The authors thank Tom Kodger, Michael Landry, and Christopher J. Barrett for assistance with bead synthesis. A.J.E. acknowledges Natural Sciences and Engineering Research Council grants RGPIN/05843-2014 and EQPEQ/472339-2015, Canadian Institutes of Health Research grant no. 143327, Canadian Cancer Society grant no. 703930, and Canadian Foundation for Innovation Project #32749. R. Krishnan acknowledges National Institutes of Health grant no. R21HL123522 and R01HL136209. H.Y. was supported by Fonds de recherche Sant&#233; Qu&#233;bec, and Fonds de recherche Nature et Technologies Qu&#233;bec. The authors thank Johanan Idicula for assistance with the video and manuscript and Zixin He for assistance in preparing the video.

NOTE: The following protocol will guide researchers in fabricating and using the multi-well TFM dish shown in Figure 1.
1. Preparation of PDMS silicone substrates
<ol>
	<li>Preparation of PDMS silicone rubber mixture based on a composite mixture of two commercially available kits.
	<ol>
		<li>Add Part A and Part B of PDMS kit (e.g., GEL-8100, see the Table of Materials) in a 1:1 weight ratio into the 50 mL tube. 
		NOTE: The mixture is mixed on a rotator at a speed slow enough for the mixture to flow back and forth during revolution to ensure complete mixing.</li>
		<li>Add the required amount of curing agent for the desired modulus of the substrate. 
		NOTE: The amount of curing agent to be added to the mixture depends on the desired modulus of the substrate and may typically range from 0.1% to 1.8%. Refer to Table 1 and Figure 3 for a guide to specific crosslinker concentrations and resulting moduli.</li>
		<li>Mix the formulation on the rotator for 30-45 min; ensure the rotation is slow enough for thorough mixing.</li>
	</ol>
	</li>
	<li>Bottom layer: coating PDMS substrates on the glass slide
	<ol>
		<li>Place the custom-built chuck illustrated in Figure 2 on the spin-coater. Clean the glass with ethanol or isopropanol, and dry with a lint-free wipe. Place the glass slide in the chuck and turn on the vacuum to hold the slide in place.</li>
		<li>Apply uncured PDMS approximately 1 cm from the edges and work in towards the center. Apply enough (3-4 mL) PDMS to ensure the whole surface will be covered. 
		NOTE: To ensure that the PDMS is evenly spread on the surface of the glass, a pipette tip may be helpful to spread the PDMS mixture from the center to the edges.</li>
		<li>Spin the glass with the PDMS mixture on a spin-coater with the following protocol.
		<ol>
			<li>To spread the uncured PDMS on the slide, accelerate at 50 rpm/s from 0 to 200 rpm; hold at 200 rpm for 1 min.</li>
			<li>To achieve a 100 &#181;m thick PDMS layer, accelerate at 50 rpm/s to 300 rpm and hold for 1 min at 300 rpm. Different desired thicknesses other than 100 &#181;m will require specific speed values.</li>
			<li>To remove, decelerate at 50 rpm/s to 0 rpm. Disable vacuum and remove the coated slide, taking care not to touch the coated surface. 
			NOTE: It is important to include the acceleration and deceleration steps to ensure a smooth continuous surface. 
			CAUTION: To ensure that the sample does not fly off the chuck, the custom-made holder should be used to hold the slide, and not rely simply on vacuum and the existing flat chuck. The details and specifications of this holder are given in Figure 2.</li>
		</ol>
		</li>
		<li>Place the spin-coated sample in the oven at the manufacturer recommended temperature (100 &#176;C) for 2 h. 
		NOTE: The surface of the oven where the sample is placed should be solid (i.e., not a wire rack) and level surface to ensure the uniform heating and thickness of the sample. A ceramic or steel plate makes an ideal surface.</li>
	</ol>
	</li>
	<li>Top bead layer
	<ol>
		<li>Add bead solution in the appropriate ratio to the remaining PDMS mixture. 
		NOTE: This ratio depends on the concentration of the stock bead solution and the desired bead density on the sample. Typical final values are 9.2 x 1011 beads/mL and 0.05-0.2 beads/&#181;m2, and an excess of beads is generally preferable to an inadequate amount.</li>
		<li>Mix the bead solution with the uncured PDMS. This may be accomplished by placing the tube on a rotator for approximately 30 min, vortexing for 1-2 min, or sonication for 30 min. These methods may be combined. 
		NOTE: In our application, we find that sonication is effective in breaking bead aggregates, and rotation is effective in mixing. Synthesized fiduciary beads may aggregate in storage. Prior to use, they may be resuspended in hexane and sonicated. If there are significant large aggregates, one can filter the bead suspension through a 5 &#181;m syringe filter. This filtration step is optional; it helps to coat the sample with monodispersed beads, but a significant fraction of beads may be lost in the filter.</li>
		<li>Take out the slide from the oven, allow to cool to room temperature, and place it on the spin-coater.</li>
		<li>Add 3-4 mL of the bead and uncured PDMS mixture onto the surface of the coated sample. 
		NOTE: The mixture with beads added is less viscous due to the hexane. Make sure not to touch the surface of the substrate as it may damage the already-coated PDMS substrate. Additionally, the bead mixture may initially not wet the surface; take care that the mixture does not immediately flow off the cured PDMS surface.</li>
		<li>Spin the sample with the following protocol.
		<ol>
			<li>To spread the bead and uncured PDMS mixture, accelerate at 100 rpm/s from 0 to 500 rpm; hold at 500 rpm for 1 min.</li>
			<li>To achieve a thin layer of bead-embedded PDMS (~1 &#181;m), accelerate at 200 rpm/s from 500 to 5000 rpm; hold at 5000 rpm for 10 s.</li>
			<li>To remove, decelerate at 100 rpm/s to 0 rpm. Disable vacuum and remove coated slide, taking care not to touch the coated surface.</li>
		</ol>
		</li>
		<li>Place the spin-coated sample in the oven at 100 &#176;C for 1 h. 
		NOTE: Temperatures above 100 &#176;C or durations longer than 1 h can reduce the bead fluorescence. Make sure that the oven temperature is set to 100 &#176;C and not higher.</li>
		<li>The protocol can be paused here. To store the sample, cover the surface to avoid dust and light exposure. Make sure that nothing touches the surface. The sample is shelf-stable at room temperature indefinitely.</li>
	</ol>
	</li>
	<li>Assembling the plate
	<ol>
		<li>Add Part A (base) and Part B (curing agent, e.g., Sylgard) of a PDMS elastomer kit in a 10:1 weight ratio into the 50 mL tube.</li>
		<li>Mix the mixture on the rotator for 30-45 min. 
		NOTE: For one plate, mix 5 mL of base with 0.5 mL of curing agent. Up to 1 mL of hexane can be added to reduce the viscosity of the mixture.</li>
		<li>Apply the mixture to the bottom of the divider and spread the mixture. 
		NOTE: The divider should be placed upside-down.</li>
		<li>Lay the substrate onto the divider upside-down.</li>
		<li>Place the sample upside-down in the oven at 65 &#176;C for 2 h.</li>
		<li>Take out samples from the oven and clean the bottom of the glass with 70% ethanol or isopropanol to remove any PDMS residue. 
		NOTE: The protocol can be paused here. To store the sample, place a lid on the substrate and wrap the device in aluminum foil to avoid exposure to the light. The sample is shelf-stable at room temperature indefinitely. The divider utilized in this method is in a 96-well format; however, researchers may employ other formats (384-well, 2-well, 4-well, 8-well, etc.) depending on desired experiment setups and availability of dividing structures. Some further optimization may be required.</li>
	</ol>
	</li>
</ol>
2. Surface functionalization
<ol>
	<li>Dissolve 80 &#181;L of a Sulfo-SANPAH aliquot in 40 mL of 0.1 M HEPES buffer (pH 7-9). 
	NOTE: Prepare Sulfo-SANPAH aliquots by dissolving 100 mg of Sulfo-SANPAH powder in 2 mL of sterile dimethyl sulfoxide (DMSO). Prepare 0.1 M HEPES buffer by diluting 50 mL of HEPES in 450 mL of sterile deionized water and filter through a 0.22 &#181;m pore filter.</li>
	<li>Add 200 &#181;L of diluted Sulfo-SANPAH solution to each well of the 96-well plate.</li>
	<li>Expose the plate to UV (300-460nm) light at appropriate distance and duration. 
	NOTE: After UV exposure, the color of the solution should be darker. UV exposure distance and duration depend on the UV lamp power. In our application, we expose for 10-15 min at a distance of 5 cm.</li>
