Team:EPF-Lausanne/ Microfluidics

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== Microfluidics ==



== Methods ==

=== Chip design and functionality ===

=== Molds fabrication - Clean room ===

Molds were fabricated at the [http://cmi.epfl.ch Center of MicroNanoTechnology at EPFL (CMI)] on silicon wafers. The flow wafers were coated with the AZ9260 positive resist at a thickness of 8um and the control wafers were coated with SU-8 negative photoresist at a thickness of 10um. SU-8 has the advantage to be more resistant and more stable than the positive resist. But, AZ9260 has the advantage that it can be rounded when baked and this property allows to have a better closing ability of the flow channels by the control valves.

On the meantime, two glass masks corresponding to each layer of the design (flow and control) were written using a laser pattern generator (Heidelberg DWL200). The photoresist was then removed by a standard developer, the chromium was removed on the Chr etching bench and the masks were finally cleaned in a hot bath of 1165 remover.

The masks were used to expose the corresponding wafers. Wafers were then baked slowly up to 100°C and developed with PGMEA and 2-propanol. For the positive resist (AZ9260), an additional bake was performed for 20 min at 160°C in order to round the edges of the flow channels.



=== PDMS chip ===

== Chip fabrication ==
Once the wafers are ready, they are used as molds for PDMS (poly(dimethylsiloxane)). The designed chip has two layers: flow level, where the cells will ultimately grow and control layer, used to close and open certain valves by putting under pressure the thin membrane between the control and the flow layers.

As both layers serve different purposes, their fabrication also differs. 

The production of the PDMS chip is performed as follows: 
The PDMS mix for control (C) and flow (F) layers is prepared separately. C-layer PDMS is a 5:1 mix of silicone and silicone curing agent. F-layer is a 20:1 mixture. Once the correct proportions have been measured, the mix is placed in a mixing defoaming machine that mixes the silicone and the curing agent in a homogeneous substance. 

[[Image:picture0.png]]

The liquid C-layer PDMS is casted directly on the wafer and set in a vacuum pump to eliminate any bubbles. The F-layer PDMS needs to form a very thin film over the wafer, so a spin coat machine is used.

[[Image:wafer in coater.png]]

Once both wafers are cast with PDMS, they are placed at 80°C for exactly 30 min. After the baking time, the PDMS from C-layer is solid and can be cut out from the wafer. 

[[Image:picture1.png]]

We now have two distinct layers that need to be aligned with each other. This process is done manually under a microscope.

[[Image:alignment.png]]

Once the chips are aligned, they are baked again at 80°C for 90 minutes. After this final bake, the C and F layers are tightly bound together. They can be easily detached from the wafer and put on a glass film for use in experiment. Again, if needed, additional wholes are punched. In the end the result is impressive! 

[[Image:chip1.png]]

[[Image:chipfranc.png]]

== Setup of the Experiment ==

The product of the previous fabrication process can now be used in the experiment. The setup is the following: 

[[Image:[[Image:setup with legends.png]]]]

The connections with the chip are done using thin tubing and syringes. When the chip is ready to use the connections look like this: 

[[Image:connections with legends.png]]

=== Cell patterning on chip ===

=== MITOMI ===
S.Maerkl and S. Quake recently developed a high-throughput microfluidic platform capable of detecting low affinity transient binding events on the basis of the mechanically induced trapping of molecular interactions, called MITOMI (ref. 1). In the context of our project, we decided to use this technique to precisely look at the molecular interactions between our two key trans-activator molecules involved in quorum-sensing, RhlR and LuxR. We wanted to quantify the interactions of those two molecules, bounded or unbounded to their specific AHLs, with the sequences of the pRhl and pLux promoters. MITOMI is a good way to precisely characterize promoters and define cross-talks levels.

For detailed protocols, have a look at the [https://2008.igem.org/Team:EPF-Lausanne/Notebook Notebook].

== Results ==


=== Chip functionality ===

=== Cell patterning ===

=== MITOMI ===


== Discussion ==


==Reference==

[http://www.ncbi.nlm.nih.gov/pubmed/17218526?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum]
Maerkl SJ, Quake SR. A systems approach to measuring the binding energy landscapes of transcription factors. Science. 2007 Jan 12;315(5809):233-7.