The authors are grateful to Anna Labernadie, Guillaume Charri&#232;re and Patrick Delobelle for their initial contribution to this work and to Matthieu Sanchez and Fran&#231;oise Viala for their help with video filming and editing. This work has been supported by l'Agence Nationale de la Recherche (ANR14-CE11-0020-02), la Fondation pour la Recherche M&#233;dicale (FRM DEQ2016 0334894), INSERM Plan Cancer, Fondation Toulouse Cancer and Human Frontier Science Program (RGP0035/2016).

1. Preparation of Formvar-Coated Grids
<ol>
	<li>Clean electron microscopy grids with pure acetone and dry them on filter paper. Then clean a microscope slide with pure ethanol, wipe with a lens paper and remove dust with a blower.</li>
	<li>Place an ethanol-cleaned glass slide vertically in the funnel of a film casting device containing a solution of Formvar in the lower part. Cover the top of the funnel.</li>
	<li>Pump 100 mL of Formvar solution (0.5% in ethylene dichloride) with the atomizer bulb until the level reaches two thirds of the slide.</li>
	<li>Keep the slide in the solution for 1 min.</li>
	<li>Open the valve of the device to drain the Formvar solution in a steady stream. A flow rate of 10 to 15 mL/s will yield a Formvar film of 30-80 nm. The thickness of the film is determined by the concentration of the Formvar solution and by the drainage rate. 
	NOTE: The drainage rate can be controlled by venting the pressure via the air-out valve by slowly opening the valve. The faster the drainage, the thicker the film. In practice, because it is difficult to predict the film thickness from the Formvar flow rate, we prepare several batches of Formvar films and control their thickness by AFM (see Step 2).</li>
	<li>Remove the slide from the chamber and dry it delicately on filter paper to remove any liquid Formvar.</li>
	<li>Cut out a 20 mm x 50 mm rectangle from the Formvar film with a razor blade.</li>
	<li>Fill a beaker with clean distilled water and slowly plunge the slide vertically into the water to float off the film: the film should float on the water surface.</li>
	<li>Place dry acetone-cleaned grids on the film, shiny face up.</li>
	<li>Place a round glass coverslip (&#216; 12 mm) onto a few of the grids. This coverslip will serve to measure the film thickness (see Step 2).</li>
	<li>Cover a microscope slide with a white sticker resized to fit it. Dip the slide vertically at the border of the floating Formvar film until the whole film adheres to the slide. Remove excess water from the slide with filter paper and let it dry at room temperature overnight.</li>
</ol>
2. Measurement of Film Thickness
<ol>
	<li>Cut the Formvar around the coverslip with tweezers to detach it from the slide.</li>
	<li>Mark the location of the grid under the coverslip with a pen.</li>
	<li>Cut the Formvar around the marked grid to detach it from the coverslip. There will therefore be a hole in the remaining Formvar sheet, which will allow to measure the film thickness. Cover the coverslip with PBS and place it on a glass slide on the microscope.</li>
	<li>Mount a silicon nitride cantilever on the AFM glass block, making sure the golden stripe is not covered by the tip of the spring. 
	NOTE: The sensitivity and spring constant of the cantilever should have previously been calibrated in PBS.</li>
	<li>Mount the glass block onto the AFM module, and then place the module onto the microscope.</li>
	<li>Place the Formvar-coated coverslip on the observation chamber and cover it with 500 &#181;L of PBS.</li>
	<li>Scan the border of the hole in the Formvar sheet using AFM in contact mode and a 0.5 nN force set point.</li>
	<li>Use the glass coverslip surface as the reference for height measurements, and evaluate the Formvar thickness as the height of the cross-section (perform at least 10 measurements per Formvar batch).</li>
</ol>
3. Seeding Cells on Grids
<ol>
	<li>Under a sterile hood, put a strip (12 mm x 3 mm) of double-sided adhesive tape on a coverslip.</li>
	<li>Cut out a Formvar-coated grid with tweezers and put it upside-down on the adhesive strip (only the rim of the grid needs to be attached to the tape). The Formvar film needs to face the coverslip.</li>
	<li>Put this device in a culture well.</li>
	<li>Place a 10 &#181;L droplet of RPMI without FCS containing 104 macrophages differentiated from human monocytes16. 
	NOTE: Make sure not to touch the grid with the pipette tip to prevent damaging the Formvar coating.</li>
	<li>Incubate for 30 min (37 &#176;C, 5% CO2) to let cells adhere.</li>
	<li>Fill up the well with 2 mL of RPMI containing 10% FCS.</li>
	<li>Incubate the device for 2 h at 37 &#176;C and 5% CO2 to let cells adhere before AFM observation.</li>
</ol>
4. Topography Measurements of Podosome-Induced Deformations
<ol>
	<li>Stick two strips of doubled-sided adhesive tape on a glass bottom Petri dish. 
	NOTE: The distance between the two strips should be smaller than the grid diameter.</li>
	<li>Carefully detach the grid plated with macrophages from the adhesive tape.</li>
	<li>Turn the grid upside-down in order to have the cells facing the glass and stick the grid between the two adhesive strips.</li>
	<li>Fix the grid with two new strips of doubled-sided adhesive: the grid will thus be sandwiched between two adhesive strips, leaving the central area of the grid accessible to the AFM tip. 
	NOTE: Make sure that the grid is well fixed and not twisted; otherwise the AFM cantilever might not be able to approach the Formvar surface.</li>
	<li>Fill the Petri dish with 2 mL of pre-heated 37 &#176;C culture medium (RPMI with 10% FCS) supplemented with 10 mM HEPES (pH 7.4).</li>
	<li>Place the culture dish on a 37 &#176;C dish heater.</li>
	<li>Install the dish heater on the AFM stage.</li>
	<li>Let the system stabilize at 37 &#176;C.</li>
	<li>In contact mode with a 0.5 nN force, make a first global image to locate podosomes, and then scan the Formvar topography at 3 Hz with an approximately 20 nm-large pixel. 
	NOTE: Avoid scanning near the edges of the grid.</li>
</ol>

