Difference between revisions of "Team:EPF Lausanne"

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Team:EPF_Lausanne- 2015.igem.org

YEAST IS THE

ANSWER

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E. COLI

IS AlSO

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Logic Orthogonal GRNA Implemented Circuit

The aim of our project is to enable the simple and reproducible design of modular digital circuits within living cells. Cells possess the ability to accept biological data as input and process it according to predefined instructions. We plan to harness this potential by designing bio-elements that behave as transistors. Our goal is to assemble these transistors to create a programmable logic gate array.

Thinking Binary

Boolean Logic is the bedrock of the digital revolution. Developed by George Boole in the mid-19th century, it is based on a simple set of values: 0 (“FALSE”) or 1 (“TRUE”). In computers, all information is represented by strings of 0s and 1s - multiple representations of binary digits or “Bits”. Bits are physically implemented by two-state devices named transistors. The assembling of transistors forms logic gates - which enables digital circuits to exhibit incredibly complex behaviours in the everyday objects that surround us.

A Biological Computer

Creating customizable logic gates in living cells holds the promise of revolutionizing our ability to dictate the behaviour of organism and the way they react to distinct molecular cues. This involves designing logic circuits capable of linking the many genetic regulatory networks responsible for biologic operations. An ideal genetic logic device should therefore be modular and reusable, enabling scientists to implement any complex logic functions in multiple biological systems. Our goal this summer is to achieve this by using gRNA-dCas9 combinations as the biological equivalent of the wires that connect the different components of electric circuits.
Cas9 (CRISPR associated protein 9) is an RNA-guided DNA endonuclease enzyme that can target and cleave any DNA sequence complementary to its guide RNA (gRNA). Our logic gates will be based upon a derivative of this technology, the catalytically “dead” Cas9 (dCas9) that lacks the ability to cleave DNA. dCas9’s has the very interesting property of acting as programmable transcription regulator. It it can act either as repressor by preventing the binding of the RNA polymerase (RNAP) to the targeted DNA or as an activator when fused to a polymerase recruiting element (the omega subunit of RNAP in E. Coli and VP64 in Yeast).

The bio part

To create a modular system based on these elements, we will design two different plasmids: a gate array and a linker. The gate array will contain a predefined set of logic gates. The code linking the different gates will be written on the customizeable linker plasmid.
With this project, we hope to help create robust biologically based digital devices by successfully implementing modular orthogonal logic gates in living organisms. The applications of logic circuits implemented in a biological context are vast and range from the creation of smart cells able to monitor their environment for external stimuli to new forms of cellular therapeutics with improved in vivo targeting and curing.

