Name: mechanostimulation of multicellular organisms through a high-throughput microfluidic compression system
Uploaded: 2022-12-23T13:15:00
Description: Watch this Scientific Journal Video about Mechanostimulation of Multicellular Organisms Through a High-Throughput Microfluidic Compression System at JoVE.com

This work was supported by the National Science Foundation (CMMI-1946456), the Air Force Office of Scientific Research (FA9550-18-1-0262), and the National Institute of Health (R01AG06100501A1; R21AR08105201A1).

1. Preparation of the silicon wafer mold
<ol>
	<li>Clean the silicon wafer (see Table of Materials) first with acetone and then with isopropyl alcohol (IPA).</li>
	<li>Place the silicon wafer on a 250 &#176;C hot plate for 30 min for dehydration bake (Figure 3A).</li>
	<li>Coat the silicon wafer with hexamethyldisilazane (HDMS) in a vapor prime oven (see Table of Materials) (process temperature: 150 &#176;C, process pressure: 2 Torr, proce...

<ol>
	<li>Wang, J. H. -. C., Thampatty, B. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+introductory+review+of+cell+mechanobiology.">An introductory review of cell mechanobiology.</a> Biomechanics and Modeling in Mechanobiology. 5 (1), 1-16 (2006).</li><li>Ingber, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanobiology+and+diseases+of+mechanotransduction.">Mechanobiology and diseases of mechanotransduction.</a> Annals of Medicine. 35 (8), 564-577 (2003).</li><li>Nims, R. J., Pferdehirt, L., Guilak, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanogenetics:+Harnessing+mechanobiology+for+cellular+engineering.">Mechanogenetics: Harnessing mechanobiology for cellular engineering.</a> Current Opinion in Biotechnology. 73, 374-379 (2022).</li><li>Bellin, R. M., 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=Defining+the+Role+of+Syndecan-4+in+Mechanotransduction+using+Surface-Modification+Approaches.">Defining the Role of Syndecan-4 in Mechanotransduction using Surface-Modification Approaches.</a> Proceedings of the National Academy of Sciences. 106, 22102-22107 (2009).</li><li>Simpson, L. J., Reader, J. S., Tzima, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanical+regulation+of+protein+translation+in+the+cardiovascular+system.">Mechanical regulation of protein translation in the cardiovascular system.</a> Frontiers in Cell and Developmental Biology. 8, 34 (2020).</li><li>Humphrey, J. D., Schwartz, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Vascular+mechanobiology:+Homeostasis,+adaptation,+and+disease.">Vascular mechanobiology: Homeostasis, adaptation, and disease.</a> Annual Review of Biomedical Engineering. 23, 1-27 (2021).</li><li>Maurer, M., Lammerding, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+driving+force:+Nuclear+mechanotransduction+in+cellular+function,+fate,+and+disease.">The driving force: Nuclear mechanotransduction in cellular function, fate, and disease.</a> Annual Review of Biomedical Engineering. 21, 443-468 (2019).</li><li>Jennings, B. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drosophila-A+versatile+model+in+biology+&amp;+medicine.">Drosophila-A versatile model in biology &amp; medicine.</a> Materials Today. 14 (5), 190-195 (2011).</li><li>Konno, M., 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=State-of-the-art+technology+of+model+organisms+for+current+human+medicine.">State-of-the-art technology of model organisms for current human medicine.</a> Diagnostics. 10 (6), 392 (2020).</li><li>Morgan, T. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sex+limited+inheritance+in+Drosophila.">Sex limited inheritance in Drosophila.</a> Science. 32 (812), 120-122 (1910).</li><li>Wu, Q., Kumar, N., Velagala, V., Zartman, J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tools+to+reverse-engineer+multicellular+systems:+Case+studies+using+the+fruit+fly.">Tools to reverse-engineer multicellular systems: Case studies using the fruit fly.</a> Journal of Biological Engineering. 13 (1), 1-16 (2019).</li><li>Jayamohan, H., et al., Patrinos, G., 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=Chapter+11+-+Advances+in+Microfluidics+and+Lab-on-a-Chip+Technologies.">Chapter 11 - Advances in Microfluidics and Lab-on-a-Chip Technologies.</a> Molecular Diagnostics. , 197-217 (2017).</li><li>Scheler, O., Postek, W., Garstecki, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recent+developments+of+microfluidics+as+a+tool+for+biotechnology+and+microbiology.">Recent developments of microfluidics as a tool for biotechnology and microbiology.</a> Current Opinion in Biotechnology. 55, 60-67 (2019).</li><li>Mohammed, D., 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=Innovative+tools+for+mechanobiology:+Unraveling+outside-in+and+inside-out+mechanotransduction.">Innovative tools for mechanobiology: Unraveling outside-in and inside-out mechanotransduction.</a> Frontiers in Bioengineering and Biotechnology. 7, 162 (2019).</li><li>Shorr, A. Z., S&#246;nmez, U. M., Minden, J. S., LeDuc, P. R. <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+mechanotransduction+in+Drosophila+embryos+with+mesofluidics.">High-throughput mechanotransduction in Drosophila embryos with mesofluidics.</a> Lab on a Chip. 19 (7), 1141-1152 (2019).</li><li>Kim, Y. T., 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=Mechanochemical+Actuators+of+Embryonic+Epithelial+Contractility.">Mechanochemical Actuators of Embryonic Epithelial Contractility.</a> Proceedings of the National Academy of Sciences. 40, 14366-14371 (2014).</li><li>Ashburner, 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> Drosophila. A Laboratory Handbook. , (1989).</li><li>Qin, D., Xia, Y., Whitesides, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Soft+lithography+for+micro-and+nanoscale+patterning.">Soft lithography for micro-and nanoscale patterning.</a> Nature Protocols. 5 (3), 491 (2010).</li><li>Lee, 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=A+new+fabrication+process+for+uniform+SU-8+thick+photoresist+structures+by+simultaneously+removing+edge+bead+and+air+bubbles.">A new fabrication process for uniform SU-8 thick photoresist structures by simultaneously removing edge bead and air bubbles.</a> Journal of Micromechanics and Microengineering. 21 (12), 125006 (2011).</li><li>Xia, Y., Whitesides, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Soft+lithography.">Soft lithography.</a> Annual Review of Materials Science. 28 (1), 153-184 (1998).</li><li>Sonmez, U. M., Coyle, S., Taylor, R. E., LeDuc, P. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Polycarbonate+heat+molding+for+soft+lithography.">Polycarbonate heat molding for soft lithography.</a> Small. 16 (16), 2000241 (2020).</li><li>Levario, T. J., Zhan, M., Lim, B., Shvartsman, S. Y., Lu, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microfluidic+trap+array+for+massively+parallel+imaging+of+Drosophila+embryos.">Microfluidic trap array for massively parallel imaging of Drosophila embryos.</a> Nature Protocols. 8 (4), 721-736 (2013).</li></ol>