	<li>Remove the Sulfo-SANPAH solution from the wells and add 200 &#181;L of 5 &#181;g/mL fibronectin solution to each well. 
	NOTE: Researcher-specified protein can be used for surface coating. Some commonly used proteins are collagen, fibronectin, and laminin. We have found Sulfo-SANPAH to be the most effective method, and plasma cleaning while sometimes employing in PDMS is discouraged as it creates a silicon dioxide layer and visibly damages the surface.</li>
	<li>Incubate the plate at 4 &#176;C overnight. 
	NOTE: Different incubation methods can be applied depending on the protein used for coating.</li>
	<li>Remove the fibronectin solution and wash each well with phosphate-buffered saline (PBS)&#160;twice.</li>
	<li>Place a lid on the sample.</li>
	<li>Add 200 &#181;L of PBS to each well. 
	NOTE: The protocol can be paused here. The fibronectin-coated samples can be stored at 4 &#176;C for up to 2 weeks.</li>
</ol>
3. UV sterilization
<ol>
	<li>Sterilize the sample under UV light in a biological safety cabinet for 30 min. 
	NOTE: Longer UV exposure times may negatively impact the bead fluorescence. All subsequent steps must be performed under sterile conditions.</li>
</ol>
4. Cell culture
<ol>
	<li>Remove PBS from each well and add 200 &#181;L of cells suspended in culture media to each well.
	<ol>
		<li>Plate the cells at the desired cell density. Cell density depends on the desired experiment. For single cell studies, cells should be minimum of 50 &#181;m apart and cells near the edges of the imaging window should be not be included in the TFM measurement. For monolayer cells, the imaging window should have the viewing field covered with a confluent layer of cells.</li>
		<li>Prepare the complete growth culture media for NMuMG cells by supplementing DMEM with 5% FBS, 10 mM HEPES, 10 &#181;g/mL insulin, 1% penicillin-streptomycin, 1 mM L-glutamine, and 0.5 &#181;g/mL amphotericin B.</li>
		<li>Prepare insulin stock by reconstituting in acidified water (2.5 mL of glacial acetic acid in 130 mL of deionized water) to a concentration of 10 mg/mL. Store the stock solution at 4 &#176;C. Wait until the solution is clear, and then filter through a 0.22 &#181;m pore filter.</li>
	</ol>
	</li>
	<li>TGF-&#946; addition
	<ol>
		<li>To prepare of TGF-&#946; stock, dissolve 2 &#181;g of TGF-&#946; in 100 &#181;L of 10 mM citric acid (pH 3.0) and filter sterilize with 0.22 &#181;m pores. Vortex the tube and aliquot into the desired volumes. Store the aliquots at -80 &#176;C.</li>
		<li>Add 1.5 &#181;L of TGF-&#946; stock solution to 10 mL of the complete cell culture media to constitute the cell culture media with the final TGF-&#946; concentration of 3 ng/mL. 
		NOTE: To make 10 mM pH 3.0 citric acid, dilute the acid in water and adjust pH to 3.0 by adding HCl.</li>
	</ol>
	</li>
</ol>
5. Data acquisition
<ol>
	<li>For each position, acquire at least one image of fiduciary particles and cells. Focus on the bead layer. 
	NOTE: Pixel size should be optimized based on size of the fiduciary particles and image processing method being used. In this application, the authors use a 10x 0.4 NA objective, and images are acquired with 1024 x 1024 resolution, with 455 nm/pixel. In general, it is helpful to retain a resolution of at least approximately 1-5 pixels per bead; here, beads are polydisperse and have an individual size of 300-500 nm. It is critical that the fluorescent fiduciary beads be in focus for images to be used for TFM calculations. The focus and imaging quality of the beads should be prioritized over imaging the cells themselves. There should be no cross-talk between different channels, particularly any fluorescence not from the fiduciary beads which appears in the imaging spectra of the beads.</li>
	<li>Once all the positions of interest have been recorded, add detachment solution to each well to acquire force-free reference images of the fiduciary particles.
	<ol>
		<li>To prepare cell detachment solution, mix an aqueous solution containing 2% TritonX-100, 50 mM sodium azide, and 500 mM potassium hydroxide. 
		NOTE: The above is provided as an example of an effective detachment solution. Different detachment solutions at researchers&#39; discretion may be used to detach the cells off the substrate surface.</li>
	</ol>
	</li>
</ol>
6. Image analysis
<ol>
	<li>Perform appropriate image analysis as desired. 
	NOTE: Analysis software was developed in-house. Image analysis may be done with custom-made software or software available online.</li>
</ol>
7. Bead synthesis
NOTE: The following protocol is based on the synthesis method described by Klein et al.10.
<ol>
	<li>Under a fume hood, prepare the three-neck flask with a water-cooled reflux condenser. 
	CAUTION: Set up a synthesis in a well-ventilated chemical fume hood.</li>
	<li>Add 0.5 mL of PDMS stabilizer and fluorophore to the flask.</li>
	<li>Equip one neck with a rubber septum with a nitrogen inlet needle and an outlet needle and equip the other neck with a rubber septum for adding reagent with a syringe.</li>
	<li>Add 100 mL of anhydrous hexane in 250 mL to the flask and add a small magnetic stir bar.</li>
	<li>Place the flask in the mineral oil bath at 75 &#176;C and purge it with nitrogen gas for 1 h.</li>
	<li>Add 6 mL of methylmethacrylate to a 25 mL round bottom flask.</li>
	<li>Add 0.100 g of 2,2&#39;-azobisisobutyronitrile (AIBN) to the round bottom flask and purge the mixture with nitrogen gas for 1 h. 
	NOTE: Flush methylamethacrylate through prepacked column to remove inhibitors before use. Add methylamethacrylate and AIBN mixture to the three-neck flask.</li>
	<li>The solution initially becomes cloudy and turns milky. Let the reaction run for 3 h after the solution becomes cloudy.</li>
	<li>After 3 h, place the flask in an ice water bath.</li>
	<li>Vacuum-filter the solution with coarse filter paper.</li>
	<li>Centrifuge the filtrate and re-suspend the particles in hexane. 
	NOTE: The volume of the hexane to be added depends on the desired concentration of the bead solution. Sonication facilitates re-dispersion of the bead particles in hexane solution. Beads produced by the authors have polydisperse diameters of approximately 300-500nm. Due to the use of cross-correlation pattern tracking to determine displacements, monodisperse beads are not required.</li>
</ol>
8. Rheology measurement protocol
NOTE: Rheology is not required for every researcher or experiment, but is necessary to quantify the moduli for new formulations of PDMS. In this protocol, we employ a shear rheometer to measure the effects of crosslinker, frequency, and strain on moduli of PDMS samples. Depending on the available tools and expertise, moduli may also be measured using many other mechanical analysis approaches. Additionally, researchers using this protocol may elect to use our published moduli presented in Table 1, Figure 3 and Figure 4.
<ol>
	<li>Use a rheometer with a 25 mm diameter parallel plate geometry. Other geometries may be used.</li>
	<li>Initialize the system and calibrate the device and measuring system (parallel plate, d = 25 mm). After measuring the zero gap, begin loading the PDMS sample.</li>
	<li>As soon as the PDMS elastomer and crosslinking agent have been mixed, pipet the mixture onto the bottom plate of rheometer.
	<ol>
		<li>Move the spindle down to completely contact the top of the PDMS sample.</li>
		<li>Carefully trim the loaded sample excess from the bottom plate.</li>
	</ol>
	</li>
	<li>In a strain sweep test, apply increasing strains for each composition with different crosslinking density to ensure the polymer structure remains in the linear viscoelastic regime during all shear measurements. 
	NOTE: Strain values relevant for cell studies are typically in the range of 0.1-10%. We have found PDMS to be linear up to approximately 100% strain.</li>
	<li>Measure the dynamic shear storage modulus (G&#39;), and loss modulus (G&#8242;&#8242;) of the PDMS network in a time sweep test with frequency of 1 Hz and oscillatory shear strain of 0.5% at 100 &#176;C.</li>
	<li>To determine the viscoelasticity and time dependency of the final PDMS network, apply a frequency sweep test with frequency ranging 0.1-100 Hz and oscillatory shear strain of 0.5%.</li>
</ol>

