Name: nanoparticle tracking analysis for the quantification and size determination of extracellular vesicles
Uploaded: 2021-03-28T14:00:00
Description: Watch this Scientific Journal Video about Nanoparticle Tracking Analysis for the Quantification and Size Determination of Extracellular Vesicles at JoVE.com

This work was supported by the National Institutes of Health (ES030973-01A1, R01ES025225, R01DK066525, P30DK026687, P30DK063608). We acknowledge Jeffrey Bodycomb, Ph.D. of HORIBA Instruments Incorporated for his help calibrating the instrument.

All work with these samples was performed in compliance with Institutional Animal Care and Use Committee and Institutional Review Board guidelines. A schematic overview of the NTA method is depicted in Figure 2.
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/62447/62447fig02.jpg" /> 
Figure 2: Overview of NTA method using the particle tracking instrument. The sample is...

<ol>
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Here, we demonstrate a protocol for NTA of EVs to measure the size distribution of a wide range of particle sizes simultaneously and measure total EV concentration in a polydisperse sample. In this study, mouse perigonadal adipose tissue and human plasma were used as the source of EVs. However, EVs isolated from other tissues or biological fluids such as serum, urine, saliva, breast milk, amniotic fluid, and cell culture supernatant may also be used for NTA. Measurements of polystyrene bead standards ensured that the ins...