The article describes the development of a microfluidic device to automatically align, immobilize, and precisely apply mechanical stimulation to hundreds of whole Drosophila embryos. The integration of the microfluidic system with a thin glass coverslip allowed for the imaging of embryos with high-resolution confocal microscopy during the stimulation. The microfluidic device also enabled the collection of the embryos right after the stimulation for running downstream biological assays. The design considerations,...

Living systems constantly experience and respond to various mechanical inputs throughout their lifetimes1. Mechanotransduction has been linked to many diseases, including developmental disorders, muscle and bone loss, and neuropathologies through signaling pathways directly or indirectly affected by the mechanical environment2. However, the genes and proteins that are regulated by mechanical stimulation3 in the mechanosensitive signaling pathways4 remain largely unknown5, preventing the elucidation of the mechanical regulation mechanisms and the identification of molecular targets for diseases associated with pathological mechanotransduction6,7. One limiting factor in projecting mechanobiology studies onto the related physiological processes is using individual cells with conventional culture dishes instead of intact multicellular organisms. Model organisms, such as Drosophila melanogaster (fruit fly), have contributed greatly to understanding the genes, signaling pathways, and proteins involved in animal development8,9,10. Nevertheless, using Drosophila and other multicellular model organisms in mechanobiology research has been hindered by challenges with experimental tools. Conventional techniques for preparing, sorting, imaging, or applying various stimuli require mostly manual manipulation; these approaches are time-consuming, require expertise, introduce variability, and limit the experimental design and sample size11. Recent microtechnological advancements are a great resource for enabling novel biological assays with very high throughput and highly controlled experimental parameters12,13,14.
This article describes the development of an enhanced microfluidic device to align, immobilize, and precisely apply mechanical stimulation in the form of uniaxial compression to hundreds of whole Drosophila embryos15&#160;(Figure 1). Integration of the microfluidic system with a glass coverslip allowed high-resolution confocal imaging of the samples during the stimulation. The microfluidic device also enabled fast collection of the embryos after the stimulation for running -omics assays (Figure 2). Explanations of the design considerations of this device, as well as the fabrication using soft lithography and experimental characterization, are described herein. Since making a silicon wafer mold of such a device requires a uniform coating of thick photoresist (thickness &#62;200 &#181;m) over large areas with high aspect ratio (AR) trenches (AR &#62;5), this method considerably modified the traditional photolithographic mold fabrication protocol. In this way, this method facilitated the handling, adhesion, coating, patterning, and development of the photoresist. Additionally, potential pitfalls and their solutions are discussed. Lastly, the versatility of this design and fabrication strategy was demonstrated using other multicellular systems such as Drosophila egg chambers and brain organoids16.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>100 mL tri-cornered perforated plastic beakers with 60 mm Petri dishes</td>
			<td>Fisher</td>
			<td>14-955-111B</td>
			<td>Perferate with air holes</td>
		</tr>
		<tr>
			<td>100 mm P B &#60;100&#62; 0-100 500um SSP Test Grade Si Wafer</td>
			<td>University Wafer</td>
			<td>452</td>
			<td></td>
		</tr>
		<tr>
			<td>Biopsy punches</td>
			<td>Ted Pella</td>
			<td>15110</td>
			<td></td>
		</tr>
		<tr>
			<td>Bleach</td>
			<td></td>
			<td></td>
			<td>Not brand specific</td>
		</tr>
		<tr>
			<td>Blunt needle set</td>
			<td>CML Supply</td>
			<td>901</td>
			<td></td>
		</tr>
		<tr>
			<td>Contact Mask Aligner</td>
			<td>Quintel</td>
			<td>Q4000 MA</td>
			<td></td>
		</tr>
		<tr>
			<td>Cutting mat</td>
			<td>Dahle</td>
			<td>Vantage 10670</td>
			<td>size: 24&#34; x 36&#34;</td>
		</tr>
		<tr>
			<td>Developer</td>
			<td>Kayaku Advance Materials</td>
			<td>SU-8 2000</td>
			<td></td>
		</tr>
		<tr>
			<td>Direct Write Lithographer</td>
			<td>Heidelberg</td>
			<td>MLA100</td>
			<td></td>
		</tr>
		<tr>
			<td>Dissecting microscope</td>
			<td></td>
			<td></td>
			<td>Any commericailly availble dissecting microscope with transmitted light</td>
		</tr>
		<tr>
			<td>Glass petri dish</td>
			<td>Fisher</td>
			<td>FB0875713A</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass slide</td>
			<td>Warner Instruments</td>
			<td>64-0710&#160; (CS-24/60)</td>
			<td></td>
		</tr>
		<tr>
			<td>HMDS Vapor Prime Oven</td>
			<td>Yes Engineering</td>
			<td>YES-3TA</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td></td>
			<td></td>
			<td>Not brand specific</td>
		</tr>
		<tr>
			<td>Oven</td>
			<td>Labnet</td>
			<td>I5110A</td>
			<td></td>
		</tr>
		<tr>
			<td>Paintbrush</td>
			<td></td>
			<td></td>
			<td>Not brand specific</td>
		</tr>
		<tr>
			<td>PDMS</td>
			<td>Dow Corning</td>
			<td>Sylgard 184</td>
			<td></td>
		</tr>
		<tr>
			<td>Photoresist</td>
			<td>MicroChem</td>
			<td>SU-8 2100</td>
			<td></td>
		</tr>
		<tr>
			<td>Plasma cleaner</td>
			<td>Harrick Plasma</td>
			<td>PDC-32G</td>
			<td></td>
		</tr>
		<tr>
			<td>Portable pressure source</td>
			<td>hygger Quietest</td>
			<td>HGD946</td>
			<td></td>
		</tr>
		<tr>
			<td>Pressure gauge</td>
			<td>Cole-Parmer</td>
			<td>EW-68950-25</td>
			<td></td>
		</tr>
		<tr>
			<td>Spin Coater</td>
			<td>Laurell</td>
			<td>WS-650-8B</td>
			<td></td>
		</tr>
		<tr>
			<td>Trichloro(1H,1H,2H,2H-perfluorooctyl)silane (PFOCTS)</td>
			<td>Sigma-Aldrich</td>
			<td>448931-10G</td>
			<td></td>
		</tr>
		<tr>
			<td>Triton-X 100</td>
			<td>Fisher</td>
			<td>AAA16046AP</td>
			<td></td>
		</tr>
		<tr>
			<td>Tubing</td>
			<td>Saint-Gobain</td>
			<td>02-587-1A</td>
			<td></td>
		</tr>
		<tr>
			<td>Ultrasonic Cleaner</td>
			<td>Cole-Parmer</td>
			<td>UX-08895-05</td>
			<td></td>
		</tr>
		<tr>
			<td>Vacuum Pump</td>
			<td>Cole-Parmer</td>
			<td>EW-07164-87</td>
			<td></td>
		</tr>
	</tbody>
</table>

mechanostimulation of multicellular organisms through a high-throughput microfluidic compression system