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No conflicts of interest declared.

Material properties
The choice of the material for the deformable membrane, in our case Formvar, needs to fulfill a few requirements. The material must be transparent to visible light and exhibit limited auto fluorescence to allow observations in bright field and fluorescence microscopy. The roughness of the thin film must be well below 10 nm to avoid any topographical effect on cell adhesion and to allow clear observation of the cell-induced protrusions by AFM imaging. Finall...

Animal cells interact physically with the matrix and the other cells that constitute their environment1. This is required for them to migrate, internalize bodies, acquire external information, or differentiate. In such processes, the cell must generate mechanical forces and, as numerous studies have shown over the recent years, the ability of a cell to generate forces and probe its environment influences its biological behavior, directing for instance proliferation or differentiation2,3. In turn, the measurement of cellular forces is a major aid to study the regulation of force generation and understand its implication in cell behavior and tissue fate4,5.
Recent years have witnessed the development of numerous techniques to measure the forces that a cell can exert on its environment6. The majority of these have been instrumental in revealing the traction forces that cells exert as they pull on mobile probes or a deformable substrate. However, the mechanical forces involved in protrusion into the extracellular environment suffer from a lack of measurement techniques and are to date not well characterized.
To overcome this limitation, we present a method to measure forces exerted orthogonally to the substrate. It consists in plating living cells on a thin elastic sheet that can deform in the orthogonal direction, making it possible to measure substrate deformation by the cells and deduce the forces involved. Substrate topography is measured with nanoscale resolution using atomic force microscopy and the evaluation of forces from deformation relies on the knowledge of the geometry of the protrusive cellular structures7,8,9.
Here, we describe the setup and its application to measure the forces generated by podosomes, protrusive adhesion structures formed by macrophages for their mesenchymal migration in three-dimensional environments10,11,12,13,14,15,16,17. We believe that this technique will advance the understanding of force generation and its regulation in the many cellular processes involving protrusion.

