Name: quantitative analysis of viscoelastic properties of red blood cells using optical tweezers and defocusing microscopy
Uploaded: 2022-03-25T14:30:00
Description: Watch this Scientific Journal Video about Quantitative Analysis of Viscoelastic Properties of Red Blood Cells Using Optical Tweezers and Defocusing Microscopy at JoVE.com

The authors would like to acknowledge all the members of CENABIO advanced microscopy facility for all-important help. This work was supported by the Brazilian agencies Conselho Nacional de Desenvolvimento Cient&#237;fico e Tecnol&#243;gico (CNPq), Coordena&#231;&#227;o de Aperfei&#231;oamento de Pessoal de N&#237;vel Superior (CAPES) - Financial Code 001, Funda&#231;&#227;o de Amparo &#224; Pesquisa do Estado do Rio de Janeiro (FAPERJ), and Instituto Nacional de Ci&#234;ncia e Tecnologia de Fluidos Complexos (INCT-FCx) together with Funda&#231;&#227;o de Amparo &#224; Pesquisa do Estado de S&#227;o Paulo (FAPESP). B.P. was supported by a JCNE grant from FAPERJ.

Human blood samples were provided by adult men and women volunteers according to protocols approved by the Research Ethics Committee of the Federal University of Rio de Janeiro (Protocol 2.889.952) and registered in Brazil Platform under CAAE number 88140418.5.0000.5699. A written form of consent was issued to and collected from all volunteers. Those with any hemoglobinopathy and/or taking controlled medication were excluded. The entire process followed the guidelines approved by the institute&#39;s ethical committee.</p...

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In this protocol, an integrated method based on optical tweezers and defocusing microscopy is presented to quantitatively map the viscoelastic properties of RBCs. Results for the storage and loss shear moduli, together with the scaling exponent that characterizes the soft glassy rheology of RBC are determined. Application of this protocol for different experimental conditions, such as in physiological situation8 or along each stage of P. falciparum intra-erythrocytic cycle<sup class="xref...