During embryogenesis, coordinated cell movement generates mechanical forces that regulate gene expression and activity. To study this process, tools such as aspiration or coverslip compression have been used to mechanically stimulate whole embryos. These approaches limit experimental design as they are imprecise, require manual handling, and can process only a couple of embryos simultaneously. Microfluidic systems have great potential for automating such experimental tasks while increasing throughput and precision. This article describes a microfluidic system developed to precisely compress whole Drosophila melanogaster (fruit fly) embryos. This system features microchannels with pneumatically actuated deformable sidewalls and enables embryo alignment, immobilization, compression, and post-stimulation collection. By parallelizing these microchannels into seven lanes, steady or dynamic compression patterns can be applied to hundreds of Drosophila embryos simultaneously. Fabricating this system on a glass coverslip facilitates the simultaneous mechanical stimulation and imaging of samples with high-resolution microscopes. Moreover, the utilization of biocompatible materials, like PDMS, and the ability to flow fluid through the system make this device capable of long-term experiments with media-dependent samples. This approach also eliminates the requirement for manual mounting which mechanically stresses samples. Furthermore, the ability to quickly collect samples from the microchannels enables post-stimulation analyses, including -omics assays which require large sample numbers unattainable using traditional mechanical stimulation approaches. The geometry of this system is readily scalable to different biological systems, enabling numerous fields to benefit from the functional features described herein including high sample throughput, mechanical stimulation or immobilization, and automated alignment.

The microfluidic system is divided into two sub-compartments separated by deformable PDMS sidewalls. The first compartment is the liquid system where Drosophila embryos are introduced, automatically aligned, lined up, and compressed. The second compartment is a gas system where the gas pressure at either side of the compression channels is controlled via dead-end microchannels to precisely control the effective width of the compression channels. The microfluidic device is sealed with a glass slide at th...

Watch this Scientific Journal Video about Mechanostimulation of Multicellular Organisms Through a High-Throughput Microfluidic Compression System at JoVE.com

Mechanostimulation of Multicellular Organisms Through a High-Throughput Microfluidic Compression System

The present protocol describes the design, fabrication, and characterization of a microfluidic system capable of aligning, immobilizing, and precisely compressing hundreds of Drosophila melanogaster embryos with minimal user intervention. This system enables high-resolution imaging and recovery of samples for post-stimulation analysis and can be scaled to accommodate other multicellular biological systems.

During embryogenesis, coordinated cell movement generates mechanical forces that regulate gene expression and activity. To study this process, tools such ...