Extracellular vesicles (EVs) are small (0.03-2 &#181;m) membrane-bound vesicles secreted by nearly all cell types1. They are often referred to as &#34;exosomes,&#34; &#34;microvesicles,&#34; or &#34;apoptotic bodies&#34; depending on their mechanism of release and size2. While it was initially thought that EVs were simply a means of eliminating waste from the cell to maintain homeostasis3, we now know that they can also participate in intercellular communication via transfer of molecular material - including DNA, RNA (mRNA, microRNA), lipids, and proteins4,5 - and that they are important regulators of normal physiology as well as pathological processes1,5,6,7,8.
There are many different methods to isolate and quantify EVs, which have been described elsewhere9,10,11,12. The isolation protocol used as well as the source of EVs can greatly impact EV yield and purity. Even differential centrifugation, long considered the &#34;gold standard&#34; approach for exosome isolation, can be subject to substantial variability subsequently impacting the EV population obtained and downstream analyses13. Thus, the various different methodologies for EV isolation and quantification make it difficult to compare, reproduce, and interpret results of experiments reported in the literature14.&#160;Furthermore, EV release can be regulated by cellular conditions or various external factors. It has been suggested that EVs play a role in maintaining cellular homeostasis by protecting cells against intracellular stress15, as several studies have shown that cellular stress stimulates EV secretion. For example, increased EV release has been reported after cellular exposure to hypoxia, endoplasmic reticulum stress, oxidative stress, mechanical stress, cigarette smoke extract, and particulate matter air pollution16,17,18,19,20,21,22. EV release has also been shown to be modified in vivo; mice subjected to a high fat diet or fasting for sixteen hours released more adipocyte EVs23. To investigate whether a specific treatment or condition alters EV release, the number of EVs must be accurately determined. Assessment of the EV size distribution may also indicate the predominant subcellular origin of EVs (e.g., fusion of late endosomes/multivesicular bodies with the plasma membrane vs. budding of the plasma membrane)24. Thus, there is a need for robust methods to accurately measure the total concentration and the size distribution of the EV prep being studied.
A rapid and highly sensitive method for the visualization and characterization of EVs in solution is nanoparticle tracking analysis (NTA). A detailed explanation of the principles of this method and comparison with alternative methods for assessment of EV size and concentration have been described previously25,26,27,28. Briefly, during NTA measurement, EVs are visualized by the light scattered when they are irradiated with a laser beam. The scattered light is focused by a microscope onto a camera which records the particle movement. The NTA software tracks the random thermal motion of each particle, known as Brownian motion, to determine the diffusion coefficient which is used to calculate the size of each particle using the Stokes-Einstein equation. NTA was first applied to measurement of EVs in a biological sample in 201125. Until recently, there were only two mainstream companies offering commercial NTA instruments29 until the introduction of the ViewSizer 3000 (hereafter referred to as the particle tracking instrument) which uses a combination of novel hardware and software solutions to overcome significant limitations of other NTA techniques.
The particle tracking instrument characterizes nanoparticles in liquid samples by analyzing their Brownian motion and characterizes larger micron-sized particles by analyzing gravitational settling. This instrument&#39;s unique optical system, which includes multispectral illumination with three laser light sources (at 450 nm, 520 nm, and 635 nm), allows researchers to analyze a wide range of particle sizes (e.g., exosomes, microvesicles) simultaneously. A schematic of the instrument setup is shown in Figure 1.
Here, we demonstrate how to perform particle size distribution and concentration measurements of isolated mouse and human EVs using a novel NTA instrument.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/62447/62447fig01.jpg" /> 
Figure 1: Particle tracking instrument optical system. The NTA instrument illuminates particles using three lasers with the following wavelengths: 450 nm, 520 nm, 635 nm. Video recording of the scattered light from individual particles is detected and tracked by a digital video camera oriented 90&#176; from the cuvette. <a href="https://www.jove.com/files/ftp_upload/62447/62447fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1X dPBS</td>
			<td>VWR</td>
			<td>02-0119-1000</td>
			<td>To dilute samples</td>
		</tr>
		<tr>
			<td>100 nm bead standard</td>
			<td>Thermo Scientific</td>
			<td>3100A</td>
			<td>To test ViewSizer 3000 calibration</td>
		</tr>
		<tr>
			<td>400 nm bead standard</td>
			<td>Thermo Scientific</td>
			<td>3400A</td>
			<td>To test ViewSizer 3000 calibration</td>
		</tr>
		<tr>
			<td>Centrifugal Filter Unit</td>
			<td>Amicon</td>
			<td>UFC901024</td>
			<td>To filter PBS diluent</td>
		</tr>
		<tr>
			<td>Collection tubes, 2 mL</td>
			<td>Qiagen</td>
			<td>19201</td>
			<td>For isolation of human plasma extracellular vesicles</td>
		</tr>
		<tr>
			<td>Compressed air duster</td>
			<td>DustOff</td>
			<td>DPSJB-12</td>
			<td>To clean cuvettes</td>
		</tr>
		<tr>
			<td>Cuvette insert</td>
			<td>HORIBA Scientific</td>
			<td>-</td>
			<td>Provided with purchase of ViewSizer 3000</td>
		</tr>
		<tr>
			<td>Cuvette jig</td>
			<td>HORIBA Scientific</td>
			<td>-</td>
			<td>To align magnetic stir bar while placing inserts inside cuvette; Provided with purchase of ViewSizer 3000</td>
		</tr>
		<tr>
			<td>De-ionized water</td>
			<td>VWR</td>
			<td>02-0201-1000</td>
			<td>To clean cuvettes</td>
		</tr>
		<tr>
			<td>Desktop computer with monitor, keyboard, mouse, and all necessary cables</td>
			<td>Dell</td>
			<td>-</td>
			<td>Provided with purchase of ViewSizer 3000</td>
		</tr>
		<tr>
			<td>Ethanol (70-100%)</td>
			<td>Millipore Sigma</td>
			<td>-</td>
			<td>To clean cuvettes</td>
		</tr>
		<tr>
			<td>ExoQuick ULTRA</td>
			<td>System Biosciences</td>
			<td>EQULTRA-20A-1</td>
			<td>For isolation of human plasma extracellular vesicles</td>
		</tr>
		<tr>
			<td>Glass scintillation vials with lids</td>
			<td>Thermo Scientific</td>
			<td>B780020</td>
			<td>To clean cuvettes</td>
		</tr>
		<tr>
			<td>&#34;Hook&#34; tool</td>
			<td>Excelta</td>
			<td>-</td>
			<td>Provided with purchase of ViewSizer 3000</td>
		</tr>
		<tr>
			<td>Lint-free microfiber cloth</td>
			<td>Texwipe</td>
			<td>TX629</td>
			<td>To clean cuvettes and cover work surface</td>
		</tr>
		<tr>
			<td>Microcentrifuge tubes, 2 mL</td>
			<td>Eppendorf</td>
			<td>22363344</td>
			<td>For isolation of human plasma extracellular vesicles</td>
		</tr>
		<tr>
			<td>Stir bar</td>
			<td>Sp Scienceware</td>
			<td>F37119-0005</td>
			<td></td>
		</tr>
		<tr>
			<td>Suprasil Quartz cuvette with cap</td>
			<td>Agilent Technologies</td>
			<td>AG1000-0544</td>
			<td>Initially provided with purchase of ViewSizer 3000</td>
		</tr>
		<tr>
			<td>ViewSizer 3000</td>
			<td>HORIBA Scientific</td>
			<td>-</td>
			<td>Nanoparticle tracking instrument</td>
		</tr>
	</tbody>
</table>