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		<tr height="51">
			<td height="51" style="height:51px;width:216px;">200 mesh nickel grids</td>
			<td style="width:71px;">Electron Microscopy Sciences</td>
			<td style="width:119px;">G200-Ni</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:216px;">Filter paper</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td style="width:119px;">1001-055</td>
			<td></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:216px;">Microscope slides</td>
			<td style="width:71px;">Fisher Scientific</td>
			<td style="width:119px;">10235612</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">White stickers 26 x 70 mm</td>
			<td style="width:71px;">Avery</td>
			<td style="width:119px;">DP033-100</td>
			<td></td>
		</tr>
		<tr height="51">
			<td height="51" style="height:51px;width:216px;">Film casting device with valve in its outlet</td>
			<td style="width:71px;">Electron Microscopy Sciences</td>
			<td style="width:119px;">71305-01</td>
			<td></td>
		</tr>
		<tr height="51">
			<td height="51" style="height:51px;width:216px;">Razorblades</td>
			<td style="width:71px;">Electron Microscopy Sciences</td>
			<td style="width:119px;">72000</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Ethanol</td>
			<td style="width:71px;">VWR</td>
			<td style="width:119px;">1.08543.0250</td>
			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Acetone</td>
			<td style="width:71px;">VWR</td>
			<td style="width:119px;">20066.321</td>
			<td></td>
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		<tr height="51">
			<td height="51" style="height:51px;width:216px;">Formvar 0.5% solution in ethylene dichloride</td>
			<td style="width:71px;">Electron Microscopy Sciences</td>
			<td style="width:119px;">15820</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">12 mm coverslips</td>
			<td style="width:71px;">VWR</td>
			<td style="width:119px;">631-0666</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Inverted microscope</td>
			<td style="width:71px;">Carl Zeiss</td>
			<td style="width:119px;">Axiovert 200</td>
			<td></td>
		</tr>
		<tr height="51">
			<td height="51" style="height:51px;width:216px;">Atomic Force Microscope</td>
			<td style="width:71px;">JPK Instruments</td>
			<td style="width:119px;">NanoWizard III</td>
			<td></td>
		</tr>
		<tr height="51">
			<td height="51" style="height:51px;width:216px;">Temperature-controlled sample holder&#160;</td>
			<td style="width:71px;">JPK Instruments</td>
			<td style="width:119px;">BioCell</td>
			<td></td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:216px;">Silicon nitride cantilever with a nominal spring constant of 0.01 N/m</td>
			<td style="width:71px;">Veeco Instruments</td>
			<td style="width:119px;">MLCT-AUHW</td>
			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;width:216px;">PBS</td>
			<td style="width:71px;">Gibco</td>
			<td style="width:119px;">14190-094</td>
			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Double-sided adhesive tape</td>
			<td style="width:71px;">APLI AGIPA</td>
			<td style="width:119px;">118100</td>
			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;width:216px;">RPMI 1640</td>
			<td style="width:71px;">Gibco</td>
			<td style="width:119px;">31870-025</td>
			<td></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:216px;">FCS</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td style="width:119px;">F7524</td>
			<td></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:216px;">HEPES&#160;</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td style="width:119px;">H0887</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">35 mm glass-bottom Petri dishes</td>
			<td style="width:71px;">WPI</td>
			<td style="width:119px;">FD35-100</td>
			<td></td>
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protrusion force microscopy: a method to quantify forces developed by cell protrusions

In numerous biological contexts, animal cells need to interact physically with their environment by developing mechanical forces. Among these, traction forces have been well-characterized, but there is a lack of techniques allowing the measurement of the protrusion forces exerted by cells orthogonally to their substrate. We designed an experimental setup to measure the protrusion forces exerted by adherent cells on their substrate. Cells plated on a compliant Formvar sheet deform this substrate and the resulting topography is mapped by atomic force microscopy (AFM) at the nanometer scale. Force values are then extracted from an analysis of the deformation profile based on the geometry of the protrusive cellular structures. Hence, the forces exerted by the individual protruding units of a living cell can be measured over time. This technique will enable the study of force generation and its regulation in the many cellular processes involving protrusion. Here, we describe its application to measure the protrusive forces generated by podosomes formed by human macrophages.

The above protocol describes how to prepare the experimental setup to quantify protrusion forces applied by macrophage podosomes on a Formvar substrate. This is achieved using AFM and is illustrated in Figure 1.
When analyzing a topographical image of bulges beneath podosomes using the JPK data processing software, a third-degree polynomial fit should be subtracted from each scan line independently....

Watch this Scientific Journal Video about Protrusion Force Microscopy: A Method to Quantify Forces Developed by Cell Protrusions at JoVE.com

Protrusion Force Microscopy: A Method to Quantify Forces Developed by Cell Protrusions

Here, we detail the experimental techniques used to evaluate the protrusion forces that podosomes apply on a compliant film, from the preparation of the film to the automated analysis of topographical images.