This protocol explains how to fabricate and use microfluidics technologies to leverage the experimental benefits in sample throughput, automated handling, and the ability to precisely apply mechanical stress while simultaneously visualizing samples. This technique minimizes the manual handling of multicellular biological organisms, such as embryos and organoids, for their immobilization, alignment, and live imaging. It also enables the application of mechanical compression to them for mechanobiology studies.Fabrication of molds with high aspect ratio features for this microfluidic chip can be challenging with conventional microfabrication techniques. The tips explained in this video article can overcome these challenges. To begin, clean the silicon wafer first with acetone, and then with isopropyl alcohol.Place the silicon wafer on a 250-degree Celsius hot plate for 30 minutes. for dehydration bake. Coat the silicon wafer with hexamethyldisiloxane in a vapor prime oven.Place a bottle of SU-8 2100 Photoresist in a 60-degrees Celsius oven for 15 minutes to reduce its viscosity. Pour one milliliter of the heated Photoresist for each inch of the silicon wafer placed on the hot plate until the Photoresist covers most of the surface. Apply pre-spin first at 250 rotations per minute for 30 seconds, and then at 350 rotations per minute for another 30 seconds, both with 100 RPM per second acceleration.Next, apply a spin first at 500 rotations per minute for 15 seconds with 100 RPM per second acceleration, and then at 1, 450 rotations per minute for 30 seconds with 300 RPM per second acceleration. Remove the edge bead with a clean room swab, and spray acetone on the wafer to remove imperfections and promote uniform coating. Expose the silicone wafer to 350 millijoule per centimeter square UV light through the photo mask.Using the contact mask aligner, apply post-exposure bake to the silicon wafer, and let it cool down to room temperature. Place the beaker inside another larger beaker, and fill the larger beaker with a fresh developer solution. Place a metal mesh on the beaker.Place the silicon wafer on the metal mesh upside down. Leave the silicon wafer submerged in the developer for 30 minutes with the stirrer turned on. Transfer the silicon wafer into an ultrasonic bath sonicator filled with the fresh developer for one hour at 40 kilohertz.Then take the wafer out from the beaker, and wash it with a fresh developer solution. Prepare the pre-cured PDMS solution by mixing the PDMS base with the curing agent at a 10-to-one ratio. Degas the mixture by placing it into a centrifuge for 500 g for five minutes at room temperature.Pour the pre-cured PDMS on a silicon wafer, and degas it again. Finally, place the uncured PDMS into 60-degrees Celsius oven for curing. Use a scalpel to cut the borders of the cured PDMS region corresponding to the microfluidic chip geometry.Punch the inlet and outlet holes on PDMS using a biopsy punch, or a needle with a blunt tip. Place the PDMS on the glass slide with its patterned surface facing toward the glass slide after plasma treatment to seal the microchannels via covalent bonding. Allow Oregon-R adult flies to lay eggs on apple juice agar plates, and collect the plates at the desired developmental time after egg laying for the given experiment.Flood the agar with embryo egg wash, and gently agitate the embryos with a paintbrush to dislodge them from the agar. Transfer the embryos to a 50%bleach solution for 90 seconds, stirring occasionally. Strain the embryos through a tissue sieve, and thoroughly wash away the bleach solution with water.Transfer the embryos to a 90-millimeter glass Petri dish with enough embryo egg wash to fully cover the embryos. Examine the embryos with transillumination on a dissecting microscope, and select embryos of the desired developmental stage for loading into the microfluidic device. Prime all seven embryo microchannels by filling them with 0.4 micrometers of filtered IPA through the main embryo inlet port.Replace the IPA with 0.4 micrometers of filtered deionized water. Then replace the DI water with embryo egg wash solution. Collect approximately 100 pre-selected embryos from the glass Petri dish using a glass pipette.Next, pipette the embryos