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+                            <h2>YEAST IS THE </h2>
+                            <h2>ANSWER</h2>
+                        </div>
+                        <a href="#" class="slider-button">Read More</a>
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+                            <h2>E. COLI</h2>
+                            <h2>IS AlSO</h2>
+                        </div>
+                        <a href="#" class="slider-button">Read More</a>
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+                    <h3>Logic Orthogonal GRNA Implemented Circuit</h3>
+                    <p>The aim of our project is to enable the simple and reproducible design of modular digital circuits within living cells. Cells possess the ability to accept biological data as input and process it according to predefined instructions. We plan to harness this potential by designing bio-elements that behave as transistors. Our goal is to assemble these transistors to create a programmable logic gate array.</p>
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-      <h1>EPF Lausanne<br>
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-        <small>Bio LOGIC</small></h1>
+                    <h4>Thinking binary</h4>
-        <!--<img src="https://static.igem.org/mediawiki/2014/d/dc/Aalto_Helsinki_Logov_Oma.png" class="img-responsive omalogo center-block">-->
+                    <p>Boolean Logic is the bedrock of the digital revolution. Developed by George Boole in the mid-19th century, it is based on a simple set of values: 0 (“FALSE”) or 1 (“TRUE”).  In computers, all information is represented by strings of 0s and 1s - multiple representations of binary digits or “Bits”. Bits are physically implemented by two-state devices named transistors. The assembling of transistors forms logic gates - which enables digital circuits to exhibit incredibly complex behaviours in the everyday objects that surround us.</p>
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-        Single cell computing
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+                    <h4>Command our plasmids</h4>
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-                Scroll down to read more
+                    <h4>Save the world</h4>
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-<article>
-<div class="link" id="Abstract"></div>
-  <h2>EPF-Lausanne<br>
-    <small>An orthogonal complex system in a single cell</small></h2>
-  <h3>Project Description</h3>
+    <div class="third-section">
-  <p>
+        <div class="container">
-    Logic gates are the main components of every modern digital circuit. Digital circuits work with binary values that are either 0 or 1 and we can think of this values as representing a false or true state respectively; physically 0 and 1 (false or true), are represented by 0V or 5V. Logic gates are ‘’black boxes’’ that can take many binary inputs and gives generally one binary output. For example the NOT gate takes one binary input and invert it: if the input is 0 the output will be 1, while if the input is 1 the output will be 0.  The NOT gate is one of the simplest logic gates we can imagine but many other gates with different functionalities exists. For example the AND  gate takes two inputs and gives an output: the output is true (i.e. the output value is 1) if both the inputs are true, otherwise the output is false (i.e. the output value is 0). Another common example is the OR gate, which takes two inputs and gives an output: the output is false if both inputs are false, otherwise the output is true. By combining different logic gates in sequence and in parallel (each gate having its own characteristic truth table) it is possible to create digital circuits with complex behaviours.
+            <div class="row">
-  </p>
+                <div class="col-md-6">
-  <p>
+                    <h2>Thinking Binary</h2>
-    The aim of our project, is to create a general framework allowing simple design of digital circuits inside living cells, using dCas9 proteins with specific gRNAs as activators or inhibitors of gene transcription.
+                    <p>Boolean Logic is the bedrock of the digital revolution. Developed by George Boole in the mid-19th century, it is based on a simple set of values: 0 (“FALSE”) or 1 (“TRUE”).  In computers, all information is represented by strings of 0s and 1s - multiple representations of binary digits or “Bits”. Bits are physically implemented by two-state devices named transistors. The assembling of transistors forms logic gates - which enables digital circuits to exhibit incredibly complex behaviours in the everyday objects that surround us.</p>
-  </p>
+                </div>
-  <p>
+            </div>
-   Cas9 (CRISPR associated protein 9) is an RNA-guided DNA endonuclease enzyme which can target nearly any DNA sequence complementary to its guide RNA (gRNA). The original function of the CRISPR-Cas9 system in bacteria is to cleave foreign DNA after positive match. However, a dead version of Cas9 (dCas9) unable to cut the DNA can be used as a repressor (by preventing the binding of the RNA polymerase to promoter sequences) or as an activator (our dCas9 is fused with a a polymerase recruiting element).
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-  </p>
+                <div class="col-md-6">
+                    <h2>A Biological Computer</h2>
-<p>Our project relies on a three plasmids system. The first one will produce dCas9, another will gather gates acting like a gate array and the last one will act as a linker for the gates and can represent the programm.
+                    <p>Creating customizable logic gates in living cells holds the promise of revolutionizing our ability to dictate the behaviour of organism and the way they react to distinct molecular cues. This involves designing logic circuits capable of linking the many genetic regulatory networks responsible for biologic operations.  An ideal genetic logic device should therefore be modular and reusable, enabling scientists to implement any complex logic functions in multiple biological systems. Our goal this summer is to achieve this by using gRNA-dCas9 combinations as the  biological equivalent of the wires that connect the different components of electric circuits.<br>
-</p>
+                    Cas9 (CRISPR associated protein 9) is an RNA-guided DNA endonuclease enzyme that can target and cleave any DNA sequence complementary to its guide RNA (gRNA). Our logic gates will be based upon a derivative of this technology, the catalytically “dead” Cas9 (dCas9) that lacks the ability to cleave DNA. dCas9’s has the very interesting property of acting as  programmable transcription regulator. It it can act either as repressor by preventing the binding of the RNA polymerase (RNAP) to the targeted DNA or as an activator when fused to a polymerase recruiting element (the omega subunit of RNAP in E. Coli and VP64 in Yeast).</p>
-<p>This modified Cas9 will form a complex with a chosen produced gRNA (guideRNA) that will allow the complex to complementary bind to the plasmids. That way dCas9 will induce the production of other gRNAs or inhibit them. The output of a gate would then be the production or not of gRNA that will go back to the linker that will induce also a gRNA to continue the program etc…
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+                    <h2>The bio part</h2>
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+                    <p>To create a modular system based on these elements, we will design two different plasmids: a gate array and a linker. The gate array will contain a predefined set of logic gates. The code linking the different gates will be written on the customizeable linker plasmid. <br>
-             <a href="https://www.youtube.com/watch?v=Fa6qf7avM1s" target="_blank"><img src="https://static.igem.org/mediawiki/2014/7/79/Aaltohelsinki_pitc_capture.png" class="img-responsive smallerimg"></img></a>
+                    With this project, we hope to help create robust biologically based digital devices by successfully implementing modular orthogonal logic gates in living organisms. The applications of logic circuits implemented in a biological context are vast and range from the creation of smart cells able to monitor their environment for external stimuli to new forms of cellular therapeutics with improved in vivo targeting and curing. </p>
-            <p class="kuvateksti">
+                </div>
-                Vidéo descriptive de Logic Gates ou dCas9?
+             </div>
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-     <li>Incoming</li>
+                    <h2>Still under construction</h2>
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-              <big><big><big>Team</big></big></big><br>
-              We are a team of twelve students with a multicultural background.
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-              We explored the possibilities of biotech and synthetic biology business.
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-              <big><big><big>Research</big></big></big><br>
-              We engineered a three-channel switch that can be controlled with the intensity of blue light.
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-              <big><big><big>Modeling</big></big></big><br>
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-              We made mathematic models of the interactions behind our gene switch.
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-              <big><big><big>Cooperation</big></big></big><br>
-              We got to know other iGEM teams and developed tools for everyone to use.
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