In numerous biological contexts, animal cells need to interact physically with their environment by developing mechanical forces. Among these, traction ...

protrusion-force-microscopy-method-to-quantify-forces-developed-cell

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5.5K Views.  IPBS, Université de Toulouse, CNRS, UPS. Here, we detail the experimental techniques used to evaluate the protrusion forces that podosomes apply on a compliant film, from the preparation of the film to the automated analysis of topographical images. 

Video: Protrusion Force Microscopy: A Method to Quantify Forces Developed by Cell Protrusions

Microfabricated Post-Array-Detectors (mPADs): an Approach to Isolate Mechanical Forces

In this video, we will present our approach to measure cellular traction forces using a microfabricated array of posts.  Traction forces are generated through myosin-actin interactions and play an important role in our physiology.  During development, they enable cells to move from one location to the next in order to form the early structures of tissue.  Traction forces help in the healing processes.  They are necessary for the proper closure of wounds or the migration and crawling of leukocytes through our body.  These same forces can be detrimental to our health in the case of cancer metastasis or vascular growth towards a tumor.  The most common method by which to study cells in vitro has been to use a glass or polystyrene dish.  However, the rigidity of the substrates makes it impossible to physically measure cell traction forces, and there are relatively few methods to study traction forces.  Our lab has developed a technique to overcome these limitations.  The method is based on a vertical array of flexible cantilevers, the stiffness and size scale of which are such that individual cells spread across many cantilevers and deflect them in the process.  The pillars we use are 3 &mu;m in diameter, 10 &mu;m tall, and are configured in a regular array with 9 &mu;m center-to-center spacing.  But these physical dimensions can be readily varied to accommodate a variety of studies.  We start with a silicon master, but the final posts are made out of silicone rubber called poly (dimethyl siloxane), or PDMS.  We can measure the deflections under a microscope and calculate the magnitude and direction of traction forces required to produce the observed deflections.  We call these substrates microfabricated post-array-detectors, or mPADs.  Here, we will show you how we fabricate and use the mPADs to assess modulations of cellular contractility.

Microfabricated Post-Array-Detectors mPADs: an Approach to Isolate Mechanical Forces

In this video, we demonstrate how to fabricate and utilize microfabricated post array detectors (mPADs) to assess modulations of cellular contractility.

In this video, we will present our approach to measure cellular traction forces using a microfabricated array of posts.  Traction forces are generated ...

Live Cell Response to Mechanical Stimulation Studied by Integrated Optical and Atomic Force Microscopy

To understand the mechanism by which living cells sense mechanical forces, and how they respond and adapt to their environment, a new technology able to investigate cells behavior at sub-cellular level with high spatial and temporal resolution was developed. Thus, an atomic force microscope (AFM) was integrated with total internal reflection fluorescence (TIRF) microscopy and fast-spinning disk (FSD) confocal microscopy. The integrated system is broadly applicable across a wide range of molecular dynamic studies in any adherent live cells, allowing direct optical imaging of cell responses to mechanical stimulation in real-time. Significant rearrangement of the actin filaments and focal adhesions was shown due to local mechanical stimulation at the apical cell surface that induced changes into the cellular structure throughout the cell body. These innovative techniques will provide new information for understanding live cell restructuring and dynamics in response to mechanical force. A detailed protocol and a representative data set that show live cell response to mechanical stimulation are presented.

This paper aims to instruct the reader in the operation of an integrated atomic force-optical imaging microscope for mechanical stimulation of live cells in culture. A step-by-step protocol is presented. A representative data set that shows live cell response to mechanical stimulation is presented.

To understand the mechanism by which living cells sense mechanical forces, and how they respond and adapt to their environment, a new technology able to ...

Identifying Targets of Human microRNAs with the LightSwitch Luciferase Assay System using 3'UTR-reporter Constructs and a microRNA Mimic in Adherent Cells

MicroRNAs (miRNAs) are important regulators of gene expression and play a role in many biological processes. More than 700 human miRNAs have been identified so far with each having up to hundreds of unique target mRNAs. Computational tools, expression and proteomics assays, and chromatin-immunoprecipitation-based techniques provide important clues for identifying mRNAs that are direct targets of a particular miRNA. In addition, 3'UTR-reporter assays have become an important component of thorough miRNA target studies because they provide functional evidence for and quantitate the effects of specific miRNA-3'UTR interactions in a cell-based system. To enable more researchers to leverage 3'UTR-reporter assays and to support the scale-up of such assays to high-throughput levels, we have created a genome-wide collection of human 3'UTR luciferase reporters in the highly-optimized LightSwitch Luciferase Assay System. The system also includes synthetic miRNA target reporter constructs for use as positive controls, various endogenous 3'UTR reporter constructs, and a series of standardized experimental protocols.
Here we describe a method for co-transfection of individual 3'UTR-reporter constructs along with a miRNA mimic that is efficient, reproducible, and amenable to high-throughput analysis.