Mature red blood cells (RBCs), also known as erythrocytes, are able to extend more than twice their size when passing through the narrowest capillaries of the human body1. Such capacity is attributed to their unique ability to deform when subjected to external loads.
In recent years, different studies have characterized this feature in RBC surfaces2,3. The area of physics that describes the elastic and viscous responses of materials due to external loads is called rheology. In general, when an external force is applied, the resulting deformation depends on the material&#39;s properties and can be divided into elastic deformations, that store energy, or viscous deformations, that dissipate energy4. All cells, including RBCs, exhibit a viscoelastic behavior; in other words, energy is both stored and dissipated. The viscoelastic response of a cell can thus be characterized by its complex shear modulus G*(&#969;) = G&#39;(&#969;) + iG&#34;(&#969;), where G&#39;&#160;(&#969;) is the storage modulus, related to the elastic behavior, and G&#34; (&#969;)&#160;is the loss modulus, related to its viscosity4. Moreover, phenomenological models have been used to describe cell responses, one of the most used is called the soft glassy rheology model5, characterized by a power-law dependence of the complex shear modulus with the load frequency.
Single-cell-based methods have been employed to characterize the viscoelastic properties of RBCs, by applying force and measuring displacement as a function of the imposed load2,3. However, for the complex shear modulus, few results can be found in the literature. Using dynamic light scattering, values for RBC storage and loss moduli were reported varying from 0.01-1 Pa, in the frequency range of 1-100 Hz6. By using optical magnetic twisting cytometry, an apparent complex elastic modulus was obtained7, and for comparison purposes, a multiplicative factor was claimed to possibly clarify the discrepancies.
More recently, a new methodology based on optical tweezers (OT) together with defocusing microscopy (DM), as an integrated tool to quantitatively map the storage and loss of shear moduli of human erythrocytes over time-dependent loads, was established8,9. In addition, a soft glassy rheology model was used to fit the results and obtain a power-law coefficient that characterizes the RBCs8,9.
Overall, the developed methodology8,9, the protocol for which is described in detail below, clarifies previous discrepancies by using the measured values for the form factor, Ff, that relates forces and deformations to stresses and strains in the RBC surface and can be utilized as a novel diagnostic method capable of quantitatively determining the viscoelastic parameters and soft glassy features of RBCs obtained from individuals with different blood pathologies. Such characterization, using the protocol described below, may open up new possibilities to understand the behavior of RBCs from a mechanobiological perspective.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>35mm culture dishes</td>
			<td>Corning</td>
			<td>430165</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine serum albumin</td>
			<td>Sigma-Aldrich</td>
			<td>A9418</td>
			<td></td>
		</tr>
		<tr>
			<td>Coverslips</td>
			<td>Knittel Glass</td>
			<td>VD12460Y1A.01 and VD12432Y1A.01</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass-bottom dishes</td>
			<td>MatTek Life Sciences</td>
			<td>P35G-0-10-C</td>
			<td></td>
		</tr>
		<tr>
			<td>Glucose</td>
			<td>Sigma-Aldrich</td>
			<td>G7021</td>
			<td></td>
		</tr>
		<tr>
			<td>ImageJ</td>
			<td>NIH</td>
			<td>https://imagej.nih.gov/ij/</td>
			<td></td>
		</tr>
		<tr>
			<td>Immersion oil</td>
			<td>Nikon</td>
			<td>MXA22165</td>
			<td></td>
		</tr>
		<tr>
			<td>Inverted microscope</td>
			<td>Nikon</td>
			<td>Eclipse TE300</td>
			<td></td>
		</tr>
		<tr>
			<td>KaleidaGraph</td>
			<td>Synergy Software</td>
			<td>https://www.synergy.com/</td>
			<td></td>
		</tr>
		<tr>
			<td>KCl</td>
			<td>Sigma-Aldrich</td>
			<td>P5405</td>
			<td></td>
		</tr>
		<tr>
			<td>KH2PO4</td>
			<td>Sigma-Aldrich</td>
			<td>P5655</td>
			<td></td>
		</tr>
		<tr>
			<td>Microscope camera</td>
			<td>Hamamatsu</td>
			<td>C11440-10C</td>
			<td></td>
		</tr>
		<tr>
			<td>Na2HPO4</td>
			<td>Sigma-Aldrich</td>
			<td>S5136</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Sigma-Aldrich</td>
			<td>S5886</td>
			<td></td>
		</tr>
		<tr>
			<td>Neubauer chamber</td>
			<td>Sigma-Aldrich</td>
			<td>BR717805-1EA</td>
			<td></td>
		</tr>
		<tr>
			<td>Objective lens</td>
			<td>Nikon</td>
			<td>PLAN APO 100X 1.4 NA DIC H; PLAN APO 60x 1.4 NA DIC H and Plan APO 10x XXNA PH2</td>
			<td></td>
		</tr>
		<tr>
			<td>Optical table</td>
			<td>Thorlabs</td>
			<td>T1020CK</td>
			<td></td>
		</tr>
		<tr>
			<td>OT laser</td>
			<td>IPG Photonics</td>
			<td>YLR-5-1064-LP</td>
			<td></td>
		</tr>
		<tr>
			<td>Polystyrene microspheres</td>
			<td>Polysciences</td>
			<td>17134-15</td>
			<td></td>
		</tr>
		<tr>
			<td>rubber ring</td>
			<td>Forever Seals</td>
			<td>NBR O-Ring</td>
			<td></td>
		</tr>
		<tr>
			<td>Silicone grease</td>
			<td>Dow Corning</td>
			<td>Z273554</td>
			<td></td>
		</tr>
		<tr>
			<td>Stage positioning</td>
			<td>PI</td>
			<td>P-545.3R8S</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipette</td>
			<td>Gilson</td>
			<td>P1000</td>
			<td></td>
		</tr>
	</tbody>
</table>

quantitative analysis of viscoelastic properties of red blood cells using optical tweezers and defocusing microscopy

The viscoelastic properties of erythrocytes have been investigated by a range of techniques. However, the reported experimental data vary. This is not only attributed to the normal variability of cells, but also to the differences in methods and models of cell response. Here, an integrated protocol using optical tweezers and defocusing microscopy is employed to obtain the rheological features of red blood cells in the frequency range of 1 Hz to 35 Hz. While optical tweezers are utilized to measure the erythrocyte-complex elastic constant, defocusing microscopy is able to obtain the cell height profile, volume, and its form factor a parameter that allows conversion of complex elastic constant into complex shear modulus. Moreover, applying a soft glassy rheology model, the scaling exponent for both moduli can be obtained. The developed methodology allows to explore the mechanical behavior of red blood cells, characterizing their viscoelastic parameters, obtained under well-defined experimental conditions, for several physiological and pathological conditions.