<ol>
	<li>Harris, A., Wild, P., Stopak, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Silicone+rubber+substrata:+a+new+wrinkle+in+the+study+of+cell+locomotion.">Silicone rubber substrata: a new wrinkle in the study of cell locomotion.</a> Science. 208 (4440), 177-179 (1980).</li><li>Oliver, T., Dembo, M., Jacobson, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Traction+forces+in+locomoting+cells.">Traction forces in locomoting cells.</a> Cell Motil Cytoskeleton. 31 (3), 225-240 (1995).</li><li>Dembo, M., Wang, Y. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stresses+at+the+Cell-to-Substrate+Interface+during+Locomotion+of+Fibroblasts.">Stresses at the Cell-to-Substrate Interface during Locomotion of Fibroblasts.</a> Biophysical Journal. 76 (4), 2307-2316 (1999).</li><li>Yoshie, H., Koushki, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Traction+Force+Screening+Enabled+by+Compliant+PDMS+Elastomers.">Traction Force Screening Enabled by Compliant PDMS Elastomers.</a> Biophysical Journal. 114 (9), 2194-2199 (2018).</li><li>Park, C. Y., Zhou, E. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+screening+for+modulators+of+cellular+contractile+force.">High-throughput screening for modulators of cellular contractile force.</a> Integrative biology quantitative biosciences from nano to macro. 7 (10), 1318-1324 (2015).</li><li>Kraning-Rush, C. M., Califano, J. P., Reinhart-King, C. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cellular+traction+stresses+increase+with+increasing+metastatic+potential.">Cellular traction stresses increase with increasing metastatic potential.</a> PLoS ONE. 7 (2), e32572 (2012).</li><li>Agus, D. B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+physical+sciences+network+characterization+of+non-tumorigenic+and+metastatic+cells.">A physical sciences network characterization of non-tumorigenic and metastatic cells.</a> Scientific Reports. 3 (1), 1449 (2013).</li><li>Guo, M., Ehrlicher, A. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Probing+the+Stochastic,+Motor-Driven+Properties+of+the+Cytoplasm+Using+Force+Spectrum+Microscopy.">Probing the Stochastic, Motor-Driven Properties of the Cytoplasm Using Force Spectrum Microscopy.</a> Cell. 158 (4), 822-832 (2014).</li><li>Ngan, E., Northey, J. J., Brown, C. M., Ursini-Siegel, J., Siegel, P. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+complex+containing+LPP+and+alpha-actinin+mediates+TGFbeta-induced+migration+and+invasion+of+ErbB2-expressing+breast+cancer+cells.">A complex containing LPP and alpha-actinin mediates TGFbeta-induced migration and invasion of ErbB2-expressing breast cancer cells.</a> Journal of Cell Science. 126 (Pt 9), 1981-1991 (2013).</li><li>Klein, S. M., Manoharan, V. N., Pine, D. J., Lange, F. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preparation+of+monodisperse+PMMA+microspheres+in+nonpolar+solvents+by+dispersion+polymerization+with+a+macromonomeric+stabilizer.">Preparation of monodisperse PMMA microspheres in nonpolar solvents by dispersion polymerization with a macromonomeric stabilizer.</a> Colloid &amp; Polymer Science. 282 (1), 7-13 (2003).</li></ol>

AJE and RK have interest in Live Cell Technologies, a company which fabricates materials described in this article.

For the success of this method, it is critical to have a uniformly coated sample with a constant thickness of approximately 100 &#181;m. The modulus should be carefully chosen to examine the physical significance of the biological system of interest. When fabricating a top layer, the concentration of the fiducial fluorescent particles should be optimized for accurate analysis of displacement and traction stress. Analyzing isolated single cells requires a denser fiduciary layer than measuring confluent monolayers. Additio...

Acto-myosin contractility is an essential element of active cell mechanics, impacting cell behaviors from motility and proliferation to stem cell differentiation. In tissues, contractility drives activity from polar separation in embryogenesis, to airway constriction and cardiac activity. Critically, to generate tension, cells must first adhere to their extracellular environment. In doing so, this contractility generates traction forces on their surroundings. Traction Force Microscopy (TFM) has emerged in a multitude of forms as a way to quantify these forces from diverse cells under different conditions.
The field of TFM has seen an exceptional breadth of innovation and application, and the results have paved the way for new perspectives in biology, which incorporate mechanics and physical forces. Starting with wrinkling silicone substrates1, researchers have applied various techniques to measure cell traction forces. These approaches have been continuously improved and have now reached a level of resolution on the order of several microns2. However, one principal problem has emerged, which is the difficulty in creating substrates of suitably low moduli using the available silicones. To circumvent this problem, polyacrylamide was adopted as a replacement due to the ease of creating substrates on the order of 1-20 kPa3. We recently implemented very compliant silicones in TFM4, allowing us to fabricate the same range of moduli as polyacrylamide, but with the advantages of inert and robust silicone.
TFM approaches have enabled valuable mechano-biological discoveries, however, a persistent shortcoming is their complexity, often restricting their use to researchers in the engineering or physical sciences disciplines. This is due&#160;in large part&#160;to the detailed calibrations and challenging calculations that are required to quantify contractility. Another significant challenge is that TFM methods are largely low-throughput and therefore ill-suited to study many different conditions or populations simultaneously5. This has presented a bottleneck, which has hampered transfer of TFM from a specialist biophysics setting into broader biological and pharmacological&#160;applications.
We have recently developed a multi-well format TFM plate, which allows researchers to parallelize their TFM measurements for faster quantification of contractility metrics, while exploring the impact of different compounds and also using less reagents4. This methodology has broad utility in diverse mechanobiology studies, from evaluating the effects of compounds on cellular activity, to quantifying the contractile changes in differentiation or disease.
One area of biomedical research that will benefit greatly from TFM is the study of how physical cues impact the malignant phenotypes of cancer cells. Metastasis, responsible for 90% of cancer-related deaths, is characterized by cancerous cells leaving their original tumor site and colonizing a secondary site. For cells to migrate through tissue and pass in and out of the vascular system, they must radically change their shapes to squeeze through these physical barriers while generating substantial forces to pull their way along extracellular matrix or move between other cells. These forces are transmitted to the substrate through focal adhesion interactions2,3, and can be quantified using TFM. While cancers are biochemically exceptionally diverse, with an expanding repertoire of known mutations and protein changes, some common physical changes have been observed; in a variety of cancers, including breast, prostate, and lung cancers, metastatic cells have been shown to exert 2-3 times the traction forces of non-metastatic cells6,7,8. These results suggest that there may be a strong correlation between metastatic progression and the traction forces exerted by cells; however, the detailed time-dependent changes in contractility are difficult to examine.
The epithelial-to-mesenchymal transition (EMT) is a process whereby cells reduce adherens- and tight-junction mediated cell-cell adhesion, becoming more migratory and invasive. In addition to physiological functions that include wound healing and developmental processes, EMT is also a process exploited during metastasis, making it a useful model system to study this process. Using TGF-&#946;, we can induce the EMT in&#160;murine mammary epithelial cells (NMuMG)9 to directly quantify the physical changes during this transformation, and characterize the time and dose-dependent effects of TGF-&#946; on EMT and cell contractility. In this article, we demonstrate the utility of this approach by measuring the changes in contractility during an induced EMT.