nanoparticle tracking analysis for the quantification and size determination of extracellular vesicles

The physiological and pathophysiological roles of extracellular vesicles (EVs) have become increasingly recognized, making the EV field a quickly evolving area of research. There are many different methods for EV isolation, each with distinct advantages and disadvantages that affect the downstream yield and purity of EVs. Thus, characterizing the EV prep isolated from a given source by a chosen method is important for interpretation of downstream results and comparison of results across laboratories. Various methods exist for determining the size and quantity of EVs, which can be altered by disease states or in response to external conditions. Nanoparticle tracking analysis (NTA) is one of the prominent technologies used for high-throughput analysis of individual EVs. Here, we present a detailed protocol for quantification and size determination of EVs isolated from mouse perigonadal adipose tissue and human plasma using a breakthrough technology for NTA representing major advances in the field. The results demonstrate that this method can deliver reproducible and valid total particle concentration and size distribution data for EVs isolated from different sources using different methods, as confirmed by transmission electron microscopy. The adaptation of this instrument for NTA will address the need for standardization in NTA methods to increase rigor and reproducibility in EV research.

Before this demonstration, the calibration of the instrument was first tested to ensure the validity of the acquired data by measuring the size distribution of polystyrene bead standards. We tested the size distribution of 100 nm and 400 nm beads using the default recording parameters and the processing settings recommended in this protocol (Figure 8).
For the 100 nm polystyrene bead standard, a concentration of 4.205 x 107 particles/mL was measured. Th...

Watch this Scientific Journal Video about Nanoparticle Tracking Analysis for the Quantification and Size Determination of Extracellular Vesicles at JoVE.com

Nanoparticle Tracking Analysis for the Quantification and Size Determination of Extracellular Vesicles

We demonstrate how to use a novel nanoparticle tracking analysis instrument to estimate the size distribution and total particle concentration of extracellular vesicles isolated from mouse perigonadal adipose tissue and human plasma.

The physiological and pathophysiological roles of extracellular vesicles (EVs) have become increasingly recognized, making the EV field a quickly evolving ...

