Difference between revisions of "Team:Uppsala/Project/Microfluidics"

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      <h2> Microfluidics </h2>
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                 <h2> Microfluidics </h2>
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                 <img class="img-responsive img-circle" src="https://static.igem.org/mediawiki/2016/e/e4/Uppsala_Introchip.jpg" />
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<figcaption> This picture shows a microfluidic device with different inlets and corresponding tubes with
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different colors.
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<br>
 
  
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Image source: http://news.stanford.edu/news/2006/january18/fluidics-011806.html
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<br>
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                    <img class="img-responsive img-circle" src="http://placehold.it/400x400" />
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This picture was uploaded: 2006/01/18
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We took the picture: 2016/07/06 at 10:59
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                        Stuff about Unag
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                <p>
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                    Microfluidics is both a science and a technology that is currently an active field of academic
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research and study. It consists of systems that work with small volumes of fluids in the
 
  
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nanoliter/microliter scale, through channels ranging from tens to hundreds of micrometers in diameter.
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Microfluidic devices have been readily used in chemistry and molecular biology and this
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provides a good base for further use in life sciences.
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                <h3> Why microfluidics? </h3>
 
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                <p> There are two essential qualities in
 
  
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microfluidic devices that make them attractive to life science research. Firstly, the size of the
 
  
−
device is small which makes them ideal platforms for point-of-care diagnostics that are
 
  
−
portable. Secondly, their small size is also convenient since the volume of the liquids required
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                    <a data-toggle="collapse" data-target="#collapsible-4" data-parent="#myAccordion">
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                        <div class="mybutton text-center results panel-default">
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                            <div class="panel-body"> Results</div>
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to perform complex experiments is minimal, a property that can lower the cost of reactions.
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                </div>
  
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Thanks to fluidic components that approach the scale of a single cell, microfluidics in cell
 
  
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biology increases the throughput of biological and chemical assays. Small fluidic devices can
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                <hr>
  
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perform a wide range of experimental designs and are also able to executed fully automated
 
  
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computer protocols. This reduces the human error and makes experiments highly efficient and
 
  
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reproducible. The advantages that this field brings to life science research are proof that
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                    <div class="col-lg-8 collapse" id="collapsible-1">
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                        <h3> About Microfluidics </h3>
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                        <p> Microfluidics is both a science and a technology that is currently an active field of academic
 +
research and study. It consists of systems that work with small volumes of fluids in the
 +
nanoliter/microliter scale, through channels ranging from tens to hundreds of micrometers in diameter.
 +
Microfluidic devices have been readily used in chemistry and molecular biology and this
 +
provides a good base for further use in life sciences.
 +
                    </div>
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                </div>
  
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microfluidics shows broad potential use in medicine as well. In our project, we are using
 
  
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microfluidic techniques to transform bacterial and yeast cells in an efficient and more
 
  
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automated manner. </p>
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                <h3> What we have been up to </h3>
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                <p>We are in the process of making a microfluidic device that will be used for cell transformation. Hitherto, we have been able to 3D print a couple of designs and discuss our final design. After we 3D print a mold that is satisfactory, we will bake PDMS on it and can later begin to test our chip. During our first trials we would like to keep things simple in order to make troubleshooting as painless of a process as possible. Therefore, we have decided to start off with the heat shock method of transformation. Our initial thoughts are to have a channel on the chip running with cells and plasmids and a parallel channel with temperature regulated water. With this technique we hope to be able to expose CaCl2 competent cells to a heat shock preceded and followed by low temperatures; much like a conventional heat shock. Moreover we are in the process of calculating the cost for an ordinary heat shock. The reason for this being that one of our main goals is to make cell transformation more affordable. </p>
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                        <h3> Why microfluidcs? </h3>
 +
                        <p> There are two essential qualities in microfluidic devices that make them attractive to life science research. Firstly, the size of the device is small which makes them ideal platforms for point-of-care diagnostics that are
 +
portable. Secondly, their small size is also convenient since the volume of the liquids required
 +
to perform complex experiments is minimal, a property that can lower the cost of reactions. Thanks to fluidic components that approach the scale of a single cell, microfluidics in cell biology increases the throughput of biological and chemical assays. Small fluidic devices can perform a wide range of experimental designs and are also able to executed fully automated computer protocols. This reduces the human error and makes experiments highly efficient andreproducible. The advantages that this field brings to life science research are proof that microfluidics shows broad potential use in medicine as well. In our project, we are using microfluidic techniques to transform bacterial and yeast cells in an efficient and more automated manner.  
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                        <h3> What we did. </h3>
 +
                        <p> Our first step in fabricating a microfluidics device was to plan how it is was going to function. In this process the design of the micropattern is paramount. Generally you want the channels of the microchannels kept small and use low flow rates. These parameters together with the viscosity of the fluid combine into a dimensionless number called the Reynolds number. Microfluidic devices usually have flows with low Re numbers < 2000. When flows have low Re they are labeled laminar. For a laminar flow, properties change such as its bulk motion predictability and how species in the fluid are transported via convection/diffusion as opposed to a turbulent flow where such phenomena can be very difficult to predict. How laminar the flow in your chip will be is determined by the flow rate, the fluid's viscosity and the dimensions of the channels. When designing the channels it is important to think about the range of flow rates that can be used so that the flow inside the chip are within the laminar domain.
 +
 