Figure 1&#160;represents the schematics of the OT system used for the rheology measurements. Figure 2 shows the schematics of the microrheology experiment with both spheres and a representative RBC is also shown. Figure 3 shows a typical curve for the amplitudes of both spheres as a function of time when the sinusoidal movements are produced by the piezoelectric stage. While the reference sphere (Figure 3</stron...

Watch this Scientific Journal Video about Quantitative Analysis of Viscoelastic Properties of Red Blood Cells Using Optical Tweezers and Defocusing Microscopy at JoVE.com

Quantitative Analysis of Viscoelastic Properties of Red Blood Cells Using Optical Tweezers and Defocusing Microscopy

Here, an integrated protocol based on optical tweezers and defocusing microscopy is described to measure the rheological properties of cells. This protocol has wide applicability in studying the viscoelastic properties of erythrocytes under variable physio-pathological conditions.

The viscoelastic properties of erythrocytes have been investigated by a range of techniques. However, the reported experimental data vary. This is not ...

This methodology allows to explore the mechanical behavior of erythrocytes, characterizing their viscoelastic parameters and soft glassy features for several physiological and pathological conditions. Our single-cell based method verifies video references by using the metal values for the form factor that relates forces and displacements, the stresses and scrapes in the erythrocyte surface. Begin by pouring silicone grease over the rubber ring surface in a way that covers the entire perimeter.Next, place the rubber ring on the coverslip with the grease side facing the coverslip. Wait for five minutes for proper attachment, and the sample holders are then ready to receive the cell culture. Next, with the solution of cells previously prepared following the written protocol, seed the cells in the sample holder.Add 0.2 microliters of a 10%volume by volume polystyrene sphere solution to the sample. Place the second coverslip above the rubber ring. Close the setup and finish the sample preparation.Finally, move the entire sample to the microscope. To start with the experimentation, use the OT system, trap the sphere with the OT laser, and then attach it to the coverslip, close to the cell. Then, trap another sphere and repeat the same attachment procedure by pressing the sphere against the cell surface, near the top surface and close to the cell edge.Add a sinusoidal function of amplitude and varying frequencies. Next, press the start"button, using the piezoelectric stage to allow the piezoelectric displacement. Keep the RBC sphere in the trap and submit the sample to a cycle of movements using the previously set sinusoidal function.For analysis, open the ImageJ software and import the entire movie obtained during the sinusoidal movements. Click on adjust, and then select option threshold. Adjust the threshold with both scroll bars, and select the reference sphere by clicking on file, followed by rectangle.Then in the analyze tab, click on set measurements"and select the center of mass"option. Click again on the analyze tab and select analyze particles. A new window containing a table with xy coordinates for the center of the mass will appear.Repeat the procedure for the other sphere attached to the RBC surface. Open the analysis software and import the txt files previously obtained. Generate a plot with the centers of mass on the y-axis and time on the x-axis.Plot the results on a graph using the x-axis for loss constant, denoted by K double prime, and the y-axis for storage constant, denoted by K prime. First, for video acquisition, move the piezoelectric stage in the xy direction, using the software to search for an isolated cell attached to the coverslip. Trap and attach a polystyrene sphere of known diameter to the RBC surface.Next, using the piezoelectric stage, move the trapped bead attached to the RBC surface to deform the cell, and then attach the bead to the coverlip. Now, change the z-axis position to find the focused image. After fixing the position, use the camera software to create a movie of the entire cell.Then, move the z-axis position two micrometers down or up to obtain a defocused image for the chosen cell. Finally, without changing the z-axis position, search for a region without cells to repeat the same procedure, and create a movie of the image background. For contrast image acquisition, first find the value of N zero, click on the polygon selection icon, then click on the analyze tab and select measure.Next, use the contrast equation to determine N image minus N zero, and execute this by selecting math"under process, followed by subtract. Later, divide the result by N zero minus B.Finally, find the contrast for the focused and defocused images. Now, use the Hartley transform to obtain the RBC thickness.In ImageJ, click on process, followed by FFT"and FFT options, and then choose FHT. Then perform the inverse transform FHT by selecting process, followed by FFT"and FFT. Use the resulting image to obtain the height profile.After finding the image that contains the RBC height profile use the two micrometers defocused contrast to create a set of two images in ImageJ. To find the form factor, use an ImageJ customized macro to analyze the stack. The macro will deliver a table with the edge's position, the perimeter, the inverse of the perimeter, and an image of the analyzed cell.Check whether the edges of this image are similar to the edges of the reference figure. Otherwise, repeat the procedure, and use the sum of the inverse of the perimeter to find the form factor. Start by organizing the experimental data in a table.Create a new table in the analysis software by clicking on the file tab. Determine 10 different columns for the parameters. To plot the curve G prime and G double prime in the analysis software, use the data from the previous table and click on the plot"button.To obtain parameters Gamma and GM, click on the curve fit tab and select fit1"to open a new window. Select the square, click on the define button, and type the equation. Click on the okay"button in both the windows, and the fitting will appear.Next, create two other plots, namely G prime and G double prime as a function of omega. Place the error bars only on the y-axis, as previously demonstrated. Repeat the curve fitting procedure, select G"option.Click curve definition"under general fit, and then write the concerned equation. Finally, click on okay, and a curve fitting will appear along with the values for Alpha and G zero. Again, perform another curve fitting procedure.Select G"option, click curve definition"under general fit, and then write the concerned equation. Finally, click on okay, and a curve fitting will appear. The figure shows the storage elastic constant as a function of the loss elastic constant.The linear dependence observed demonstrates that the RBC surface can be considered a soft glassy material. By applying the values for overall cell form factor and RBC surface thickness, the values for the exponent Alpha can be determined. This technique may provide the basis for novel diagnostic methods that correlates changes in erythrocytes'viscoelastic properties with modifications in blood flow of individuals with different pathologies.