NTA results are very prone to operator bias. This protocol demonstrates the effects of altered NTA parameters on obtained results. A standardized method will help increase rigor and reproducibility in NTA analysis.Analyzing the sample in a cuvette allows for a statistically random sample to be captured in each video. This results in more reproducible data and the visualization of particles over a wide range of sizes. As getting a sample in the recommended particle concentration range can be difficult, be sure to perform a serial dilution to identify the ideal dilution factor.Demonstrating the procedure will be Kungheng Cai, a PhD student from Anthony Ferrante's laboratory. To prepare cuvette for nanoparticle tracking analysis, cover the workspace with a lint-free material to prevent fibers from entering the cuvettes. Wearing gloves, place a cuvette containing a stir bar onto the magnetic cuvette jig.Use a hook tool to place the insert into the cuvette with the notch of the insert visible at the front of the cuvette. Use a pipette to slowly add 400 to 500 microliters of purified extracellular vesicles onto the cuvette through the hole in the insert and mix the sample by gently pipetting without introducing air bubbles, then cap the cuvette, tapping out bubbles as necessary and use a lint-free cloth to wipe the outside surface of the cuvette. To analyze the particle concentration of the diluent or a sample, turn on the computer workstation and instrument and start the particle tracking analysis program.When prompted, click NTA and open the recording tab. Follow the onscreen instructions to fill out all the necessary sample information. For EV tracking analysis, set the diluent to PBS.The salinity will auto-populate to 9%To obtain the diluent or sample particle concentration, open the instrument lid and remove the protective cap covering where the cuvette will be placed. Load the cuvette into the instrument in the correct orientation with the notch of the insert facing the camera and replace the cap and instrument lid. Click the streaming arrow to turn on the camera and click the chevron arrow to expand the record settings.Adjust the focus until the relatively small particles are clearly visible. To set the analysis for a small EV quantification, set the frame rate to 30 frames per second, the exposure to 15 milliseconds, the stir time to five seconds, the wait time to three seconds, the blue, green, and red laser powers to 210, 12, and 8 milliwatts respectively, the frames per video to 300, and the gain to 30 decibels. Adjust the focus until the relatively small particles are clearly visible.Increasing the zoom and/or the gain can help with particle focusing. But if you increase the gain, remember to set it to 30 decibels prior to recording. Once particles are in focus, set the zoom setting to 0.5X to save bandwidth and to prevent loss frames and click record to begin recording the video.When a prompt appears stating that the videos have been recorded, click OK to complete the recording and select the process tab. If very large particles were visible in any video while recording, navigate to the directory of recorded videos and remove any problematic video prior to processing. Check the disable audio detection override box and set the feature diameter to 30.Click process to initiate video processing and view a live distribution graph. When the processing is complete, click OK and select the plot tab. For EVs, display the main chart as log bin silica.Other features of the graph, such as changing the x-axis to set the area for integration of the figure produced, can be customized. To create a PDF report of the results, click the report button. The mean, median, mode size, and concentration adjusted for the dilution factor and distribution width will be displayed.NTA of the diluent should be performed before any sample so that the concentration of this blank can be subtracted from the EV sample particle concentration. To clean the cuvettes after analysis, empty the cuvette and completely fill the cuvettes 10 to 15 times with deionized water and the three times with 70 to 100%ethanol to remove any residual sample. Dry the outside of the cuvettes with a lint-free microfiber cloth and dry the inside with a compressed air duster.To clean the inserts and stir bars, place the materials in a glass scintillation vial containing 70 to 100%ethanol and shake the vial vigorously. Then rinse the inserts and stir bars in deionized water with shaking as demonstrated and dry them using lint-free cloths. After drying, immediately place all of the clean components into storage until the next analysis.Before performing an analysis, the instrument calibration was tested using polystyrene beads to ensure the validity of the acquired data. As observed, the particle tracking instrument accurately reported the size of the 100 nanometer manodisperse beads, but only closely reported the size of the 400 nanometer beads. Therefore, the instrument settings for this protocol were more accurate for smaller particles, closer to 100 nanometers in size.Using these settings, reported particle concentration scales accordingly with the dilution factor demonstrating that the instrument can accurately detect the particle concentration at various dilutions with little variability between technical replicants. The optimum dilution for a 4.41 times 10 to the 10th particles per milliliter mouse tissue-derived EV sample was determined to be between 1, 000 and 3, 000. In this analysis, increasing the gain increased the sensitivity of the camera, allowing an increase in the visualization of a higher number of smaller particles.Increasing the blue laser power from 70 to 210 milliwatts while keeping the green and red laser powers constant shifted the reported average particle size from 122 to 105 nanometers and increased the reported total particle concentration from 1.1 times 10 to the eighth to 1.7 times 10 to the eighth. Increasing the power of the red laser increased the reported average particle size from 175 to 246 nanometers and decreased the reported total particle concentration. Increasing the green laser power resulted in a decrease in the reported average particle size and an increase in reported total particle concentration.Finding the right dilution to place a sample within the optimal detection range can take a few tries for each sample. The cuvette cleaning also requires extra careful handling. We recommend applying more than one orthogonal method for EV particle size and concentration measurements.Dynamic light scattering, resistive pulse sensing, transmission electron microscopy, and single-particle interferometric reflectance imaging sensing can also be performed to characterize EVs.

