Name: a microfluidic device for studying multiple distinct strains
Uploaded: 2012-11-09T12:00:00
Description: Watch this Scientific Journal Video about A Microfluidic Device for Studying Multiple Distinct Strains at JoVE.com

YG is supported by a fellowship from IDB. IN is an Alon fellow and a faculty fellow of the Edmond J&#x202D;. &#x202C;Safra Center for Bioinformatics at Tel Aviv University&#x202D;.&#x202C; This research was supported by ISF grant 1499/10.

1. Creating a Scotch-tape Master5
<ol>
	<li>Draw or print out desired microchannel layout, to scale, on paper. In our case the design consists of two Y-shaped channels, each 3 mm wide (Figure 2).</li>
	<li>Cover a glass-slide with layers of scotch tape. The number of layers will determine the height of the channel (about 60 &mu;m per layer). We used 3 scotch tape layers.</li>
	<li>Place the layout design on a flat surface. Align the slide over the design pattern. Carefully cut the tape on th...

<ol>
	<li>Dertinger, S. K., Jiang, X., Li, Z., Murthy, V. N., 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=Gradients+of+substrate-bound+laminin+orient+axonal+specification+of+neurons.">Gradients of substrate-bound laminin orient axonal specification of neurons.</a> Proceedings of the National Academy of Sciences of the United States of America. 99, 12542-12547 (2002).</li><li>Hersen, P., McClean, M. N., Mahadevan, L., Ramanathan, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Signal+processing+by+the+HOG+MAP+kinase+pathway.">Signal processing by the HOG MAP kinase pathway.</a> Proc. Natl. Acad. Sci. U.S.A. 105, 7165-7170 (2008).</li><li>Paliwal, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MAPK-mediated+bimodal+gene+expression+and+adaptive+gradient+sensing+in+yeast.">MAPK-mediated bimodal gene expression and adaptive gradient sensing in yeast.</a> Nature. 446, 46-51 (2007).</li><li>Bennett, M. R., Hasty, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microfluidic+devices+for+measuring+gene+network+dynamics+in+single+cells.">Microfluidic devices for measuring gene network dynamics in single cells.</a> Nat. Rev. Genet. 10, 628-638 (2009).</li><li>Shrirao, A. B., Perez-Castillejos, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simple+Fabrication+of+Microfluidic+Devices+by+Replicating+Scotch-tape+Masters.">Simple Fabrication of Microfluidic Devices by Replicating Scotch-tape Masters.</a> Chips &#38; Tips. , (2010).</li><li>Haubert, K., Drier, T., Beebe, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PDMS+bonding+by+means+of+a+portable,+low-cost+corona+system.">PDMS bonding by means of a portable, low-cost corona system.</a> Lab Chip. 6, 1548-1549 (2006).</li><li>Gerber, D., Maerkl, S. J., Quake, S. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+in+vitro+microfluidic+approach+to+generating+protein-interaction+networks.">An in vitro microfluidic approach to generating protein-interaction networks.</a> Nat. Methods. 6, 71-74 (2009).</li></ol>

In this paper we present a simple benchtop method for creating a microfluidic device that allows following several yeast strains simultaneously under dynamic conditions. Following several strains in one channel provides a reliable tool for comparing dynamics of single cell responses in multiple strains. One advantage of our approach is the ability to fabricate the device with simple techniques without the need for a clean room. In fact, we have also carried out the protocol skipping the plasma treatment operations (in st...