<table border="0" cellpadding="0" cellspacing="0" style="border-collapse:
 collapse;width:824pt" width="1100">
	<tbody>
		<tr height="21" style="height:15.6pt">
			<td class="xl75" colspan="4" height="21" style="height:15.6pt;
 width:824pt" width="1100">Plate</td>
		</tr>
		<tr height="42" style="height:31.2pt">
			<td class="xl69" height="42" style="height:31.2pt;width:206pt" width="275">GEL-8100</td>
			<td class="xl69" style="width:206pt" width="275">Nusil Technology</td>
			<td class="xl69" style="width:206pt" width="275">GEL-8100</td>
			<td class="xl70" style="width:206pt" width="275">High Purity Dielectric, Soft Silicone Gel kit</td>
		</tr>
		<tr height="42" style="height:31.2pt">
			<td class="xl70" height="42" style="height:31.2pt;width:206pt" width="275">Dow Corning Sylgard 184 Silicone Encapsulant Clear 0.5 kg Kit</td>
			<td class="xl69" style="width:206pt" width="275">Ellsworth Adhesives</td>
			<td class="xl69" style="width:206pt" width="275">184 SIL ELAST KIT 0.5KG</td>
			<td class="xl69" style="width:206pt" width="275">curing agent</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl69" height="21" style="height:15.6pt;width:206pt" width="275">Custom Cut Glass&#160;</td>
			<td class="xl69" style="width:206pt" width="275">Hausser Scientific Company</td>
			<td class="xl69" style="width:206pt" width="275"></td>
			<td class="xl69" style="width:206pt" width="275">109.6mm&#177; x 72.8mm&#177; x 1mm thickness</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl69" height="21" style="height:15.6pt;width:206pt" width="275">Target 2TM Nylon Syringe Filter</td>
			<td class="xl69" style="width:206pt" width="275">ThermoFisher Scientific</td>
			<td class="xl69" style="width:206pt" width="275">F2513-4</td>
			<td class="xl69" style="width:206pt" width="275"></td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl69" height="21" style="height:15.6pt;width:206pt" width="275">96-well Stripwell Egg Crate Strip Holder</td>
			<td class="xl69" style="width:206pt" width="275">Corning</td>
			<td class="xl69" style="width:206pt" width="275">2572</td>
			<td class="xl69" style="width:206pt" width="275"></td>
		</tr>
		<tr height="42" style="height:31.2pt">
			<td class="xl69" height="42" style="height:31.2pt;width:206pt" width="275">Polystyrene Universal Microplate Lid With Corner Notch&#160;</td>
			<td class="xl69" style="width:206pt" width="275">Corning</td>
			<td class="xl69" style="width:206pt" width="275">3099</td>
			<td class="xl69" style="width:206pt" width="275"></td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl69" height="21" style="height:15.6pt;width:206pt" width="275">Ethyl alcohol</td>
			<td class="xl69" style="width:206pt" width="275">Greenfield Global</td>
			<td class="xl69" style="width:206pt" width="275">P016EA95</td>
			<td class="xl69" style="width:206pt" width="275">0.95</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl69" height="21" style="height:15.6pt;width:206pt" width="275">2-Propanol</td>
			<td class="xl69" style="width:206pt" width="275">Sigma-Aldrich</td>
			<td class="xl69" style="width:206pt" width="275">190764</td>
			<td class="xl69" style="width:206pt" width="275">ACS reagent, &#8805;99.5%</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl76" colspan="4" height="21" style="height:15.6pt;
 width:824pt" width="1100">Surface Coating</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl66" height="21" style="height:15.6pt;width:206pt" width="275">Sulfo-SANPAH Crosslinker</td>
			<td class="xl65" style="width:206pt" width="275">Proteochem</td>
			<td class="xl66" style="width:206pt" width="275">c1111-100mg</td>
			<td class="xl65" style="width:206pt" width="275"></td>
		</tr>
		<tr height="42" style="height:31.2pt">
			<td class="xl66" height="42" style="height:31.2pt;width:206pt" width="275">Fibronectin bovine plasma</td>
			<td class="xl65" style="width:206pt" width="275">Sigma-Aldrich</td>
			<td class="xl65" style="width:206pt" width="275">F1141-1MG</td>
			<td class="xl65" style="width:206pt" width="275">solution, sterile-filtered, BioReagent, suitable for cell culture</td>
		</tr>
		<tr height="42" style="height:31.2pt">
			<td class="xl65" height="42" style="height:31.2pt;width:206pt" width="275">PBS, 1X</td>
			<td class="xl65" style="width:206pt" width="275">Wisent</td>
			<td class="xl65" style="width:206pt" width="275">319-005-CL</td>
			<td class="xl66" style="width:206pt" width="275">pH 7.4, without calcium and magnesium</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl64" height="21" style="height:15.6pt;width:206pt" width="275">DMSO</td>
			<td class="xl64" style="width:206pt" width="275">Sigma-Aldrich</td>
			<td align="right" class="xl64" style="width:206pt" width="275">472301</td>
			<td class="xl64" style="width:206pt" width="275"></td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl77" colspan="4" height="21" style="height:15.6pt;
 width:824pt" width="1100">Cell Culture</td>
		</tr>
		<tr height="42" style="height:31.2pt">
			<td class="xl65" height="42" style="height:31.2pt;width:206pt" width="275">DMEM, 1X</td>
			<td class="xl65" style="width:206pt" width="275">Wisent</td>
			<td class="xl65" style="width:206pt" width="275">319-005-CL</td>
			<td class="xl65" style="width:206pt" width="275">4.5g/L glucose, with L-glutamine, sodium pyruvate and phenol red</td>
		</tr>
		<tr height="42" style="height:31.2pt">
			<td class="xl65" height="42" style="height:31.2pt;width:206pt" width="275">FBS (Fetal Bovine Serum)</td>
			<td class="xl65" style="width:206pt" width="275">Wisent</td>
			<td class="xl65" style="width:206pt" width="275">080-150</td>
			<td class="xl66" style="width:206pt" width="275">Premium Quality,&#160;Endotoxin &#60;1, Hemoglobin &#60;25</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl65" height="21" style="height:15.6pt;width:206pt" width="275">HEPES</td>
			<td class="xl65" style="width:206pt" width="275">Wisent</td>
			<td class="xl65" style="width:206pt" width="275">330-050-EL</td>
			<td class="xl65" style="width:206pt" width="275">1M, free acid</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl65" height="21" style="height:15.6pt;width:206pt" width="275">Human Insulin Recombinant</td>
			<td class="xl65" style="width:206pt" width="275">Wisent</td>
			<td class="xl65" style="width:206pt" width="275">511-016-CM</td>
			<td class="xl66" style="width:206pt" width="275">USP grade</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl66" height="21" style="height:15.6pt;width:206pt" width="275">Penicillin-Streptomycin Solution</td>
			<td class="xl65" style="width:206pt" width="275">Wisent</td>
			<td class="xl65" style="width:206pt" width="275">450-201-EL</td>
			<td class="xl65" style="width:206pt" width="275">100 X, sterile filtered for cell culture</td>
		</tr>
		<tr height="42" style="height:31.2pt">
			<td class="xl65" height="42" style="height:31.2pt;width:206pt" width="275">L-Glutamine solution</td>
			<td class="xl65" style="width:206pt" width="275">Wisent</td>
			<td class="xl65" style="width:206pt" width="275">609-065-EL</td>
			<td class="xl65" style="width:206pt" width="275">200mM solution, sterile filtered for cell culture</td>
		</tr>
		<tr height="42" style="height:31.2pt">
			<td class="xl65" height="42" style="height:31.2pt;width:206pt" width="275">Amphotericine B</td>