into the embryo inlet port, and apply approximately three PSI negative pressure to the gas inlet using a portable vacuum pump to open up the embryo microchannels. Then tilt the microfluidic chip downward for the embryos to automatically align and settle into the embryo microchannels. If the embryo microchannel inlets get clogged by multiple embryos entering simultaneously, tilt the microfluidic chip upward, and then down again to clear the clogging.Based on the required throughput, introduce as many as 300 embryos into the embryo microchannels. Once the embryo loading is completed, remove the vacuum to immobilize the embryos. Then tilt the micro fluidic chip back to the horizontal position.Connect a portable positive pressure source with a pressure gauge to the gas inlet to apply three PSI compression. If live imaging experiments will be conducted on the mechanically stimulated embryos, place the microfluidic chip on a standard microscope stage glass slide holder with the gas inlet connected to the pressure source. Examine the embryos under a fluorescent microscope inside the microfluidic channels.Once the compression experiment is completed, the embryos can be collected for downstream analysis. To do this, first, apply the vacuum to the gas inlet to free the embryos. Then tilt the microfluidic chip upward for the embryos to move downward toward the embryo introduction port.Collect the embryos from the microfluidic chip using a glass pipette. The functionality of the microfluidic device was experimentally determined by loading Drosophila embryos into the compression channels and applying positive pressure to the gas channels. The embryos do not experience significant compression under vacuum, or in neutral pressure states.They are compressed when positive pressure is applied. Measurements of the decreasing width of the embryos under a microscope demonstrate how gas pressure can be used to obtain a target compression level. Microfluidic devices made in this way allow for chemical stimulation of immobilized samples.The stimulation allows for high spatiotemporal imaging. A fundamental question in developmental biology is how do mechanical forces regulate protein and gene expression during development? This technology allows us to apply mechanical stimulation to a large number of embryos at once, so that we can isolate sufficient amounts of protein and RNA to perform comparative proteomics, or transcriptomics experiments.This will enable researchers to learn more about the proteins and genes that are sensitive to mechanical forces.

mechanostimulation-multicellular-organisms-through-high-throughput

Research

JoVE Journal

Bioengineering

Polymer Microarrays for High Throughput Discovery of Biomaterials

The discovery of novel biomaterials that are optimized for a specific biological application is readily achieved using polymer microarrays, which allows a combinatorial library of materials to be screened in a parallel, high throughput format1. Herein is described the formation and characterization of a polymer microarray using an on-chip photopolymerization technique 2. This involves mixing monomers at varied ratios to produce a library of monomer solutions, transferring the solution to a glass slide format using a robotic printing device and curing with UV irradiation. This format is readily amenable to many biological assays, including stem cell attachment and proliferation, cell sorting and low bacterial adhesion, allowing the ready identification of 'hit' materials that fulfill a specific biological criterion3-5. Furthermore, the use of high throughput surface characterization (HTSC) allows the biological performance to be correlated with physio-chemical properties, hence elucidating the biological-material interaction6. HTSC makes use of water contact angle (WCA) measurements, atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). In particular, ToF-SIMS provides a chemically rich analysis of the sample that can be used to correlate the cell response with a molecular moiety. In some cases, the biological performance can be predicted from the ToF-SIMS spectra, demonstrating the chemical dependence of a biological-material interaction, and informing the development of hit materials5,3.