MicroRNAs (miRNAs) are important regulators of gene expression and have been shown to play a role in numerous biological processes. To better understand miRNA-UTR interactions, we have created a genome-wide collection of 3 UTR luciferase reporters paired with a novel luciferase gene and assay reagent, the LightSwitch system.

MicroRNAs (miRNAs) are important regulators of gene expression and play a role in many biological processes.  More than 700 human miRNAs have been ...

Sample Preparation for Single Virion Atomic Force Microscopy and Super-resolution Fluorescence Imaging

Immobilization of virions to glass surfaces is a critical step in single virion imaging. Here we present a technique&#160;adopted from single molecule imaging assays which allows adhesion of single virions to glass surfaces with specificity. This preparation is based on grafting the surface of the glass with a mixture of PLL-g-PEG and PLL-g-PEG-Biotin, adding a layer of avidin, and finally creating virion anchors through attachment of biotinylated virus specific antibodies. We have applied this technique across a range of experiments including atomic force microscopy (AFM) and super-resolution fluorescence imaging. This sample preparation method results in a control adhesion of the virions to the surface.

The attachment of virions to a surface is a requirement for single virion imaging by Super-resolution fluorescence imaging or atomic force microscopy (AFM). Here we demonstrate a sample preparation method for controlled adhesion of virions to glass surfaces suitable for use in AFM and super-resolution fluorescence imaging.

Immobilization of virions to glass surfaces is a critical step in single virion imaging. Here we present a technique&#160;adopted from single molecule ...

In Vivo 4-Dimensional Tracking of Hematopoietic Stem and Progenitor Cells in Adult Mouse Calvarial Bone Marrow

Through a delicate balance between quiescence and proliferation, self renewal and production of differentiated progeny, hematopoietic stem cells (HSCs) maintain the turnover of all mature blood cell lineages. The coordination of the complex signals leading to specific HSC fates relies upon the interaction between HSCs and the intricate bone marrow microenvironment, which is still poorly understood[1-2].
We describe how by combining a newly developed specimen holder for stable animal positioning with multi-step confocal and two-photon in vivo imaging techniques, it is possible to obtain high-resolution 3D stacks containing HSPCs and their surrounding niches and to monitor them over time through multi-point time-lapse imaging. High definition imaging allows detecting ex vivo labeled hematopoietic stem and progenitor cells (HSPCs) residing within the bone marrow. Moreover, multi-point time-lapse 3D imaging, obtained with faster acquisition settings, provides accurate information about HSPC movement and the reciprocal interactions between HSPCs and stroma cells.
Tracking of HSPCs in relation to GFP positive osteoblastic cells is shown as an exemplary application of this method. This technique can be utilized to track any appropriately labeled hematopoietic or stromal cell of interest within the mouse calvarium bone marrow space.

In Vivo 4-Dimensional Tracking of Hematopoietic Stem and Progenitor Cells in Adult Mouse Calvarial Bone Marrow

The nature of the interactions between hematopoietic stem and progenitor cells (HSPCs) and bone marrow niches is poorly understood. Custom hardware modifications and a multi-step acquisition protocol allow the use of two-photon and confocal microscopy to image ex vivo labeled HSPCs homed within bone marrow areas, tracking interactions and movement.

Through a delicate balance between quiescence and proliferation, self renewal and production of differentiated progeny, hematopoietic stem cells (HSCs) ...