			<td class="xl65" style="width:206pt" width="275">Wisent</td>
			<td class="xl65" style="width:206pt" width="275">450-105-QL</td>
			<td class="xl66" style="width:206pt" width="275">250&#956;g/ml, sterile filtered for cell culture</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl66" height="21" style="height:15.6pt;width:206pt" width="275">Recombinant Human TGF-&#946;1</td>
			<td class="xl65" style="width:206pt" width="275">Peprotech</td>
			<td class="xl65" style="width:206pt" width="275">100-21</td>
			<td class="xl65" style="width:206pt" width="275">HEK293 Derived</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl65" height="21" style="height:15.6pt;width:206pt" width="275">Acetic acid</td>
			<td class="xl65" style="width:206pt" width="275">Sigma-Aldrich</td>
			<td align="right" class="xl65" style="width:206pt" width="275">537020</td>
			<td class="xl65" style="width:206pt" width="275">Glacial, &#8805;99.85%</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl65" height="21" style="height:15.6pt;width:206pt" width="275">Cictric acid</td>
			<td class="xl65" style="width:206pt" width="275">Sigma-Aldrich</td>
			<td class="xl65" style="width:206pt" width="275">251275&#160;</td>
			<td class="xl65" style="width:206pt" width="275">ACS reagent, &#8805;99.5%</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl64" height="21" style="height:15.6pt;width:206pt" width="275">NMuMG</td>
			<td class="xl64" style="width:206pt" width="275">ATCC</td>
			<td class="xl64" style="width:206pt" width="275">CRL-1636</td>
			<td class="xl64" style="width:206pt" width="275">Mouse Mammary Gland Cell Line</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl64" height="21" style="height:15.6pt;width:206pt" width="275">Sodium azide</td>
			<td class="xl64" style="width:206pt" width="275">Fisher Schientific</td>
			<td class="xl64" style="width:206pt" width="275">AC190385000</td>
			<td class="xl64" style="width:206pt" width="275">99%, extra pure, ACROS Organics</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl64" height="21" style="height:15.6pt;width:206pt" width="275">Potassium hydroxide</td>
			<td class="xl64" style="width:206pt" width="275">Sigma-Aldrich</td>
			<td align="right" class="xl64" style="width:206pt" width="275">221473</td>
			<td class="xl65" style="width:206pt" width="275">ACS reagent, &#8805;85%, pellets</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl64" height="21" style="height:15.6pt;width:206pt" width="275">TritonX-100</td>
			<td class="xl64" style="width:206pt" width="275">Sigma-Aldrich</td>
			<td class="xl64" style="width:206pt" width="275">X100</td>
			<td class="xl64" style="width:206pt" width="275">laboratory grade</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl76" colspan="4" height="21" style="height:15.6pt;
 width:824pt" width="1100">Bead Synthesis</td>
		</tr>
		<tr height="62" style="height:46.8pt">
			<td class="xl67" height="62" style="height:46.8pt;width:206pt" width="275">1,1&#8242;-Dioctadecyl-3,3,3&#8242;,3&#8242;-tetramethylindocarbocyanine perchlorate (DiI)</td>
			<td class="xl67" style="width:206pt" width="275">Sigma-Aldrich&#160;</td>
			<td class="xl65" style="width:206pt" width="275">468495-100MG</td>
			<td align="right" class="xl72" style="width:206pt" width="275">97%</td>
		</tr>
		<tr height="42" style="height:31.2pt">
			<td class="xl67" height="42" style="height:31.2pt;width:206pt" width="275">Methyl methacrylate</td>
			<td class="xl67" style="width:206pt" width="275">Sigma-Aldrich&#160;</td>
			<td class="xl65" style="width:206pt" width="275">M55909-500ML</td>
			<td class="xl65" style="width:206pt" width="275">contains &#8804;30&#160;ppm MEHQ as inhibitor, 99%</td>
		</tr>
		<tr height="62" style="height:46.8pt">
			<td class="xl67" height="62" style="height:46.8pt;width:206pt" width="275">Inhibitor Remover</td>
			<td class="xl67" style="width:206pt" width="275">Sigma-Aldrich&#160;</td>
			<td class="xl65" style="width:206pt" width="275">306312-1EA</td>
			<td class="xl65" style="width:206pt" width="275">Prepacked column for removing hydroquinone and monomethyl ether hydroquinone</td>
		</tr>
		<tr height="42" style="height:31.2pt">
			<td class="xl68" height="42" style="height:31.2pt;width:206pt" width="275">Methacryloxylpropyl Terminated Polydimethylsiloxane</td>
			<td class="xl67" style="width:206pt" width="275">Gelest&#160;</td>
			<td class="xl65" style="width:206pt" width="275">DMS-R31 (25,000g/mol)</td>
			<td class="xl65" style="width:206pt" width="275">Polydimethylsiloxane stabilizer, 25,000g/mol, 1,000 cSt</td>
		</tr>
		<tr height="42" style="height:31.2pt">
			<td class="xl67" height="42" style="height:31.2pt;width:206pt" width="275">2,2&#8242;-Azobis(2-methylpropionitrile) (AIBN)</td>
			<td class="xl67" style="width:206pt" width="275">Sigma-Aldrich&#160;</td>
			<td class="xl65" style="width:206pt" width="275">441090-25G</td>
			<td align="right" class="xl72" style="width:206pt" width="275">98%</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl67" height="21" style="height:15.6pt;width:206pt" width="275">Hexane&#160;</td>
			<td class="xl67" style="width:206pt" width="275">Sigma-Aldrich&#160;</td>
			<td class="xl65" style="width:206pt" width="275">296090-2L</td>
			<td class="xl65" style="width:206pt" width="275">anhydrous, 95%</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl67" height="21" style="height:15.6pt;width:206pt" width="275">Hexane, mixture of isomers</td>
			<td class="xl67" style="width:206pt" width="275">Sigma-Aldrich&#160;</td>
			<td class="xl65" style="width:206pt" width="275">227064-1L</td>
			<td class="xl65" style="width:206pt" width="275">anhydrous, &#8805;99%</td>
		</tr>
		<tr height="42" style="height:31.2pt">
			<td class="xl66" height="42" style="height:31.2pt;width:206pt" width="275">Whatman&#160;qualitative filter paper, Grade 1</td>
			<td class="xl65" style="width:206pt" width="275">Sigma-Aldrich&#160;</td>
			<td class="xl65" style="width:206pt" width="275">WHA1001055</td>
			<td class="xl65" style="width:206pt" width="275">circles, diam. 55&#160;mm,</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl76" colspan="4" height="21" style="height:15.6pt;
 width:824pt" width="1100">Equipment</td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl73" height="21" style="height:15.6pt;width:206pt" width="275">Laurell WS-650Mz-23NPPB</td>
			<td class="xl64" style="width:206pt" width="275">Laurell Technologies</td>
			<td class="xl64" style="width:206pt" width="275"></td>
			<td class="xl71" style="width:206pt" width="275"></td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl74" height="21" style="height:15.6pt;width:206pt" width="275">UVP Handheld UV Lamp Model UVGL-58</td>
			<td class="xl64" style="width:206pt" width="275">VWR</td>
			<td class="xl74" style="width:206pt" width="275">21474-622</td>
			<td class="xl71" style="width:206pt" width="275"></td>
		</tr>
		<tr height="21" style="height:15.6pt">
			<td class="xl64" height="21" style="height:15.6pt;width:206pt" width="275">Rheometer</td>
			<td class="xl64" style="width:206pt" width="275">Anton Paar</td>
			<td class="xl64" style="width:206pt" width="275">MCR 302 WESP</td>
			<td class="xl71" style="width:206pt" width="275"></td>
		</tr>
	</tbody>
</table>

