, the added separation steps are tedious and make collection of kinetic time courses difficult, as each time point must be separated and measured individually. Furthermore, in the time it takes the separation to occur, the interaction of interest can dissociate, which is a problem specific to low-affinity assemblies. Nonetheless, by using rapid chemical quench techniques, reaction times as short as a few milliseconds can be observed. Homogenous assays can be separated into solution- or surface-based assays. Solutionbased assays measure an optical signal generated by the assembly to quantify an interaction. High component concentrations (micromolar) allow changes in intrinsic molecular properties, such as protein fluorescence or circular dichroism, to be used to study molecular assemblies. For greater sensitivity (nanomole component concentrations), resonance energy transfer or polarization assays using exogenous fluorescent labels can be used. In combination with stopped-flow spectroscopy methodologies, solution-based assays allow reactions to monitored in a continuous fashion with submillisecond dead times.

Current Protocols in Cytometry (CPC), published in affiliation with the International Society for Analytical Cytology, features carefully edited flow and image cytometry methods provided by leading laboratories from around the world. All methods included in the one-volume looseleaf manual are rigorously tested and proven before being selected for CPC. Carefully edited, step-by-step protocols replete with material lists, expert commentaries, and safety and troubleshooting tips ensure that you can duplicate the experimental results in your own laboratory. This publication also includes extensive coverage of cytometry instrumentation, safety and quality control, and data processing and analysis. Quarterly updates, which are filed into the looseleaf, keep the set current with the latest developments in cytometry methods. The initial purchase includes one year of updates and then subscribers may renew their annual subscriptions. Current Protocols publishes a family of laboratory manuals for bioscientists, including Molecular Biology, Immunology, Human Genetics, Protein Science, Cell Biology, Neuroscience, Pharmacology, and Toxicology.

This study is concerned with the application of advanced multimedia technology to the development of a programme aimed at raising awareness of information and communications technology (ICT) amongst health professionals in Ireland. The programme is delivered in the form of a symposium supplemented by a multimedia CD and associated web site. It examines how ICT can be used effectively in healthcare across all sectors - primary, secondary and tertiary - with a strong emphasis on supporting shared care. The aim is to empower users to make informed technological choices and to actively participate in the exploitation of ICT in the health sector. The programme was successfully completed and delivered to over 2300 health professionals across Ireland and follow-up activities include the active encouragement of leaders and champions within the sector. This will be supported by interactive web-based education and training material focused on specialised topics of particular interest within the broader context of continuing medical education (CME).

The analysis of macromolecular interactions is an essential element of biomedical research. Flow cytometry is uniquely capable of making sensitive and quantitative measurements of molecular interactions. These measurements can be made in real time with subsecond kinetic resolution using purified biomolecules or living cells. Combined with automated sample handling, these features make flow cytometry a versatile and robust technology for the analysis of molecular interactions.

Flow cytometry is uniquely capable of making sensitive and quantitative multiparameter fluorescence measurements with discrimination of free from particle-bound fluorophore. Recent advances in mixing and sample delivery have extended these capabilities into the sub-second time domain. Access to these time scales has enabled us to use flow cytometry to measure molecular interactions. Using the general approach of immobilizing one molecule on a microsphere and fluorescently labeling another, we have been able to make real-time measurements of ligand-receptor and enzyme-substrate interactions involving proteins, nucleic acids, carbohydrates, and lipids. We are developing schemes for immobilizing active biological molecules in defined and homogeneous orientations relative to the surface. We are also developing approaches for homogeneous fluorescent labeling of active biomolecules and calibration schemes for quantitative measurements by flow cytometry. We will present several examples of applications of this new technology, including DNA- and protein-protein interactions, nucleic acid hybridization, and interactions on artificial membrane surfaces. These approaches should have wide applications for mechanistic analysis, diagnostics, and drug development.