 +
The plan for our two chips was to utilize small volumes to minimize the amount of reagents we would need. We also wanted to make the chip itself small to keep the amount of PDMS needed for curing down. The whole work of designing our lithographic molds started in AutoCAD (AutoCAD 2015 AutoDesk), a CAD software used for drawing 2D & 3D object with scientific accuracy. Although 3D modelling software such as Blender can be used these programs tend to be more difficult to work with as they are more focused on aesthetics instead of accurate angles and lengths.  
 +
 
 +
Since our CAD drawings in the end was being 3D printed we needed to consider the resolution of the printer and how to best print our design. It is important that the mold is flat so that the cured PDMS chip is flat in order to achieve a good bonding between PDMS and whatever substrate used to seal the channels. We wanted to be able to easily pour the PDMS into the mold, simplifying handling of sticky uncured PDMS, and also easily remove the cured chip without the risk of tearing it. The design should also use as little printer resin as possible to keep costs and print time to a minimum. The 3D printer in the end also determines how small the microchannels can be made, in our case we chose the shortest out of plane height that the printer could print without large deviations in the actual printed height. With these requirements in mind we designed the following chips.
 +
 
 +
The design consists of 4 main parts. The bottom plate 33 mm L / 22 mm W, the wall structure 10 mm height / 3 mm thick, the separate detachable wall and the lithographic pattern, please see our designs for more info. The design makes it possible to reuse the box and draw new patterns depending on the application for the cured chip. The benefits of reusing the box design are to minimize future unforeseen problems concerning how well the PDMS is curing, removing of chip form the mold and the flatness of the fabricated PDMS chip, increasing repeatability.
 +
<br> ----IMG HERE---- <br>
 +
 
 +
We designed a pattern for a heat shock transformation chip. This pattern consisted of two larger channels that would warm the smaller channel in between by circulating hot water. The cells would be injected into the middle channel and left in the channel for 45 sec and then ejected. As with the electroporation chip our thoughts was that the heating chip design easily could be included with other types of structures on “lab in a chips”.
 +
<br> ----IMG HERE---- <br>
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                        <h3> Results </h3>
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                        <p> Lorem ipsum dolor sit amet, consectetur adipiscing elit. Morbi commodo mollis mauris et euismod. Nullam pulvinar ultricies massa ac sagittis. Sed ex odio, venenatis non nisi sit amet, vulputate varius quam. Donec iaculis, orci a malesuada tempor, eros ex aliquam sem, eu laoreet odio erat at leo. Donec felis risus, aliquam eget blandit in, dignissim et arcu. Etiam id lectus sed augue ultrices condimentum. Donec bibendum eget leo tempus porttitor. Curabitur hendrerit ligula quis molestie scelerisque. Nunc quis ex a est finibus aliquam ac ac risus. Nam finibus ligula sed dignissim volutpat. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Morbi egestas eros sit amet fringilla viverra. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Etiam tempus aliquet turpis vitae posuere. Nam ante turpis, suscipit et nibh id, posuere porttitor justo. Nam vulputate tempus nulla, vel sagittis felis lobortis at. In tempor elit sit amet pellentesque pharetra. Fusce congue erat non lobortis aliquam. Aliquam consectetur nunc eros, pellentesque consectetur libero fermentum a. Sed condimentum tellus sapien, id laoreet velit dapibus ac. Praesent vitae commodo eros, vel posuere mi. </p>
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                <h3>Plans for electroporation </h3>
 
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                <p>One of our final goals is to produce a chip that enables electroporation. The best way to perform electroporation on a chip (as read in literature) is to use droplet techniques. That is, droplets of cell growth medium and cells separated by nonconductive material. The most common nonconductive material used is fluorinated oil. These oils are generally expensive, hard to find and may be toxic. For this reason we are considering separating droplets with gas; more precisely N2.</p>
 
  
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                Next week, we hope to bake our chip and start running experiments with it.
 
 
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Revision as of 13:35, 12 October 2016

Microfluidics

Stuff about Unag

About UnaG/Intro
Dig deeper into UnaG
Dig deeper into Bilirubin
Results

About Microfluidics

Microfluidics is both a science and a technology that is currently an active field of academic research and study. It consists of systems that work with small volumes of fluids in the nanoliter/microliter scale, through channels ranging from tens to hundreds of micrometers in diameter. Microfluidic devices have been readily used in chemistry and molecular biology and this provides a good base for further use in life sciences.