quantitative-analysis-viscoelastic-properties-red-blood-cells-using

Research

JoVE Journal

Biology

Phase Contrast and Differential Interference Contrast (DIC) Microscopy

Phase-contrast microscopy is often used to produce contrast for transparent, non light-absorbing, biological specimens. The technique was discovered by Zernike, in 1942, who received the Nobel prize for his achievement. DIC microscopy, introduced in the late 1960s, has been popular in biomedical research because it highlights edges of specimen structural detail, provides high-resolution optical sections of thick specimens including tissue cells, eggs, and embryos and does not suffer from the  phase halos  typical of phase-contrast images. This protocol highlights the principles and practical applications of these microscopy techniques.

Phase Contrast and Differential Interference Contrast DIC Microscopy

This protocol highlights the principles and practical applications of Phase and Differential Interference Contrast (DIC) Microscopy

Phase-contrast microscopy is often used to produce contrast for transparent, non light-absorbing, biological specimens. The technique was discovered by ...

Isolation and Culture of Pulmonary Endothelial Cells from Neonatal Mice

Endothelial cells provide a useful research model in many areas of vascular biology. Since its first isolation 1, human umbilical vein endothelial cells (HUVECs) have shown to be convenient, easy to obtain and culture, and thus are the most widely studied endothelial cells. However, for research focused on processes like angiogenesis, permeability or many others, microvascular endothelial cells (ECs) are a much more physiologically relevant model to study 2. Furthermore, ECs isolated from knockout mice provide a useful tool for analysis of protein function ex vivo. Several approaches to isolate and culture microvascular ECs of different origin have been reported to date 3-7, but consistent isolation and culture of pure ECs is still a major technical problem in many laboratories. Here, we provide a step-by-step protocol on a reliable and relatively simple method of isolating and culturing mouse lung endothelial cells (MLECs). In this approach, lung tissue obtained from 6- to 8-day old pups is first cut into pieces, digested with collagenase/dispase (C/D) solution and dispersed mechanically into single-cell suspension. MLECS are purified from cell suspension using positive selection with anti-PECAM-1 antibody conjugated to Dynabeads using a Magnetic Particle Concentrator (MPC). Such purified cells are cultured on gelatin-coated tissue culture (TC) dishes until they become confluent. At that point, cells are further purified using Dynabeads coupled to anti-ICAM-2 antibody. MLECs obtained with this protocol exhibit a cobblestone phenotype, as visualized by phase-contrast light microscopy, and their endothelial phenotype has been confirmed using FACS analysis with anti-VE-cadherin 8 and anti-VEGFR2 9 antibodies and immunofluorescent staining of VE-cadherin. In our hands, this two-step isolation procedure consistently and reliably yields a pure population of MLECs, which can be further cultured. This method will enable researchers to take advantage of the growing number of knockout and transgenic mice to directly correlate in vivo studies with results of in vitro experiments performed on isolated MLECs and thus help to reveal molecular mechanisms of vascular phenotypes observed in vivo.