high throughput traction force microscopy using pdms reveals dose-dependent effects of transforming growth factor-&#946; on the epithelial-to-mesenchymal transition

Cellular contractility is essential in diverse aspects of biology, driving processes that range from motility and division, to tissue contraction and mechanical stability, and represents a core element of multi-cellular animal life. In adherent cells, acto-myosin contraction is seen in traction forces that cells exert on their substrate. Dysregulation of cellular contractility appears in a myriad of pathologies, making contractility a promising target in diverse diagnostic approaches using biophysics as a metric. Moreover, novel therapeutic strategies can be based on correcting the apparent malfunction of cell contractility. These applications,&#160;however, require direct quantification of these forces.
We have developed silicone elastomer-based traction force microscopy (TFM) in a parallelized multi-well format. Our use of a silicone rubber, specifically polydimethylsiloxane (PDMS), rather than the commonly employed hydrogel polyacrylamide (PAA) enables us to make robust and inert substrates with indefinite shelf-lives requiring no specialized storage conditions. Unlike pillar-PDMS based approaches that have a modulus in the GPa range, the PDMS used here is very compliant, ranging from approximately 0.4 kPa to 100 kPa. We create a high-throughput platform for TFM by partitioning these large monolithic substrates spatially into biochemically independent wells, creating a multi-well platform for traction force screening that is compatible with existing multi-well systems.
In this manuscript, we use this multi-well traction force system to examine the Epithelial to Mesenchymal Transition (EMT); we induce EMT in NMuMG cells by exposing them to TGF-&#946;, and to quantify the biophysical changes during EMT. We measure the contractility as a function of concentration and duration of TGF-&#946; exposure. Our findings here demonstrate the utility of parallelized TFM in the context of disease biophysics.

Before addition of TGF-&#946;, a confluent monolayer of cells has a cobblestone like shape and is tightly packed. Upon TGF-&#946; treatment, cells become more elongated in morphology, enlarging the cell area and acquiring a more mesenchymal phenotype. Utilizing the multi-well device fabricated with soft PDMS elastomers, the physical properties of cells in a total 17 different conditions were studied. The cells were treated with four different TGF-&#946; concentrations (0.5, 1, 2, and 4 ng...

Watch this Scientific Journal Video about High Throughput Traction Force Microscopy Using PDMS Reveals Dose-Dependent Effects of Transforming Growth Factor-ÃŽÂ² on the Epithelial-to-Mesenchymal Transi

High Throughput Traction Force Microscopy Using PDMS Reveals Dose-Dependent Effects of Transforming Growth Factor-&#946; on the Epithelial-to-Mesenchymal Transition

We present a high throughput traction force assay fabricated with silicone rubber (PDMS). This novel assay is suitable for studying physical changes in cell contractility during various biological and biomedical processes and diseases. We demonstrate this method's utility by measuring a TGF-&#946; dependent increase in contractility during the epithelial-to-mesenchymal transition.

Cellular contractility is essential in diverse aspects of biology, driving processes that range from motility and division, to tissue contraction and ...

high-throughput-traction-force-microscopy-using-pdms-reveals-dose

Research

JoVE Journal

Bioengineering

9.3K Views.  McGill University. We present a high throughput traction force assay fabricated with silicone rubber (PDMS). This novel assay is suitable for studying physical changes in cell contractility during various biological and biomedical processes and diseases. We demonstrate this method's utility by measuring a TGF-β dependent increase in contractility during the epithelial-to-mesenchymal transition.

Video: High Throughput Traction Force Microscopy Using PDMS Reveals Dose-Dependent Effects of Transforming Growth Factor-β on the Epithelial-to-Mesenchymal Transition

Visualization of Recombinant DNA and Protein Complexes Using Atomic Force Microscopy

Atomic force microscopy (AFM) allows for the visualizing of individual proteins, DNA molecules, protein-protein complexes, and DNA-protein complexes. On the end of the microscope's cantilever is a nano-scale probe, which traverses image areas ranging from nanometers to micrometers, measuring the elevation of macromolecules resting on the substrate surface at any given point. Electrostatic forces cause proteins, lipids, and nucleic acids to loosely attach to the substrate in random orientations and permit imaging. The generated data resemble a topographical map, where the macromolecules resolve as three-dimensional particles of discrete sizes (Figure 1) 1,2. Tapping mode AFM involves the repeated oscillation of the cantilever, which permits imaging of relatively soft biomaterials such as DNA and proteins. One of the notable benefits of AFM over other nanoscale microscopy techniques is its relative adaptability to visualize individual proteins and macromolecular complexes in aqueous buffers, including near-physiologic buffered conditions, in real-time, and without staining or coating the sample to be imaged. 
The method presented here describes the imaging of DNA and an immunoadsorbed transcription factor (i.e. the glucocorticoid receptor, GR) in buffered solution (Figure 2). Immunoadsorbed proteins and protein complexes can be separated from the immunoadsorbing antibody-bead pellet by competition with the antibody epitope and then imaged (Figure 2A). This allows for biochemical manipulation of the biomolecules of interest prior to imaging. Once purified, DNA and proteins can be mixed and the resultant interacting complex can be imaged as well. Binding of DNA to mica requires a divalent cation 3,such as Ni2+ or Mg2+, which can be added to sample buffers yet maintain protein activity. Using a similar approach, AFM has been utilized to visualize individual enzymes, including RNA polymerase 4 and a repair enzyme 5, bound to individual DNA strands. These experiments provide significant insight into the protein-protein and DNA-protein biophysical interactions taking place at the molecular level. Imaging individual macromolecular particles with AFM can be useful for determining particle homogeneity and for identifying the physical arrangement of constituent components of the imaged particles. While the present method was developed for visualization of GR-chaperone protein complexes 1,2 and DNA strands to which the GR can bind, it can be applied broadly to imaging DNA and protein samples from a variety of sources.

