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Current Protocols in Cytometry

Jared M Eller, Melissa L Stewart, Alexandria J Slepian, Sheila Markwardt, Jack Wiedrick, Michael S Cohen, Richard H Goodman, Xiaolu A Cambronne
Flow cytometry approaches combined with a genetically encoded targeted fluorescent biosensor are used to determine the subcellular compartmental availability of the oxidized form of nicotinamide adenine dinucleotide (NAD+ ). The availability of free NAD+ can affect the activities of NAD+ -consuming enzymes such as sirtuin, PARP/ARTD, and cyclic ADPR-hydrolase family members. Many methods for measuring the NAD+ available to these enzymes are limited because they cannot determine free NAD+ as it exists in various subcellular compartments distinctly from bound NAD+ or NADH...
December 17, 2018: Current Protocols in Cytometry
Martin Büscher
The term flow cytometry, used since the seventies, describes a technology employed mainly in biology and medicine to measure and classify suspended particles, e.g., cells or microspheres. Measurable cell parameters include: geometric properties, such as cell size (diameter, surface area, volume); physiological properties (membrane potential, integrity, vitality); and quantities of DNA, RNA, cytokines, surface antigens, nuclear antigens, enzymes, and proteins. © 2018 by John Wiley & Sons, Inc.
January 2019: Current Protocols in Cytometry
Nithianandan Selliah, Steven Eck, Cherie Green, Teri Oldaker, Jennifer Stewart, Alessandra Vitaliti, Virginia Litwin
Analytical method validation provides a means to ensure that data are credible and reproducible. This unit will provide a brief introduction to analytical method validation as applied to cellular analysis by flow cytometry. In addition, the unit will provide practical procedures for three different types of validation. The first is a limited validation protocol that is applicable for research settings and non-regulated laboratories. The second is validation protocol that presents the minimum validation requirements in regulated laboratories...
January 2019: Current Protocols in Cytometry
Piyusha S Gade, Anne M Robertson, Chih-Yuan Chuang
Multiphoton-induced second-harmonic generation and two-photon excitation enable imaging of collagen and elastin fibers at micron-level resolution to depths of hundreds of microns, without the use of exogenous stains. These attributes can be leveraged for quantitative analysis of the 3D architecture of collagen and elastin fibers within intact, soft tissue specimens such as the artery and bladder wall. This architecture influences the function of intramural cells and also plays a primary role in determining tissue passive mechanical properties...
October 31, 2018: Current Protocols in Cytometry
Amy Galvin, Meredith Weglarz, Kat Folz-Donahue, Maris Handley, Misa Baum, Michael Mazzola, Hannah Litwa, David T Scadden, Lev Silberstein
Maintenance of hematopoietic stem cell (HSC) quiescence is critical for self-renewal and differentiation into mature lineages. Therefore, the ability to reliably detect abnormal HSC cycling is essential for experiments that seek to investigate abnormalities of HSC function. The ability to reproducibly evaluate cell cycle status in a rare cell subset requires careful optimization of multiple parameters during cell preparation and sample processing. Here, we describe a method where data acquisition parameters and fluorochrome combination for long-term HSC staining have been specifically designed for concurrent use with DAPI and Ki-67 antibodies...
October 18, 2018: Current Protocols in Cytometry
Sindhu Cherian, Maryalice Stetler-Stevenson
The use of targeted therapy is growing in the setting of hematopoietic neoplasms. Flow cytometry is a cornerstone of residual disease monitoring post therapy in this group of malignancies. Often, there is overlap between antigens targeted by immunotherapies and gating reagents utilized for population identification by flow cytometry. Such overlap can render a previously excellent gating reagent inadequate for disease detection. Recently, several anti-CD19 T cell-engaging immunotherapeutic agents and an anti-CD22 immunotoxin have been FDA approved for use in B lymphoblastic leukemia (B-LL), with an anti-CD22 T cell-engaging agent in development...