Why microfluidcs?

There are two essential qualities in microfluidic devices that make them attractive to life science research. Firstly, the size of the device is small which makes them ideal platforms for point-of-care diagnostics that are portable. Secondly, their small size is also convenient since the volume of the liquids required to perform complex experiments is minimal, a property that can lower the cost of reactions. Thanks to fluidic components that approach the scale of a single cell, microfluidics in cell biology increases the throughput of biological and chemical assays. Small fluidic devices can perform a wide range of experimental designs and are also able to executed fully automated computer protocols. This reduces the human error and makes experiments highly efficient andreproducible. The advantages that this field brings to life science research are proof that microfluidics shows broad potential use in medicine as well. In our project, we are using microfluidic techniques to transform bacterial and yeast cells in an efficient and more automated manner.

What we did.

Our first step in fabricating a microfluidics device was to plan how it is was going to function. In this process the design of the micropattern is paramount. Generally you want the channels of the microchannels kept small and use low flow rates. These parameters together with the viscosity of the fluid combine into a dimensionless number called the Reynolds number. Microfluidic devices usually have flows with low Re numbers < 2000. When flows have low Re they are labeled laminar. For a laminar flow, properties change such as its bulk motion predictability and how species in the fluid are transported via convection/diffusion as opposed to a turbulent flow where such phenomena can be very difficult to predict. How laminar the flow in your chip will be is determined by the flow rate, the fluid's viscosity and the dimensions of the channels. When designing the channels it is important to think about the range of flow rates that can be used so that the flow inside the chip are within the laminar domain. The plan for our two chips was to utilize small volumes to minimize the amount of reagents we would need. We also wanted to make the chip itself small to keep the amount of PDMS needed for curing down. The whole work of designing our lithographic molds started in AutoCAD (AutoCAD 2015 AutoDesk), a CAD software used for drawing 2D & 3D object with scientific accuracy. Although 3D modelling software such as Blender can be used these programs tend to be more difficult to work with as they are more focused on aesthetics instead of accurate angles and lengths. Since our CAD drawings in the end was being 3D printed we needed to consider the resolution of the printer and how to best print our design. It is important that the mold is flat so that the cured PDMS chip is flat in order to achieve a good bonding between PDMS and whatever substrate used to seal the channels. We wanted to be able to easily pour the PDMS into the mold, simplifying handling of sticky uncured PDMS, and also easily remove the cured chip without the risk of tearing it. The design should also use as little printer resin as possible to keep costs and print time to a minimum. The 3D printer in the end also determines how small the microchannels can be made, in our case we chose the shortest out of plane height that the printer could print without large deviations in the actual printed height. With these requirements in mind we designed the following chips. The design consists of 4 main parts. The bottom plate 33 mm L / 22 mm W, the wall structure 10 mm height / 3 mm thick, the separate detachable wall and the lithographic pattern, please see our designs for more info. The design makes it possible to reuse the box and draw new patterns depending on the application for the cured chip. The benefits of reusing the box design are to minimize future unforeseen problems concerning how well the PDMS is curing, removing of chip form the mold and the flatness of the fabricated PDMS chip, increasing repeatability.
----IMG HERE----
We designed a pattern for a heat shock transformation chip. This pattern consisted of two larger channels that would warm the smaller channel in between by circulating hot water. The cells would be injected into the middle channel and left in the channel for 45 sec and then ejected. As with the electroporation chip our thoughts was that the heating chip design easily could be included with other types of structures on “lab in a chips”.
----IMG HERE----

Results

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Morbi commodo mollis mauris et euismod. Nullam pulvinar ultricies massa ac sagittis. Sed ex odio, venenatis non nisi sit amet, vulputate varius quam. Donec iaculis, orci a malesuada tempor, eros ex aliquam sem, eu laoreet odio erat at leo. Donec felis risus, aliquam eget blandit in, dignissim et arcu. Etiam id lectus sed augue ultrices condimentum. Donec bibendum eget leo tempus porttitor. Curabitur hendrerit ligula quis molestie scelerisque. Nunc quis ex a est finibus aliquam ac ac risus. Nam finibus ligula sed dignissim volutpat. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Morbi egestas eros sit amet fringilla viverra. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Etiam tempus aliquet turpis vitae posuere. Nam ante turpis, suscipit et nibh id, posuere porttitor justo. Nam vulputate tempus nulla, vel sagittis felis lobortis at. In tempor elit sit amet pellentesque pharetra. Fusce congue erat non lobortis aliquam. Aliquam consectetur nunc eros, pellentesque consectetur libero fermentum a. Sed condimentum tellus sapien, id laoreet velit dapibus ac. Praesent vitae commodo eros, vel posuere mi.