A description of the formation of a polymer microarray using an on-chip photopolymerization technique. The high throughput surface characterization using atomic force microscopy, water contact angle measurements, X-ray photoelectron spectroscopy and time of flight secondary ion mass spectrometry and a cell attachment assay is also described.

The discovery of novel biomaterials that are optimized for a specific biological application is readily achieved using polymer microarrays, which allows a ...

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 ...

High Throughput Microfluidic Rapid and Low Cost Prototyping Packaging Methods

In this work, 3 different packaging and assembly techniques are presented. They can be classified into two categories: one-time use and reusable packaging techniques.
The one-time use packaging technique employs UV-based and temperature curing epoxies to connect microtubes to access holes, wire-bonding for integrated circuit connections, and silver epoxy for electrical connections. This method is based on a robust assembly technique that can support relatively high pressure close to 1 psi and does not need any support to strengthen the microfluidic architecture.
Reusable packaging techniques consist of PDMS-based microtube interconnectors and anisotropic adhesive films for electrical connections. These devices are more sensitive and fragile. Consequently, Plexiglas support is added to the microfluidic structure to improve the electrical contact when anisotropic adhesive films are used, and also to strengthen the microfluidic architecture. In addition, a micromanipulator is needed to maintain tubes while using a thin PDMS layer to connect them to the access holes. Different PDMS layer thicknesses, ranging from 0.45-3 mm, are tested to compare the best adherence versus injection rates. Applied injection rates are varied from 50-300 &#956;l/hr for 0.45-3 mm PDMS layers, respectively. These techniques are mainly applicable for low-pressure applications. However, they can be extended for high-pressure ones through plasma-oxygen process to permanently seal the PDMS to glass substrates. The main advantage of this technique, besides the fact that it is reusable, consists of keeping the device observable when the microchannel length is very short (in the range of 3 mm or lower).

In this article we describe different techniques for microfluidic rapid prototyping platforms. The proposed techniques are based on ultraviolet (UV) sensitive and temperature curing epoxies, polydimethylsiloxane (PDMS) based tubing, wire-bonding, and anisotropic adhesive films. The assembling procedures presented are developed for both one-time use devices as well as reusable microfluidic systems.

In this work, 3 different packaging and assembly techniques are presented. They can be classified into two categories: one-time use and reusable packaging ...

Systematic Analysis of In Vitro Cell Rolling Using a Multi-well Plate Microfluidic System

A major challenge for cell-based therapy is the inability to systemically target a large quantity of viable cells with high efficiency to tissues of interest following intravenous or intraarterial infusion. Consequently, increasing cell homing is currently studied as a strategy to improve cell therapy. Cell rolling on the vascular endothelium is an important step in the process of cell homing and can be probed in-vitro using a parallel plate flow chamber (PPFC). However, this is an extremely tedious, low throughput assay, with poorly controlled flow conditions. Instead, we used a multi-well plate microfluidic system that enables study of cellular rolling properties in a higher throughput under precisely controlled, physiologically relevant shear flow1,2. In this paper, we show how the rolling properties of HL-60 (human promyelocytic leukemia) cells on P- and E-selectin-coated surfaces as well as on cell monolayer-coated surfaces can be readily examined. To better simulate inflammatory conditions, the microfluidic channel surface was coated with endothelial cells (ECs), which were then activated with tumor necrosis factor-&#945; (TNF-&#945;), significantly increasing interactions with HL-60 cells under dynamic conditions. The enhanced throughput and integrated multi-parameter software analysis platform, that permits rapid analysis of parameters such as rolling velocities and rolling path, are important advantages for assessing cell rolling properties in-vitro. Allowing rapid and accurate analysis of engineering approaches designed to impact cell rolling and homing, this platform may help advance exogenous cell-based therapy.

Systematic Analysis of In Vitro Cell Rolling Using a Multi-well Plate Microfluidic System

This study used a multi-well plate microfluidic system, significantly increasing throughput of cell rolling studies under physiologically relevant shear flow. Given the importance of cell rolling in the multi-step cell homing cascade and the importance of cell homing following systemic delivery of exogenous populations of cells in patients, this system offers potential as a screening platform to improve cell-based therapy.