nanoparticle-tracking-analysis-for-quantification-size-determination

Research

JoVE Journal

Biology

An Innovative Method for Exosome Quantification and Size Measurement

Although the biological importance of exosomes has recently gained an increasing amount of scientific and clinical attention, much is still unknown about their complex pathways, their bioavailability and their diverse functions in health and disease. Current work focuses on the presence and the behavior of exosomes (in vitro as well as in vivo) in the context of different human disorders, especially in the fields of oncology, gynecology and cardiology.
Unfortunately, neither a consensus regarding a gold standard for exosome isolation exists, nor is there an agreement on such a method for their quantitative analysis. As there are many methods for the purification of exosomes and also many possibilities for their quantitative and qualitative analysis, it is difficult to determine a combination of methods for the ideal approach. 
Here, we demonstrate nanoparticle tracking analysis (NTA), a semi-automated method for the characterization of exosomes after isolation from human plasma by ultracentrifugation. The presented results show that this approach for isolation, as well as the determination of the average number and size of exosomes, delivers reproducible and valid data, as confirmed by other methods, such as scanning electron microscopy (SEM).

A method for isolation of exosomes from whole blood and further analysis by nanoparticle tracking using a semi-automatic instrument is presented in this article. The presented technology provides an extremely sensitive method for visualizing and analyzing particles in liquid suspension.

Although the biological importance of exosomes has recently gained an increasing amount of scientific and clinical attention, much is still unknown about ...

A Rapid and Specific Microplate Assay for the Determination of Intra- and Extracellular Ascorbate in Cultured Cells

Vitamin C (ascorbate) plays numerous important roles in cellular metabolism, many of which have only come to light in recent years. For instance, within the brain, ascorbate acts in a neuroprotective and neuromodulatory manner that involves ascorbate cycling between neurons and vicinal astrocytes - a relationship that appears to be crucial for brain ascorbate homeostasis. Additionally, emerging evidence strongly suggests that ascorbate has a greatly expanded role in regulating cellular and systemic iron metabolism than is classically recognized. The increasing recognition of the integral role of ascorbate in normal and deregulated cellular and organismal physiology demands a range of medium-throughput and high-sensitivity analytic techniques that can be executed without the need for highly expensive specialist equipment. Here we provide explicit instructions for a medium-throughput, specific and relatively inexpensive microplate assay for the determination of both intra- and extracellular ascorbate in cell culture.

Ascorbate plays numerous important roles in cellular metabolism, many of which have only come to light in recent years. Here we describe a medium-throughput, specific and inexpensive microplate assay for the determination of both intra- and extracellular ascorbate in cell culture.

Vitamin C (ascorbate) plays numerous important roles in cellular metabolism, many of which have only come to light in recent years. For instance, within ...