A tapping mode atomic force microscope (AFM) method for the visualization of plasmid DNA, cytoplasmic proteins, and DNA-protein complexes is described. The method includes alternate approaches for preparing samples for AFM imaging following biochemical manipulation. DNA containing specific protein interacting regions are observed in near-physiologic buffer conditions.

Atomic force microscopy (AFM) allows for the visualizing of individual proteins, DNA molecules, protein-protein complexes, and DNA-protein complexes. On ...

High-throughput Protein Expression Generator Using a Microfluidic Platform

Rapidly increasing fields, such as systems biology, require the development and implementation of new technologies, enabling high-throughput and high-fidelity measurements of large systems. Microfluidics promises to fulfill many of these requirements, such as performing high-throughput screening experiments on-chip, encompassing biochemical, biophysical, and cell-based assays1. Since the early days of microfluidics devices, this field has drastically evolved, leading to the development of microfluidic large-scale integration2,3. This technology allows for the integration of thousands of micromechanical valves on a single device with a postage-sized footprint (Figure 1). We have developed a high-throughput microfluidic platform for generating in vitro expression of protein arrays (Figure 2) named PING (Protein Interaction Network Generator). These arrays can serve as a template for many experiments such as protein-protein 4, protein-RNA5 or protein-DNA6 interactions.
The device consist of thousands of reaction chambers, which are individually programmed using a microarrayer. Aligning of these printed microarrays to microfluidics devices programs each chamber with a single spot eliminating potential contamination or cross-reactivity Moreover, generating microarrays using standard microarray spotting techniques is also very modular, allowing for the arraying of proteins7, DNA8, small molecules, and even colloidal suspensions. The potential impact of microfluidics on biological sciences is significant. A number of microfluidics based assays have already provided novel insights into the structure and function of biological systems, and the field of microfluidics will continue to impact biology.

We present a microfluidic approach for the expression of protein arrays. The device consists of thousands of reaction chambers controlled by micro-mechanical valves. The microfluidic device is mated to a microarray-printed gene library. These genes are then transcribed and translated on-chip, resulting in a protein array ready for experimental use.

Rapidly increasing fields, such as systems biology, require the development and implementation of new technologies, enabling high-throughput and ...

Low Molecular Weight Protein Enrichment on Mesoporous Silica Thin Films for Biomarker Discovery

The identification of circulating biomarkers holds great potential for non invasive approaches in early diagnosis and prognosis, as well as for the monitoring of therapeutic efficiency.1-3 The circulating low molecular weight proteome (LMWP) composed of small proteins shed from tissues and cells or peptide fragments derived from the proteolytic degradation of larger proteins, has been associated with the pathological condition in patients and likely reflects the state of disease.4,5 Despite these potential clinical applications, the use of Mass Spectrometry (MS) to profile the LMWP from biological fluids has proven to be very challenging due to the large dynamic range of protein and peptide concentrations in serum.6 Without sample pre-treatment, some of the more highly abundant proteins obscure the detection of low-abundance species in serum/plasma. Current proteomic-based approaches, such as two-dimensional polyacrylamide gel-electrophoresis (2D-PAGE) and shotgun proteomics methods are labor-intensive, low throughput and offer limited suitability for clinical applications.7-9 Therefore, a more effective strategy is needed to isolate LMWP from blood and allow the high throughput screening of clinical samples. 
Here, we present a fast, efficient and reliable multi-fractionation system based on mesoporous silica chips to specifically target and enrich LMWP.10,11 Mesoporous silica (MPS) thin films with tunable features at the nanoscale were fabricated using the triblock copolymer template pathway. Using different polymer templates and polymer concentrations in the precursor solution, various pore size distributions, pore structures, connectivity and surface properties were determined and applied for selective recovery of low mass proteins. The selective parsing of the enriched peptides into different subclasses according to their physicochemical properties will enhance the efficiency of recovery and detection of low abundance species. In combination with mass spectrometry and statistic analysis, we demonstrated the correlation between the nanophase characteristics of the mesoporous silica thin films and the specificity and efficacy of low mass proteome harvesting. The results presented herein reveal the potential of the nanotechnology-based technology to provide a powerful alternative to conventional methods for LMWP harvesting from complex biological fluids. Because of the ability to tune the material properties, the capability for low-cost production, the simplicity and rapidity of sample collection, and the greatly reduced sample requirements for analysis, this novel nanotechnology will substantially impact the field of proteomic biomarker research and clinical proteomic assessment.

We developed a technology based on mesoporous silica thin film for the selective recovery of low molecular weight proteins and peptides from human serum. The physico-chemical properties of our mesoporous chips were finely tuned to provide substantial control in peptide enrichment and consequently profile the serum proteome for diagnostic purposes.

The identification of circulating biomarkers holds great potential for non invasive approaches in early diagnosis and prognosis, as well as for the ...

Measuring the Mechanical Properties of Living Cells Using Atomic Force Microscopy

Mechanical properties of cells and extracellular matrix (ECM) play important roles in many biological processes including stem cell differentiation, tumor formation, and wound healing. Changes in stiffness of cells and ECM are often signs of changes in cell physiology or diseases in tissues. Hence, cell stiffness is an index to evaluate the status of cell cultures. Among the multitude of methods applied to measure the stiffness of cells and tissues, micro-indentation using an Atomic Force Microscope (AFM) provides a way to reliably measure the stiffness of living cells. This method has been widely applied to characterize the micro-scale stiffness for a variety of materials ranging from metal surfaces to soft biological tissues and cells. The basic principle of this method is to indent a cell with an AFM tip of selected geometry and measure the applied force from the bending of the AFM cantilever. Fitting the force-indentation curve to the Hertz model for the corresponding tip geometry can give quantitative measurements of material stiffness. This paper demonstrates the procedure to characterize the stiffness of living cells using AFM. Key steps including the process of AFM calibration, force-curve acquisition, and data analysis using a MATLAB routine are demonstrated. Limitations of this method are also discussed.

This paper demonstrates a protocol to characterize the mechanical properties of living cells by means of microindentation using an Atomic Force Microscope (AFM).

Mechanical  properties of cells and extracellular matrix (ECM) play important roles in many  biological processes including stem cell differentiation, ...

Stretching Micropatterned Cells on a PDMS Membrane

Mechanical forces exerted on cells and/or tissues play a major role in numerous processes. We have developed a device to stretch cells plated on a PolyDiMethylSiloxane (PDMS) membrane, compatible with imaging. This technique is reproducible and versatile. The PDMS membrane can be micropatterned in order to confine cells or tissues to a specific geometry. The first step is to print micropatterns onto the PDMS membrane with a deep UV technique. The PDMS membrane is then mounted on a mechanical stretcher. A chamber is bound on top of the membrane with biocompatible grease to allow gliding during the stretch. The cells are seeded and allowed to spread for several hours on the micropatterns. The sample can be stretched and unstretched multiple times with the use of a micrometric screw. It takes less than a minute to apply the stretch to its full extent (around 30%). The technique presented here does not include a motorized device, which is necessary for applying repeated stretch cycles quickly and/or computer controlled stretching, but this can be implemented. Stretching of cells or tissue can be of interest for questions related to cell forces, cell response to mechanical stress or tissue morphogenesis. This video presentation will show how to avoid typical problems that might arise when doing this type of seemingly simple experiment.