A major challenge for cell-based therapy is the inability to systemically target a large quantity of viable cells with high efficiency to tissues of ...

Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms

There are few high-throughput in vitro systems which facilitate the development of multi-species biofilms that contain numerous species commonly detected within in vivo oral biofilms. Furthermore, a system that uses natural human saliva as the nutrient source, instead of artificial media, is particularly desirable in order to support the expression of cellular and biofilm-specific properties that mimic the in vivo communities. We describe a method for the development of multi-species oral biofilms that are comparable, with respect to species composition, to supragingival dental plaque, under conditions similar to the human oral cavity. Specifically, this methods article will describe how a commercially available microfluidic system can be adapted to facilitate the development of multi-species oral biofilms derived from and grown within pooled saliva. Furthermore, a description of how the system can be used in conjunction with a confocal laser scanning microscope to generate 3-D biofilm reconstructions for architectural and viability analyses will be presented. Given the broad diversity of microorganisms that grow within biofilms in the microfluidic system (including Streptococcus, Neisseria, Veillonella, Gemella, and Porphyromonas), a protocol will also be presented describing how to harvest the biofilm cells for further subculture&#160;or DNA extraction and analysis. The limits of both the microfluidic biofilm system and the current state-of-the-art data analyses will be addressed. Ultimately, it is envisioned that this article will provide a baseline technique that will improve the study of oral biofilms and aid in the development of additional technologies that can be integrated with the microfluidic platform.

Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms

The goal of this methods paper is to describe the use of a microfluidic system for the development of multi-species biofilms that contain species typically identified in human supragingival dental plaque.&#160;Methods to describe biofilm architecture, biofilm viability, and an approach to harvest biofilm for culture-dependent or culture-independent analyses are highlighted.

There are few high-throughput in vitro systems which facilitate the development of multi-species biofilms that contain numerous species commonly detected ...

Using Tomoauto: A Protocol for High-throughput Automated Cryo-electron Tomography

Cryo-electron tomography (Cryo-ET) is a powerful three-dimensional (3-D) imaging technique for visualizing macromolecular complexes in their native context at a molecular level. The technique involves initially preserving the sample in its native state by rapidly freezing the specimen in vitreous ice, then collecting a series of micrographs from different angles at high magnification, and finally computationally reconstructing a 3-D density map. The frozen-hydrated specimen is extremely sensitive to the electron beam and so micrographs are collected at very low electron doses to limit the radiation damage. As a result, the raw cryo-tomogram has a very low signal to noise ratio characterized by an intrinsically noisy image. To better visualize subjects of interest, conventional imaging analysis and sub-tomogram averaging in which sub-tomograms of the subject are extracted from the initial tomogram and aligned and averaged are utilized to improve both contrast and resolution. Large datasets of tilt-series are essential to understanding and resolving the complexes at different states, conditions, or mutations as well as obtaining a large enough collection of sub-tomograms for averaging and classification. Collecting and processing this data can be a major obstacle preventing further analysis. Here we describe a high-throughput cryo-ET protocol based on a computer-controlled 300kV cryo-electron microscope, a direct detection device (DDD) camera and a highly effective, semi-automated image-processing pipeline software wrapper library tomoauto developed in-house. This protocol has been effectively utilized to visualize the intact type III secretion system (T3SS) in Shigella flexneri minicells. It can be applicable to any project suitable for cryo-ET.

We present a protocol on how to utilize high-throughput cryo-electron tomography to determine high resolution in situ structures of molecular machines. The protocol permits large amounts of data to be processed, avoids common bottlenecks and reduces resource downtime, allowing the user to focus on important biological questions.

Cryo-electron tomography (Cryo-ET) is a powerful three-dimensional (3-D) imaging technique for visualizing macromolecular complexes in their native ...

A Microfluidic Platform for High-throughput Single-cell Isolation and Culture

Studying the heterogeneity of single cells is crucial for many biological questions, but is technically difficult. Thus, there is a need for a simple, yet high-throughput, method to perform single-cell culture experiments. Here, we report a microfluidic chip-based strategy for high-efficiency single-cell isolation (~77%) and demonstrate its capability of performing long-term single-cell culture (up to 7 d) and cellular heterogeneity analysis using clonogenic assay. These applications were demonstrated with KT98 mouse neural stem cells, and A549 and MDA-MB-435 human cancer cells. High single-cell isolation efficiency and long-term culture capability are achieved by using different sizes of microwells on the top and bottom of the microfluidic channel. The small microwell array is designed for precisely isolating single-cells, and the large microwell array is used for single-cell clonal culture in the microfluidic chip. This microfluidic platform constitutes an attractive approach for single-cell culture applications, due to its flexibility of adjustable cell culture spaces for different culture strategies, without decreasing isolation efficiency.