Techniques for the Analysis of Extracellular Vesicles Using Flow Cytometry

Extracellular Vesicles (EVs) are small, membrane-derived vesicles found in bodily fluids that are highly involved in cell-cell communication and help regulate a diverse range of biological processes. Analysis of EVs using flow cytometry (FCM) has been notoriously difficult due to their small size and lack of discrete populations positive for markers of interest. Methods for EV analysis, while considerably improved over the last decade, are still a work in progress. Unfortunately, there is no one-size-fits-all protocol, and several aspects must be considered when determining the most appropriate method to use. Presented here are several different techniques for processing EVs and two protocols for analyzing EVs using either individual detection or a bead-based approach. The methods described here will assist with eliminating the antibody aggregates commonly found in commercial preparations, increasing signal&#8211;to-noise ratio, and setting gates in a rational fashion that minimizes detection of background fluorescence. The first protocol uses an individual detection method that is especially well suited for analyzing a high volume of clinical samples, while the second protocol uses a bead-based approach to capture and detect smaller EVs and exosomes.

Many different methods exist for the measurement of extracellular vesicles (EVs) using flow cytometry (FCM). Several aspects should be considered when determining the most appropriate method to use. Two protocols for measuring EVs are presented, using either individual detection or a bead-based approach.

Extracellular Vesicles (EVs) are small, membrane-derived vesicles found in bodily fluids that are highly involved in cell-cell communication and help ...

Flow Cytometric Analysis of Extracellular Vesicles from Cell-conditioned Media

Flow cytometry (FC) is the method of choice for semi-quantitative measurement of cell-surface antigen markers. Recently, this technique has been used for phenotypic analyses of extracellular vesicles (EV) including exosomes (Exo) in the peripheral blood and other body fluids. The small size of EV mandates the use of dedicated instruments having a detection threshold around 50-100 nm. Alternatively, EV can be bound to latex microbeads that can be detected by FC. Microbeads, conjugated with antibodies that recognize EV-associated markers/Cluster of Differentiation CD63, CD9, and CD81 can be used for EV capture. Exo isolated from CM can be analyzed with or without pre-enrichment by ultracentrifugation. This approach is suitable for EV analyses using conventional FC instruments. Our results demonstrate a linear correlation between Mean Fluorescence Intensity (MFI) values and EV concentration. Disrupting EV through sonication dramatically decreased MFI, indicating that the method does not detect membrane debris. We report an accurate and reliable method for the analysis of EV surface antigens, which can be easily implemented in any laboratory.

The protocol describes a reproducible method designed for use with cell culture supernatants to detect surface epitopes on small extracellular vesicles (EV). It utilizes specific EV immunoprecipitation using beads coupled with antibodies that recognize surface antigen CD9, CD63, and CD81. The method is optimized for downstream flow cytometry analysis.

Flow cytometry (FC) is the method of choice for semi-quantitative measurement of cell-surface antigen markers. Recently, this technique has been used for ...

Purification and Analysis of Caenorhabditis elegans Extracellular Vesicles

The secretion of small membrane-bound vesicles into the external environment is a fundamental physiological process of all cells. These extracellular vesicles (EVs) function outside the cell to regulate global physiological processes by transferring proteins, nucleic acids, metabolites, and lipids between tissues. EVs reflect the physiological state of their cells of origin. EVs are implicated to have fundamental roles in virtually every aspect of human health. Thus, EV protein and genetic cargos are being increasingly analyzed for biomarkers of health and disease. However, the EV field still lacks a tractable invertebrate model system that permits the study of EV cargo composition. C. elegans is well suited for EV research because it actively secretes EVs outside of its body into its external environment, permitting facile isolation. This article provides all the necessary information for generating, purifying, and quantifying these environmentally secreted C. elegans EVs including how to work quantitatively with very large populations of age-synchronized worms, purifying EVs, and a flow cytometry protocol that directly measures the number of intact EVs in the purified sample. Thus, the large library of genetic reagents available for C. elegans research can be tapped into for investigating the impacts of genetic pathways and physiological processes on EV cargo composition.

Purification and Analysis of Caenorhabditis elegans Extracellular Vesicles

This article presents methods for generating, purifying, and quantifying Caenorhabditis elegans extracellular vesicles.