A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay

Small molecules provide rich targets for biosensing applications due to their physiological implications as biomarkers of various aspects of human health and performance. Nucleic acid aptamers have been increasingly applied as recognition elements on biosensor platforms, but selecting aptamers toward small molecule targets requires special design considerations. This work describes modification and critical steps of a method designed to select structure-switching aptamers to small molecule targets. Binding sequences from a DNA library hybridized to complementary DNA capture probes on magnetic beads are separated from nonbinders via a target-induced change in conformation. This method is advantageous because sequences binding the support matrix (beads) will not be further amplified, and it does not require immobilization of the target molecule. However, the melting temperature of the capture probe and library is kept at or slightly above RT, such that sequences that dehybridize based on thermodynamics will also be present in the supernatant solution. This effectively limits the partitioning efficiency (ability to separate target binding sequences from nonbinders), and therefore many selection rounds will be required to remove background sequences. The reported method differs from previous structure-switching aptamer selections due to implementation of negative selection steps, simplified enrichment monitoring, and extension of the length of the capture probe following selection enrichment to provide enhanced stringency. The selected structure-switching aptamers are advantageous in a gold nanoparticle assay platform that reports the presence of a target molecule by the conformational change of the aptamer. The gold nanoparticle assay was applied because it provides a simple, rapid colorimetric readout that is beneficial in a clinical or deployed environment. Design and optimization considerations are presented for the assay as proof-of-principle work in buffer to provide a foundation for further extension of the work toward small molecule biosensing in physiological fluids.

A protocol is provided to select structure-switching aptamers for small molecule targets based on a tunable stringency magnetic bead selection method. Aptamers selected with structure-switching properties are beneficial for assays that require a conformational change to signal the presence of a target, such as the described gold nanoparticle assay.

Small molecules provide rich targets for biosensing applications due to their physiological implications as biomarkers of various aspects of human health ...

Design and Development of Aptamer&#8211;Gold Nanoparticle Based Colorimetric Assays for In-the-field Applications

The design and development of an aptamer&#8211;gold nanoparticle (AuNP) colorimetric assay for the detection of small molecules for in-the-field applications was examined. Target selective AuNP based color assays have been developed in controlled proof-of-concept laboratory settings. However, these schemes have not been exerted to a point of failure to determine their practical use beyond laboratory settings. This work describes a generic approach to design, develop, and troubleshoot an aptamer-AuNP colorimetric assay for small molecule analytes and using the assay for in-the-field settings. The assay is advantageous because adsorbed aptamers passivate the nanoparticle surfaces and provide a means to reduce and eliminate false positive responses to non-target analytes. Transitioning this system to practical uses required defining not only the shelf-life of the aptamer-AuNP assay, but establishing methods and procedures for extending the long-term storage capabilities. Also, one of the recognized concerns with colorimetric readout is the burden placed on analysts to accurately identify often subtle changes in color. To lessen the responsibility on analysts in the field, a color analysis protocol was designed to perform the color identification duties without the need for performing this task on laboratory grade equipment. The method for creating and testing the data analysis protocol is described. However to understand and influence the design of adsorbed aptamer assays, the interactions associated with the aptamer, target, and AuNPs require further study. The knowledge gained could lead to tailoring aptamers for improved functionality.

The design and development of an aptamer&#8211;gold nanoparticle colorimetric assay for the detection of small molecules for in-the-field applications was examined. Additionally, a smart-device colorimetric application (app) was validated and long-term storage of the assay was established for use in the field.

The design and development of an aptamer&#8211;gold nanoparticle (AuNP) colorimetric assay for the detection of small molecules for in-the-field ...

Novel Method of Plasmid DNA Delivery to Mouse Bladder Urothelium by Electroporation

Genetically engineered mouse models (GEMMs) are extremely valuable in revealing novel biological insights into the initiation and progression mechanisms of human diseases such as cancer. Transgenic and conditional knockout mice have been frequently used for gene overexpression or ablation in specific tissues or cell types in vivo. However, generating germline mouse models can be time-consuming and costly. Recent advancements in gene editing technologies and the feasibility of delivering DNA plasmids by viral infection have enabled rapid generation of non-germline autochthonous mouse cancer models for several organs. The bladder is an organ that has been difficult for viral vectors to access, due to the presence of a glycosaminoglycan layer covering the urothelium. Here, we describe a novel method developed in lab for efficient delivery of DNA plasmids into the mouse bladder urothelium in vivo. Through intravesical instillation of pCAG-GFP DNA plasmid and electroporation of surgically exposed bladder, we show that the DNA plasmid can be delivered specifically into the bladder urothelial cells for transient expression. Our method provides a fast and convenient way for overexpression and knockdown of genes in the mouse bladder, and can be applied to building GEMMs of bladder cancer and other urological diseases.