Here, we describe a protocol for isolation and culture of murine pulmonary endothelial cells. This method comprises mechanic and enzymatic lung tissue dissociation as well as a 2-step purification process using anti-PECAM-1 and anti-ICAM-2 antibodies conjugated to magnetic beads, which produces a pure endothelial cell population of mostly microvascular origin.

Endothelial cells provide a useful research model in many areas of vascular biology. Since its first isolation 1, human umbilical vein endothelial cells ...

Quantitative Live Cell Fluorescence-microscopy Analysis of Fission Yeast

Several microscopy techniques are available today that can detect a specific protein within the cell. During the last decade live cell imaging using fluorochromes like Green Fluorescent Protein (GFP) directly attached to the protein of interest has become increasingly popular 1. Using GFP and similar fluorochromes the subcellular localisations and movements of proteins can be detected in a fluorescent microscope. Moreover, also the subnuclear localisation of a certain region of a chromosome can be studied using this technique. GFP is fused to the Lac Repressor protein (LacR) and ectopically expressed in the cell where tandem repeats of the lacO sequence has been inserted into the region of interest on the chromosome2. The LacR-GFP will bind to the lacO repeats and that area of the genome will be visible as a green dot in the fluorescence microscope. Yeast is especially suited for this type of manipulation since homologous recombination is very efficient and thereby enables targeted integration of the lacO repeats and engineered fusion proteins with GFP 3. Here we describe a quantitative method for live cell analysis of fission yeast. Additional protocols for live cell analysis of fission yeast can be found, for example on how to make a movie of the meiotic chromosomal behaviour 4. In this particular experiment we focus on subnuclear organisation and how it is affected during gene induction. We have labelled a gene cluster, named Chr1, by the introduction of lacO binding sites in the vicinity of the genes. The gene cluster is enriched for genes that are induced early during nitrogen starvation of fission yeast 5. In the strain the nuclear membrane (NM) is labelled by the attachment of mCherry to the NM protein Cut11 giving rise to a red fluorescent signal. The Spindle Pole body (SPB) compound Sid4 is fused to Red Fluorescent Protein (Sid4-mRFP) 6. In vegetatively growing yeast cells the centromeres are always attached to the SPB that is embedded in the NM 7. The SPB is identified as a large round structure in the NM. By imaging before and 20 minutes after depletion of the nitrogen source we can determine the distance between the gene cluster (GFP) and the NM/SPB. The mean or median distances before and after nitrogen depletion are compared and we can thus quantify whether or not there is a shift in subcellular localisation of the gene cluster after nitrogen depletion.

The fission yeast, Schizosaccharomyces pombe, is a good model system to study basic cellular processes. Here we describe a method to perform quantitative live cell analysis of fission yeast. In this particular experiment we focus on organisation of the genome within the cell nucleus, but the method can also be used to study cytosolic factors.

Several microscopy techniques are available today that can detect a specific protein within the cell. During the last decade live cell imaging using ...

Quantitative Analysis of Random Migration of Cells Using Time-lapse Video Microscopy

Cell migration is a dynamic process, which is important for embryonic development, tissue repair, immune system function, and tumor invasion 1, 2. During directional migration, cells move rapidly in response to an extracellular chemotactic signal, or in response to intrinsic cues 3 provided by the basic motility machinery. Random migration occurs when a cell possesses low intrinsic directionality, allowing the cells to explore their local environment.
Cell migration is a complex process, in the initial response cell undergoes polarization and extends protrusions in the direction of migration 2. Traditional methods to measure migration such as the Boyden chamber migration assay is an easy method to measure chemotaxis in vitro, which allows measuring migration as an end point result. However, this approach neither allows measurement of individual migration parameters, nor does it allow to visualization of morphological changes that cell undergoes during migration.
Here, we present a method that allows us to monitor migrating cells in real time using video - time lapse microscopy. Since cell migration and invasion are hallmarks of cancer, this method will be applicable in studying cancer cell migration and invasion in vitro. Random migration of platelets has been considered as one of the parameters of platelet function 4, hence this method could also be helpful in studying platelet functions. This assay has the advantage of being rapid, reliable, reproducible, and does not require optimization of cell numbers. In order to maintain physiologically suitable conditions for cells, the microscope is equipped with CO2 supply and temperature thermostat. Cell movement is monitored by taking pictures using a camera fitted to the microscope at regular intervals. Cell migration can be calculated by measuring average speed and average displacement, which is calculated by Slidebook software.