The secretion of small membrane-bound vesicles into the external environment is a fundamental physiological process of all cells. These extracellular ...

Automated Imaging and Analysis for the Quantification of Fluorescently Labeled Macropinosomes

Macropinocytosis is a non-specific fluid-phase uptake pathway that allows cells to internalize large extracellular cargo, such as proteins, pathogens, and cell debris, through bulk endocytosis. This pathway plays an essential role in a variety of cellular processes, including the regulation of immune responses and cancer cell metabolism. Given this importance in biological function, examining cell culture conditions can provide valuable information by identifying regulators of this pathway and optimizing conditions to be employed in the discovery of novel therapeutic approaches. The study describes an automated imaging and analysis technique using standard laboratory equipment and a cell imaging multi-mode plate reader for the rapid quantification of the macropinocytic index in adherent cells. The automated method is based on the uptake of high molecular weight fluorescent dextran and can be applied to 96-well microplates to facilitate assessments of multiple conditions in one experiment or fixed samples mounted onto glass coverslips. This approach is aimed at maximizing reproducibility and reducing experimental variation while being both time-saving and cost-effective.

Automated assays using multi-well microplates are advantageous approaches for identifying pathway regulators by allowing the assessment of a multitude of conditions in a single experiment. Here, we have adapted the well-established macropinosome imaging and quantification protocol to a 96-well microplate format and provide a comprehensive outline for automation using a multi-mode plate reader.

Macropinocytosis is a non-specific fluid-phase uptake pathway that allows cells to internalize large extracellular cargo, such as proteins, pathogens, and ...

Extracellular Vesicle Uptake Assay via Confocal Microscope Imaging Analysis

There is a need for practical assays to visualize and quantify the cells' extracellular vesicle (EV) uptake. EV uptake plays a role in intercellular communication in various research fields; cancer biology, neuroscience, and drug delivery. Many EV uptake assays have been reported in the literature; however, there is a lack of practical, detailed experimental methodology. EV uptake can be assessed by fluorescently labeling EVs to detect their location within cells. Distinguishing between internalized EVs in cells and the superficial EVs on cells is difficult, yet critical, to accurately determine the EV uptake. Therefore, an assay that efficiently quantifies EV uptake through three-dimensional (3D) fluorescence confocal microscopy is proposed in this work. Fluorescently labeled EVs were prepared using a nano-filtration-based microfluidic device, visualized by 3D confocal microscopy, and then analyzed through advanced image-processing software. The protocol provides a robust methodology for analyzing EVs on a cellular level and a practical approach for efficient analysis.

Extracellular Vesicle Uptake Assay via Confocal Microscope Imaging Analysis

Extracellular vesicles (EVs) contribute to cellular biology and intercellular communications. There is a need for practical assays to visualize and quantify EVs uptake by the cells. The current protocol proposes the EV uptake assay by utilizing three-dimensional fluorescence imaging via confocal microscopy, following EV isolation by a nano-filtration-based microfluidic device.

There is a need for practical assays to visualize and quantify the cells' extracellular vesicle (EV) uptake. EV uptake plays a role in intercellular ...

Direct Stochastic Optical Reconstruction Microscopy of Extracellular Vesicles in Three Dimensions

Extracellular vesicles (EVs) are released by all cell types and play an important role in cell signaling and homeostasis. The visualization of EVs often require indirect methods due to their small diameter (40-250 nm), which is beneath the diffraction limit of typical light microscopy. We have developed a super-resolution microscopy-based visualization of EVs to bypass the diffraction limit in both two and three dimensions. Using this approach, we can resolve the three-dimensional shape of EVs to within +/- 20 nm resolution on the XY-axis and +/- 50 nm resolution along the Z-axis. In conclusion, we propose that super-resolution microscopy be considered as a characterization method of EVs, including exosomes, as well as enveloped viruses.