October 2018: Current Protocols in Cytometry
Leonie de Rond, Frank A W Coumans, Rienk Nieuwland, Ton G van Leeuwen, Edwin van der Pol
Flow cytometry is commonly used to investigate the potential for extracellular vesicles (EVs) to be biomarkers of disease. A typical flow cytometer detects fluorescence and scatter intensities of single EVs in arbitrary units. These arbitrary units complicate data interpretation and data comparison between different flow cytometers. For example, comparison of detected EV concentrations requires knowledge of the detectable EV sizes. Using Mie theory and knowledge of the optical configuration of the flow cytometer, EV size can be derived from the scatter intensity for a given EV refractive index...
October 2018: Current Protocols in Cytometry
Michael Muntifering, Daniel Castranova, Gregory A Gibson, Evan Meyer, Matthew Kofron, Alan M Watson
Biologic tissues are generally opaque due to optical properties that result in scattering and absorption of light. Preparation of tissues for optical microscopy often involves sectioning to a thickness of 50-100 µm, the practical limits of light penetration and recovery. A researcher who wishes to image a whole tissue must acquire potentially hundreds of individual sections before rendering them into a three-dimensional volume. Clearing removes strongly light-scattering and light-absorbing components of a tissue and equalizes the refractive index of the imaging medium to that of the tissue...
October 2018: Current Protocols in Cytometry
Gérald Grégori, Michel Denis, Sergio Sgorbati, Sandra Citterio
In aquatic environments, free heterotrophic bacteria play an extremely important role due to their high biomass, wide panel of metabolisms, and ubiquity, as well as the toxicity of certain species. This unit presents a nucleic-acid double-staining protocol (NADS) for flow cytometry that can distinguish fractions of viable, damaged, or membrane-compromised cells within the free-bacterial community. The NADS protocol is based on the simultaneous utilization of two nucleic acid stains-membrane-permeant SYBR Green and membrane-impermeant propidium iodide (PI)...
July 2018: Current Protocols in Cytometry
Claire E J Cheetham
Multiphoton intravital calcium imaging is a powerful technique that enables high-resolution longitudinal monitoring of cellular and subcellular activity hundreds of microns deep in the living organism. This unit addresses the application of 2-photon microscopy to imaging of genetically encoded calcium indicators (GECIs) in the mouse brain. The protocols in this unit enable real-time intravital imaging of intracellular calcium concentration simultaneously in hundreds of neurons, or at the resolution of single synapses, as mice respond to sensory stimuli or perform behavioral tasks...
July 2018: Current Protocols in Cytometry
Joseph R Daniele, Kartoosh Heydari, Andrew Dillin
Healthy, functional mitochondria are central to many cellular and physiological phenomena, including aging, metabolism, and stress resistance. A key feature of healthy mitochondria is a high membrane potential (Δψ) or charge differential (i.e., proton gradient) between the matrix and inner mitochondrial membrane. Mitochondrial Δψ has been extensively characterized via flow cytometry of intact cells, which measures the average membrane potential within a cell. However, the characteristics of individual mitochondria differ dramatically even within a single cell, and thus interrogation of mitochondrial features at the organelle level is necessary to better understand and accurately measure heterogeneity...
July 2018: Current Protocols in Cytometry
Peter O Bayguinov, Dennis M Oakley, Chien-Cheng Shih, Daniel J Geanon, Matthew S Joens, James A J Fitzpatrick
Since its commercialization in the late 1980's, confocal laser scanning microscopy (CLSM) has since become one of the most prevalent fluorescence microscopy techniques for three-dimensional structural studies of biological cells and tissues. The flexibility of the approach has enabled its application in a diverse array of studies, from the fast imaging of dynamic processes in living cells, to meticulous morphological analyses of tissues, and co-localization of protein expression patterns. In this chapter, we introduce the principles of confocal microscopy and discuss how the approach has become a mainstay in the biological sciences...
July 2018: Current Protocols in Cytometry
J Paul Robinson
Although in recent years flow cytometry has become commonplace in hematology and immunology laboratories, application of the technology to microbiology remains largely unrealized. This overview presents the historical background, discusses applications in various areas of the field, and speculates on the directions of future developments. The availability of high-quality methods should be a prime factor in convincing microbiologists that flow cytometry may have certain advantages over traditional methods and that it does indeed have much to contribute to microbiology...