Cells are constantly reacting to a dynamically changing environment, by changing their metabolism, transcriptional profile and cellular functions. To study these phenomena, methods that can quantify such changes are needed. One type of readout for such responses is the change in localization of stress related transcription factors in response to nutritional stress.
Microfluidic devices1 have been used to dynamically manipulate environmental conditions to cells2-4. They present several advantages for live cell imaging: the environment of the cells can be precisely controlled and dynamically changed; cells can be live-imaged at all times, including during manipulation of external conditions; and minimal reagent volumes are required. A very simple design for a microfluidic device, allowing alternation between two conditions, is a Y-shaped device2. We routinely use Y-shaped microfluidic devices that allow application of dynamic changes to the cells in the channel. We use this device to follow localization changes of fluorescently tagged stress related transcription factors in yeast cells. We follow these changes under changing nutritional conditions. For example, we can provide a pulse (or series of pulses) of glucose-containing medium within a period of no-glucose medium, at a very fine temporal resolution. Often in such experiments, one is interested in comparing the responses of different cell strains (for example, different mutants, or different wild isolates). The Y-shaped channel is limited to one strain in each channel - if more than one strain is used, there is no simple way to distinguish between the strains. To overcome this, different channels can be used. If we want to apply the same dynamics conditions to multiple strains, we would like to combine the Y-channel concept with multiple channels. There are two challenges in implementing this solution: It can be hard to apply the same conditions at the same time to all channels, and there is a geometric limitation to the number of Y-channels that can be fitted in one device. We were therefore looking for a way for viewing several strains in one channel under dynamic conditions.
Here we describe a two-layered microfluidic device intended for imaging multiple strains in one channel under the same dynamic conditions. The bottom layer consists of thin PDMS with a row of holes. This layer is attached to the glass coverslip creating wells into which we will place the different strains, adhering them with Concanavalin A to the glass. The second layer is a Y-shaped microfluidic device created using the scotch tape method5. After placing the strains in the wells the second layer is quickly aligned and attached to the first one, creating one channel with several wells that contain the different strains. This final device allows following several strains in one channel, where all strains are subjected to the same conditions at the exact same time. The whole design and production process can be done on the benchtop, using simple means, with no soft lithography.

<table border="1">
	<tbody>
 	<tr>
 	<td>Reagent/Equipment</td>
 <td>Company </td>
 <td>Catalogue number </td>
 </tr>
 <tr>
 	<td>PDMS- SYLGARD 184</td>
 <td>Dow Corning USA 	</td>
 <td></td>
 </tr>
 <tr>
 	<td>Vacuum desiccator</td>
 <td>Nalgene</td>
 <td>5310-0250</td>
 </tr>
 <tr>
 	<td>Biopsy punchers</td>
 <td>Ted Pella Inc.</td>
 <td>Harris Uni-Core 15076 (2 mm), 15074 (1.2 mm)</td>
 </tr>
 <tr>
 	<td>Syringe pumps</td>
 <td>Chemyx</td>
 <td>Fusion 200</td>
 </tr>
 <tr>
 	<td>Corona treater</td>
 <td>Electro-technic products</td>
 <td>BD-20</td>
 </tr>
 <tr>
 	<td>Tygon tubing</td>
 <td>Tygon</td>
 <td>S-54-HL</td>
 </tr>
 <tr>
 	<td>Concanavalin-A</td>
 <td>Sigma</td>
 <td>C7275</td>
 </tr>
 <tr>
 	<td>Scotch tape</td>
 <td>3M Scotch</td>
 <td>	Transparent Tape 1/2"</td>
 </tr>
 </tbody>
 </table>

a microfluidic device for studying multiple distinct strains

The study of cell responses to environmental changes poses many experimental challenges: cells need to be imaged under changing conditions, often in a comparative manner. Multiwell plates are routinely used to compare many different strains or cell lines, but allow limited control over the environment dynamics. Microfluidic devices, on the other hand, allow exquisite dynamic control over the surrounding conditions, but it is challenging to image and distinguish more than a few strains in them. Here we describe a method to easily and rapidly manufacture a microfluidic device capable of applying dynamically changing conditions to multiple distinct yeast strains in one channel. The device is designed and manufactured by simple means without the need for soft lithography. It is composed of a Y-shaped flow channel attached to a second layer harboring microwells. The strains are placed in separate microwells, and imaged under the exact same dynamic conditions. We demonstrate the use of the device for measuring protein localization responses to pulses of nutrient changes in different yeast strains.

To demonstrate the separation between different strains we imaged two distinguishable yeast strains in alternate wells. Imaging the full wells shows no cell leakage between wells (Figure 5a,b). Both strains have the transcription factor MSN2 tagged with YFP. To test the simultaneous effect of dynamically changing conditions, we switched the flow rates in the two input channels, creating a step of no-glucose medium, which resulted in localization of Msn2-YFP to the nucleus (Figure 5c,d). ...

Watch this Scientific Journal Video about A Microfluidic Device for Studying Multiple Distinct Strains at JoVE.com

A Microfluidic Device for Studying Multiple Distinct Strains

We present a simple method to produce microfluidic devices capable of applying similar dynamic conditions to multiple distinct strains, without the need for a clean room or soft lithography.

The study of cell responses to environmental changes poses many experimental challenges: cells need to be imaged under changing conditions, often in a ...

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