This manuscript presents a technique to apply or release forces on adherent cells or tissues using unidirectional stretching.

Mechanical forces exerted on cells and/or tissues  play a major role in numerous processes. We have developed a device to stretch  cells plated on a ...

A Novel Method for Localizing Reporter Fluorescent Beads Near the Cell Culture Surface for Traction Force Microscopy

PA gels have long been used as a platform to study cell traction forces due to ease of fabrication and the ability to tune their elastic properties. When the substrate is coated with an extracellular matrix protein, cells adhere to the gel and apply forces, causing the gel to deform. The deformation depends on the cell traction and the elastic properties of the gel. If the deformation field of the surface is known, surface traction can be calculated using elasticity theory. Gel deformation is commonly measured by embedding fluorescent marker beads uniformly into the gel. The probes displace as the gel deforms. The probes near the surface of the gel are tracked. The displacements reported by these probes are considered as surface displacements. Their depths from the surface are ignored. This assumption introduces error in traction force evaluations. For precise measurement of cell forces, it is critical for the location of the beads to be known. We have developed a technique that utilizes simple chemistry to confine fluorescent marker beads, 0.1 and 1 &#181;m in diameter, in PA gels, within 1.6 &#956;m of the surface. We coat a coverslip with poly-D-lysine (PDL) and fluorescent beads. PA gel solution is then sandwiched between the coverslip and an adherent surface. The fluorescent beads transfer to the gel solution during curing. After polymerization, the PA gel contains fluorescent beads on a plane close to the gel surface.

Traditional techniques for fabricating polyacrylamide (PA) gels containing fluorescent probes involve sandwiching a gel between an adherent surface and a glass slide. Here, we show that coating this slide with poly-D-lysine (PDL) and fluorescent probes localizes the probes to within 1.6 &#181;m from the gel surface.

PA gels have long been used as a platform to study cell traction forces due to ease of fabrication and the ability to tune their elastic properties. When ...

Surface Potential Measurement of Bacteria Using Kelvin Probe Force Microscopy

Surface potential is a commonly overlooked physical characteristic that plays a dominant role in the adhesion of microorganisms to substrate surfaces. Kelvin probe force microscopy (KPFM) is a module of atomic force microscopy (AFM) that measures the contact potential difference between surfaces at the nano-scale. The combination of KPFM with AFM allows for the simultaneous generation of surface potential and topographical maps of biological samples such as bacterial cells. Here, we employ KPFM to examine the effects of surface potential on microbial adhesion to medically relevant surfaces such as stainless steel and gold. Surface potential maps revealed differences in surface potential for microbial membranes on different material substrates. A step-height graph was generated to show the difference in surface potential at a boundary area between the substrate surface and microorganisms. Changes in cellular membrane surface potential have been linked with changes in cellular metabolism and motility. Therefore, KPFM represents a powerful tool that can be utilized to examine the changes of microbial membrane surface potential upon adhesion to various substrate surfaces. In this study, we demonstrate the procedure to characterize the surface potential of individual methicillin-resistant Staphylococcus aureus USA100 cells on stainless steel and gold using KPFM.

Here, we present a protocol explaining the use of Kelvin probe force microscopy as a tool for generating high resolution nano-scale surface potential maps. This tool was applied to assess the role of surface potential on the binding capacity of microorganisms to substrate surfaces.

Surface potential is a commonly overlooked physical characteristic that plays a dominant role in the adhesion of microorganisms to substrate surfaces. ...

A High-throughput Cell Microarray Platform for Correlative Analysis of Cell Differentiation and Traction Forces

Microfabricated cellular microarrays, which consist of contact-printed combinations of biomolecules on an elastic hydrogel surface, provide a tightly controlled, high-throughput engineered system for measuring the impact of arrayed biochemical signals on cell differentiation. Recent efforts using cell microarrays have demonstrated their utility for combinatorial studies in which many microenvironmental factors are presented in parallel. However, these efforts have focused primarily on investigating the effects of biochemical cues on cell responses. Here, we present a cell microarray platform with tunable material properties for evaluating both cell differentiation by immunofluorescence and biomechanical cell&#8211;substrate interactions by traction force microscopy. To do so, we have developed two different formats utilizing polyacrylamide hydrogels of varying Young&#39;s modulus fabricated on either microscope slides or glass-bottom Petri dishes. We provide best practices and troubleshooting for the fabrication of microarrays on these hydrogel substrates, the subsequent cell culture on microarrays, and the acquisition of data. This platform is well-suited for use in investigations of biological processes for which both biochemical (e.g., extracellular matrix composition) and biophysical (e.g., substrate stiffness) cues may play significant, intersecting roles.

Cell differentiation is regulated by a host of microenvironmental factors, including both matrix composition and substrate material properties. We describe here a technique utilizing cell microarrays in conjunction with traction force microscopy to evaluate both cell differentiation and biomechanical cell&#8211;substrate interactions as a function of microenvironmental context.

Microfabricated cellular microarrays, which consist of contact-printed combinations of biomolecules on an elastic hydrogel surface, provide a tightly ...

Fabrication and Implementation of a Reference-Free Traction Force Microscopy Platform

Quantifying cell-induced material deformation provides useful information concerning how cells sense and respond to the physical properties of their microenvironment. While many approaches exist for measuring cell-induced material strain, here we provide a methodology for monitoring strain with sub-micron resolution in a reference-free manner. Using a two-photon activated photolithographic patterning process, we demonstrate how to generate mechanically and bio-actively tunable synthetic substrates containing embedded arrays of fluorescent fiducial markers to easily measure three-dimensional (3D) material deformation profiles in response to surface tractions. Using these substrates, cell tension profiles can be mapped using a single 3D image stack of a cell of interest. Our goal with this methodology is to make traction force microscopy a more accessible and easier to implement tool for researchers studying cellular mechanotransduction processes, especially newcomers to the field.

This protocol provides instructions for implementing multiphoton lithography to fabricate three-dimensional arrays of fluorescent fiducial markers embedded in poly(ethylene glycol)-based hydrogels for use as reference-free, traction force microscopy platforms. Using these instructions, measurement of 3D material strain and calculation of cellular tractions is simplified to promote high-throughput traction force measurements.

Quantifying cell-induced material deformation provides useful information concerning how cells sense and respond to the physical properties of their ...

Traction Force Microscopy to Study B Lymphocyte Activation

Traction force microscopy (TFM) enables the measurement of forces produced by a cell on a substrate. This technique infers traction force measurements from an experimentally observed displacement field produced by a cell pulling on an elastic substrate. Here, we adapted TFM to investigate the spatial and temporal structure of the force field exerted by B cells when activated by antigen engagement of the B cell receptor. Gel rigidity, bead density, and protein functionalization must be optimized for the study of relatively small cells (~ 6 &#181;m) that interact with, and respond specifically to ligands for cell surface receptors.

Here we present a protocol used to perform traction force microscopy experiments on B cells. We describe the preparation of soft polyacrylamide gels and their functionalization, as well as data acquisition at the microscope and a summary of data analysis.

Traction force microscopy (TFM) enables the measurement of forces produced by a cell on a substrate. This technique infers traction force measurements ...