We describe a novel method for the delivery of DNA plasmid into the urothelial cells of mouse bladder in vivo through urethra catheterization and electroporation. It offers a fast and convenient way for generating autochthonous mouse models of bladder diseases.

Genetically engineered mouse models (GEMMs) are extremely valuable in revealing novel biological insights into the initiation and progression mechanisms ...

Applications of Spatio-temporal Mapping and Particle Analysis Techniques to Quantify Intracellular Ca2+ Signaling In Situ

Ca2+ imaging of isolated cells or specific types of cells within intact tissues often reveals complex patterns of Ca2+ signaling. This activity requires careful and in-depth analyses and quantification to capture as much information about the underlying events as possible. Spatial, temporal and intensity parameters intrinsic to Ca2+ signals such as frequency, duration, propagation, velocity and amplitude may provide some biological information required for intracellular signalling. High-resolution Ca2+ imaging typically results in the acquisition of large data files that are time consuming to process in terms of translating the imaging information into quantifiable data, and this process can be susceptible to human error and bias. Analysis of Ca2+ signals from cells in situ typically relies on simple intensity measurements from arbitrarily selected regions of interest (ROI) within a field of view (FOV). This approach ignores much of the important signaling information contained in the FOV. Thus, in order to maximize recovery of information from such high-resolution recordings obtained with Ca2+dyes or optogenetic Ca2+ imaging, appropriate spatial and temporal analysis of the Ca2+ signals is required. The protocols outlined in this paper will describe how a high volume of data can be obtained from Ca2+ imaging recordings to facilitate more complete analysis and quantification of Ca2+ signals recorded from cells using a combination of spatiotemporal map (STM)-based analysis and particle-based analysis. The protocols also describe how different patterns of Ca2+ signaling observed in different cell populations in situ can be analyzed appropriately. For illustration, the method will examine Ca2+ signaling in a specialized population of cells in the small intestine, interstitial cells of Cajal (ICC), using GECIs.

Applications of Spatio-temporal Mapping and Particle Analysis Techniques to Quantify Intracellular Ca2+ Signaling In Situ

Genetically encoded Ca2+ indicators (GECIs) have radically changed how in situ Ca2+ imaging is performed. To maximize data recovery from such recordings, appropriate analysis of Ca2+ signals is required. The protocols in this paper facilitate the quantification of Ca2+ signals recorded in situ using spatiotemporal mapping and particle-based analysis.

Ca2+ imaging of isolated cells or specific types of cells within intact tissues often reveals complex patterns of Ca2+ signaling. This activity requires ...

Live-cell Imaging of Single-Cell Arrays (LISCA) - a Versatile Technique to Quantify Cellular Kinetics

Live-cell Imaging of Single-Cell Arrays (LISCA) is a versatile method to collect time courses of fluorescence signals from individual cells in high throughput. In general, the acquisition of single-cell time courses from cultured cells is hampered by cell motility and diversity of cell shapes. Adhesive micro-arrays standardize single-cell conditions and facilitate image analysis. LISCA combines single-cell microarrays with scanning time-lapse microscopy and automated image processing. Here, we describe the experimental steps of taking single-cell fluorescence time courses in a LISCA format. We transfect cells adherent to a micropatterned array using mRNA encoding for enhanced green fluorescent protein (eGFP) and monitor the eGFP expression kinetics of hundreds of cells in parallel via scanning time-lapse microscopy. The image data stacks are automatically processed by newly developed software that integrates fluorescence intensity over selected cell contours to generate single-cell fluorescence time courses. We demonstrate that eGFP expression time courses after mRNA transfection are well described by a simple kinetic translation model that reveals expression and degradation rates of mRNA. Further applications of LISCA for event time correlations of multiple markers in the context of signaling apoptosis are discussed.

Live-cell Imaging of Single-Cell Arrays LISCA - a Versatile Technique to Quantify Cellular Kinetics

We present a method for the acquisition of fluorescence reporter time courses from single cells using micropatterned arrays. The protocol describes the preparation of single-cell arrays, the setup and operation of live-cell scanning time-lapse microscopy and an open-source image analysis tool for automated preselection, visual control and tracking of cell-integrated fluorescence time courses per adhesion site.

Live-cell Imaging of Single-Cell Arrays (LISCA) is a versatile method to collect time courses of fluorescence signals from individual cells in high ...