This method allows monitoring of cells in real time and quantitative measurements of different cell migration parameters such as speed, displacement, and velocity. Unlike the traditional methods, this real time approach is not based on endpoint quantitative migration measurements; instead it allows monitoring and calculating different parameters continuously.

Cell migration is a dynamic process, which is important for embryonic development, tissue repair, immune system function, and tumor invasion 1, 2. During ...

Quantitative Analysis of Autophagy using Advanced 3D Fluorescence Microscopy

Prostate cancer is the leading form of malignancies among men in the U.S. While surgery carries a significant risk of impotence and incontinence, traditional chemotherapeutic approaches have been largely unsuccessful. Hormone therapy is effective at early stage, but often fails with the eventual development of hormone-refractory tumors. We have been interested in developing therapeutics targeting specific metabolic deficiency of tumor cells. We recently showed that prostate tumor cells specifically lack an enzyme (argininosuccinate synthase, or ASS) involved in the synthesis of the amino acid arginine1. This condition causes the tumor cells to become dependent on exogenous arginine, and they undergo metabolic stress when free arginine is depleted by arginine deiminase (ADI)1,10. Indeed, we have shown that human prostate cancer cells CWR22Rv1 are effectively killed by ADI with caspase-independent apoptosis and aggressive autophagy (or macroautophagy)1,2,3. Autophagy is an evolutionarily-conserved process that allows cells to metabolize unwanted proteins by lysosomal breakdown during nutritional starvation4,5. Although the essential components of this pathway are well-characterized6,7,8,9, many aspects of the molecular mechanism are still unclear - in particular, what is the role of autophagy in the death-response of prostate cancer cells after ADI treatment? In order to address this question, we required an experimental method to measure the level and extent of autophagic response in cells - and since there are no known molecular markers that can accurately track this process, we chose to develop an imaging-based approach, using quantitative 3D fluorescence microscopy11,12.
Using CWR22Rv1 cells specifically-labeled with fluorescent probes for autophagosomes and lysosomes, we show that 3D image stacks acquired with either widefield deconvolution microscopy (and later, with super-resolution, structured-illumination microscopy) can clearly capture the early stages of autophagy induction. With commercially available digital image analysis applications, we can readily obtain statistical information about autophagosome and lysosome number, size, distribution, and degree of colocalization from any imaged cell. This information allows us to precisely track the progress of autophagy in living cells and enables our continued investigation into the role of autophagy in cancer chemotherapy.

Autophagy is a ubiquitous process that enables cells to degrade and recycle proteins and organelles. We apply advanced fluorescence microscopy to visualize and quantify the small, but essential, physical changes associated with the induction of autophagy, including the formation and distribution of autophagosomes and lysosomes, and their fusion into autolysosomes.

Prostate cancer is the leading form of malignancies among men in the U.S. While surgery carries a significant risk of impotence and incontinence, ...

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for using FISH to quantify the number of mRNAs in single yeast cells. Cells can be grown in any condition of interest and then fixed and made permeable. Subsequently, multiple single-stranded deoxyoligonucleotides conjugated to fluorescent dyes are used to label and visualize mRNAs. Diffraction-limited fluorescence from single mRNA molecules is quantified using a spot-detection algorithm to identify and count the number of mRNAs per cell. While the more standard quantification methods of northern blots, RT-PCR and gene expression microarrays provide information on average mRNAs in the bulk population, FISH facilitates both the counting and localization of these mRNAs in single cells at single-molecule resolution.

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

This protocol describes an experimental procedure for performing Fluorescence in situ Hybridization (FISH) for counting mRNAs in single cells at single-molecule resolution.

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for ...