April 2018: Current Protocols in Cytometry
Michael D Ward, Gregory Kaduchak
Acoustic cytometry uses radiation pressure forces instead of or in addition to hydrodynamic focusing to position cells or particles in a flowing stream for analysis. Commercial implementations to date combine both hydrodynamic and acoustic focusing together to enable high precision analysis of a broad dynamic range of volumetric sample input rates up to an order of magnitude higher than is practical with hydrodynamic focus alone. This capability allows great flexibility in reducing assay time or modifying or eliminating concentration requirements or concentration steps in sample preparation protocols...
April 2018: Current Protocols in Cytometry
Helene Barcelo, Jessica Faul, Eileen Crimmins, Bharat Thyagarajan
Large population-based cohort studies, through their prospective collection of a broad range of health information, represent an invaluable resource for novel insights into the pathogenesis of human diseases. Collection and cryopreservation of viable cells from blood samples is becoming increasingly common in large cohorts as these cells are a valuable resource for immunophenotyping and functional studies. The cryopreservation of peripheral blood mononuclear cells (PBMCs), thawing, and immunophenotyping protocols used to immunophenotype 9938 participants in the Health and Retirement Study (HRS) are described...
April 2018: Current Protocols in Cytometry
James C S Wood
A number of methods have been developed to compare single parameter histograms. Some perform a channel-by-channel analysis and others give a single statistic about how the histograms may or may not differ. If they do differ, then the significance of the difference or confidence limit is usually provided. The specific location(s) for the greatest deviations may also be given. Some are more effective at resolving severely overlapping populations and others work poorly when there is any significant overlap. Each method makes certain assumptions about the data...
January 18, 2018: Current Protocols in Cytometry
Kirsten E Diggins, Jocelyn S Gandelman, Caroline E Roe, Jonathan M Irish
Multiplexed single-cell experimental techniques like mass cytometry measure 40 or more features and enable deep characterization of well-known and novel cell populations. However, traditional data analysis techniques rely extensively on human experts or prior knowledge, and novel machine learning algorithms may generate unexpected population groupings. Marker enrichment modeling (MEM) creates quantitative identity labels based on features enriched in a population relative to a reference. While developed for cell type analysis, MEM labels can be generated for a wide range of multidimensional data types, and MEM works effectively with output from expert analysis and diverse machine learning algorithms...
January 18, 2018: Current Protocols in Cytometry
Howard M Shapiro, William G Telford
Lasers are the principal light sources for flow cytometers. Virtually all cytometers are equipped with at least one (and often many more) lasers. This unit covers the various types of lasers available and the qualities that make them suitable or unsuitable for use in flow cytometers. Also included is a discussion of future directions, particularly in the area of tunable laser development. Practical tips are provided for building multilaser cytometer systems. © 2018 by John Wiley & Sons, Inc.
January 18, 2018: Current Protocols in Cytometry
Callen T Wallace, Morgan Jessup, Tytus Bernas, Karina A Peña, Michael J Calderon, Patricia A Loughran
Modern digital microscopy combines the equipment of classical light microscopy with a computerized imaging system. The technique comprises image formation by optics, image registration by a camera, and saving of image data in a computer file. This chapter describes limitations that are particular to each of these processes, including optical resolution, efficiency of image registration, characteristics of image file formats, and data management. Further suggestions are given which serve, in turn, to help construct a set of guidelines aimed at optimization of digital microscopic imaging...
January 18, 2018: Current Protocols in Cytometry
Kenneth W Dunn, Timothy A Sutton, Ruben M Sandoval
Intravital microscopy, microscopy of living animals, is a powerful research technique that combines the resolution and sensitivity found in microscopic studies of cultured cells with the relevance and systemic influences of cells in the context of the intact animal. The power of intravital microscopy has recently been extended with the development of multiphoton fluorescence microscopy systems capable of collecting optical sections from deep within the kidney at subcellular resolution, supporting high-resolution characterizations of the structure and function of glomeruli, tubules, and vasculature in the living kidney...
January 18, 2018: Current Protocols in Cytometry
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