Here, we present a protocol for isolating and culturing single cells with a microfluidic platform, which utilizes a new microwell design concept to allow for high-efficiency single cell isolation and long-term clonal culture.

Studying the heterogeneity of single cells is crucial for many biological questions, but is technically difficult. Thus, there is a need for a simple, yet ...

High-throughput Identification of Bacteria Repellent Polymers for Medical Devices

Medical devices are often associated with hospital-acquired infections, which place enormous strain on patients and the healthcare system as well as contributing to antimicrobial resistance. One possible avenue for the reduction of device-associated infections is the identification of bacteria-repellent polymer coatings for these devices, which would prevent bacterial binding at the initial attachment step. A method for the identification of such repellent polymers, based on the parallel screening of hundreds of polymers using a microarray, is described here. This high-throughput method resulted in the identification of a range of promising polymers that resisted binding of various clinically relevant bacterial species individually and also as multi-species communities. One polymer, PA13 (poly(methylmethacrylate-co-dimethylacrylamide)), demonstrated significant reduction in attachment of a number of hospital isolates when coated onto two commercially available central venous catheters. The method described could be applied to identify polymers for a wide range of applications in which modification of bacterial attachment is important.

A high-throughput microarray method for the identification of polymers which reduce bacterial surface binding on medical devices is described.

Medical devices are often associated with hospital-acquired infections, which place enormous strain on patients and the healthcare system as well as ...

Use of High-Throughput Automated Microbioreactor System for Production of Model IgG1 in CHO Cells

Automated microscale bioreactors (15 mL) can be a useful tool for cell culture engineers. They facilitate the simultaneous execution of a wide variety of experimental conditions while minimizing potential process variability. Applications of this approach include: clone screening, temperature and pH shifts,&#160;media and supplement optimization. Furthermore, the small reactor volumes are conducive to large Design of Experiments that investigate a wide range of conditions. This allows upstream processes to be significantly optimized before scale-up where experimentation is more limited in scope due to time and economic constraints. Automated microscale bioreactor systems offer various advantages over traditional small scale cell culture units, such as shake flasks or spinner flasks. However, during pilot scale process development&#160;significant care must be taken to ensure that these advantages are realized. When run with care, the system can enable high level automation, can be programmed to run DOE&#39;s with a higher number of variables&#160;and can reduce sampling time when integrated with a nutrient analyzer or cell counter. Integration of the expert-derived heuristics presented here, with current automated microscale bioreactor experiments can minimize common pitfalls that hinder meaningful results. In the extreme, failure to adhere to the principles laid out here can lead to equipment damage that requires expensive repairs. Furthermore, the microbioreactor systems have small culture volumes&#160;making characterization of cell culture conditions difficult. The number and amount of samples taken in-process in batch mode culture is limited as operating volumes cannot fall below 10 mL. This method will discuss the benefits and drawbacks of microscale bioreactor systems.

A detailed protocol for the concurrent operation of 48 parallel cell cultures under varied conditions in a microbioreactor system is presented. Cell culture process, harvest and subsequent antibody titer analysis are described.

Automated microscale bioreactors (15 mL) can be a useful tool for cell culture engineers. They facilitate the simultaneous execution of a wide variety of ...

A Microfluidic Platform for Stimulating Chondrocytes with Dynamic Compression

Mechanical stimuli are known to modulate biological functions of cells and tissues. Recent studies have suggested that compressive stress alters growth plate cartilage architecture and results in growth modulation of long bones of children. To determine the role of compressive stress in bone growth, we created a microfluidic device actuated by pneumatic pressure, to dynamically (or statically) compress growth plate chondrocytes embedded in alginate hydrogel cylinders. In this article, we describe detailed methods for fabricating and characterizing this device. The advantages of our protocol are: 1) Five different magnitudes of compressive stress can be generated on five technical replicates in a single platform, 2) It is easy to visualize cell morphology via a conventional light microscope, 3) Cells can be rapidly isolated from the device after compression to facilitate downstream assays, and 4) The platform can be applied to study mechanobiology of any cell type that can grow in hydrogels.

This article provides detailed methods for fabricating and characterizing a pneumatically actuating microfluidic device for chondrocyte compression.

Mechanical stimuli are known to modulate biological functions of cells and tissues. Recent studies have suggested that compressive stress alters growth ...