Induction and Analysis of Epithelial to Mesenchymal Transition

Epithelial to mesenchymal transition (EMT) is essential for proper morphogenesis during development. Misregulation of this process has been implicated as a key event in fibrosis and the progression of carcinomas to a metastatic state. Understanding the processes that underlie EMT is imperative for the early diagnosis and clinical control of these disease states. Reliable induction of EMT in vitro is a useful tool for drug discovery as well as to identify common gene expression signatures for diagnostic purposes. Here we demonstrate a straightforward method for the induction of EMT in a variety of cell types. Methods for the analysis of cells pre- and post-EMT induction by immunocytochemistry are also included. Additionally, we demonstrate the effectiveness of this method through antibody-based array analysis and migration/invasion assays.

A straightforward method is described for the induction of epithelial to mesenchymal transition (EMT) in a variety of cell types. Methods for the analysis of cells in EMT states by immunocytochemistry are included.

Epithelial  to mesenchymal transition (EMT) is essential for proper morphogenesis during  development. Misregulation of this  process has been implicated ...

In vivo Clonal Tracking of Hematopoietic Stem and Progenitor Cells Marked by Five Fluorescent Proteins using Confocal and Multiphoton Microscopy

We developed and validated a fluorescent marking methodology for clonal tracking of hematopoietic stem and progenitor cells (HSPCs) with high spatial and temporal resolution to study in vivo hematopoiesis using the murine bone marrow transplant experimental model. Genetic combinatorial marking using lentiviral vectors encoding fluorescent proteins (FPs) enabled cell fate mapping through advanced microscopy imaging. Vectors encoding five different FPs: Cerulean, EGFP, Venus, tdTomato, and mCherry were used to concurrently transduce HSPCs, creating a diverse palette of color marked cells. Imaging using confocal/two-photon hybrid microscopy enables simultaneous high resolution assessment of uniquely marked cells and their progeny in conjunction with structural components of the tissues. Volumetric analyses over large areas reveal that spectrally coded HSPC-derived cells can be detected non-invasively in various intact tissues, including the bone marrow (BM), for extensive periods of time following transplantation. Live studies combining video-rate multiphoton and confocal time-lapse imaging in 4D demonstrate the possibility of dynamic cellular and clonal tracking in a quantitative manner.

In vivo Clonal Tracking of Hematopoietic Stem and Progenitor Cells Marked by Five Fluorescent Proteins using Confocal and Multiphoton Microscopy

Combinatorial 5 fluorescent proteins marking of hematopoietic stem and progenitor cells allows in vivo clonal tracking via confocal and two-photon microscopy, providing insights into bone marrow hematopoietic architecture during regeneration. This method allows non-invasive fate mapping of spectrally-coded HSPCs-derived cells in intact tissues for extensive periods of time following transplantation.

We developed and validated a fluorescent marking methodology for clonal tracking of hematopoietic stem and progenitor cells (HSPCs) with high spatial and ...

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 ...

Immunofluorescence Analysis of Endogenous and Exogenous Centromere-kinetochore Proteins

"Centromeres" and "kinetochores" refer to the site where chromosomes associate with the spindle during cell division. Direct visualization of centromere-kinetochore proteins during the cell cycle remains a fundamental tool in investigating the mechanism(s) of these proteins. Advanced imaging methods in fluorescence microscopy provide remarkable resolution of centromere-kinetochore components and allow direct observation of specific molecular components of the centromeres and kinetochores. In addition, methods of indirect immunofluorescent (IIF) staining using specific antibodies are crucial to these observations. However, despite numerous reports about IIF protocols, few discussed in detail problems of specific centromere-kinetochore proteins.1-4 Here we report optimized protocols to stain endogenous centromere-kinetochore proteins in human cells by using paraformaldehyde fixation and IIF staining. Furthermore, we report protocols to detect Flag-tagged exogenous CENP-A proteins in human cells subjected to acetone or methanol fixation. These methods are useful in detecting and quantifying endogenous centromere-kinetochore proteins and Flag-tagged CENP-A proteins, including those in human cells.

Here we report protocols to detect endogenous and exogenous centromere-kinetochore proteins in human cells and quantify these protein levels at centromeres-kinetochores by indirect immunofluorescent staining through the use of fixation (paraformaldehyde, acetone, or methanol fixation).