Direct stochastic optical reconstruction microscopy (dSTORM) is used to bypass the typical diffraction limit of light microscopy and to view exosomes at the nanometer scale. It can be employed in both two and three dimensions to characterize exosomes.

Extracellular vesicles (EVs) are released by all cell types and play an important role in cell signaling and homeostasis. The visualization of EVs often ...

Scalable Isolation and Purification of Extracellular Vesicles from Escherichia coli and Other Bacteria

Diverse bacterial species secrete ~20-300 nm extracellular vesicles (EVs), comprised of lipids, proteins, nucleic acids, glycans, and other molecules derived from the parental cells. EVs function as intra- and inter-species communication vectors while also contributing to the interaction between bacteria and host organisms in the context of infection and colonization. Given the multitude of functions attributed to EVs in health and disease, there is a growing interest in isolating EVs for in vitro and in vivo studies. It was hypothesized that the separation of EVs based on physical properties, namely size, would facilitate the isolation of vesicles from diverse bacterial cultures. 
The isolation workflow consists of centrifugation, filtration, ultrafiltration, and size-exclusion chromatography (SEC) for the isolation of EVs from bacterial cultures. A pump-driven tangential flow filtration (TFF) step was incorporated to enhance scalability, enabling the isolation of material from liters of starting cell culture. Escherichia coli was used as a model system expressing EV-associated nanoluciferase and non-EV-associated mCherry as reporter proteins. The nanoluciferase was targeted to the EVs by fusing its N-terminus with cytolysin A. Early chromatography fractions containing 20-100 nm EVs with associated cytolysin A - nanoLuc were distinct from the later fractions containing the free proteins. The presence of EV-associated nanoluciferase was confirmed by immunogold labeling and transmission electron microscopy. This EV isolation workflow is applicable to other human gut-associated gram-negative and gram-positive bacterial species. In conclusion, combining centrifugation, filtration, ultrafiltration/TFF, and SEC enables scalable isolation of EVs from diverse bacterial species. Employing a standardized isolation workflow will facilitate comparative studies of microbial EVs across species.

Scalable Isolation and Purification of Extracellular Vesicles from Escherichia coli and Other Bacteria

Bacteria secrete nanometer-sized extracellular vesicles (EVs) carrying bioactive biological molecules. EV research focuses on understanding their biogenesis, role in microbe-microbe and host-microbe interactions and disease, as well as their potential therapeutic applications. A workflow for scalable isolation of EVs from various bacteria is presented to facilitate standardization of EV research.

Diverse bacterial species secrete ~20-300 nm extracellular vesicles (EVs), comprised of lipids, proteins, nucleic acids, glycans, and other molecules ...

Isolation and Characterization of Cyanobacterial Extracellular Vesicles

Cyanobacteria are a diverse group of photosynthetic, Gram-negative bacteria that play critical roles in global ecosystems and serve as essential biotechnology models. Recent work has demonstrated that both marine and freshwater cyanobacteria produce extracellular vesicles -&#160;small membrane-bound structures released from the outer surface of the microbes. While vesicles likely contribute to diverse biological processes, their specific functional roles in cyanobacterial biology remain largely unknown. To encourage and advance research in this area, a detailed protocol is presented for isolating, concentrating, and purifying cyanobacterial extracellular vesicles. The current work discusses methodologies that have successfully isolated vesicles from large cultures of Prochlorococcus, Synechococcus, and Synechocystis. Methods for quantifying and characterizing vesicle samples from these strains are presented. Approaches for isolating vesicles from aquatic field samples are also described. Finally, typical challenges encountered with cyanobacterial vesicle purification, methodological considerations for different downstream applications, and the trade-offs between approaches are also discussed.

The present protocol providesdetailed descriptions for isolation, concentration,and characterization of extracellular vesicles from cyanobacterial cultures. Approaches for purifying vesicles from cultures at different scales, trade-offs among methodologies, and considerations for working with field samples are also discussed.