Difference between revisions of "Team:EPF Lausanne/Test"

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Find out about our project

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Biologic Orthogonal GRNA-Implemented Circuit

This summer, the EPFL iGEM team strives to pave the way for simpler implementation of digital circuits in vivo. Using the newly discovered dCas9 as a synthetic transcription factor, we aim to design biocompatible transistor-like elements. Our ultimate goal is to make cells smarters by assembling these transistors into logic gates that are both chainable and parallelizable in a homogenous logic framework.

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”). Modern computers represent all forms of information using strings of the same 0s and 1s (also named “Bits”). The processing of bits is handled by logical transistors - which can be seen as electronically controllable switches. Elementary logic operation are performed using cleverly assembled transistors. Such assemblies are named “logic gates”. Gates are the bricks with which complex behaviour is produced.

Biological computers

Since the early 2000’s, multiple synthetic biological gates have been built, revolutionizing our ability to dictate the way organisms react to stimuli. Their applications range from intelligent biosensors to cellular therapeutics with improved in vivo targeting and curing.
Unfortunately, the development of programmable cells has been hampered by difficulties in the multiplication and chaining of logic elements. This has hindered the complexification of bio-circuits as well as the automation and flexibility of their design.
To overcome these limitations, an ideal in vivo logic element should be modular, reusable, and orthogonal - i.e avoiding unwanted cross-talk with its host organism as well as other elements of the engineered circuit.

Cas9 Logic Gates

Cas9 (CRISPR associated protein 9) is an RNA-guided DNA endonuclease that targets and cleave any DNA sequence complementary to its guide RNA (gRNA). Our project will be based upon a derivative of this technology : catalytically “dead” Cas9 (dCas9) that lack the ability to cleave DNA. When fused to a RNA polymerase (RNAP) recruiting element (e.g. the omega subunit of RNAP in E. Coli or VP64 in eukaryotes), chimeric dCas9 can act as a programmable transcription activator. In addition, activating dCas9 may also act as a DNA transcription inhibitor: depending on its gRNA-determined binding site, it has been shown in yeasts to sterically hinder RNAP recruitment to promoter sequences.
Exploiting dCas9-omega/VP64’s ambivalence, we propose the creation of gRNA-controlled switch-like elements analogous to transistors. The state of the switch would be solely dependent on the position of dCas9 relative to the promoter. The content of the gRNA-targeted sequences might therefore be designed such that each transistor is orthogonal to other logic elements. Using gRNA to make what could be seen as “biological wires”, we also hope to achieve chainability of the transistors and thus complexification of bio-circuits.

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+                            <h2>Find out about our project</h2>
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+                        <a href="#Start" class="slider-button">Read More</a>
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-                     <h3>Logic Orthogonal GRNA Implemented Circuit</h3>
+                     <h3>Biologic 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>
+                     <p>This summer, the EPFL iGEM team strives to pave the way for simpler implementation of digital circuits in vivo. Using the newly discovered dCas9 as a synthetic transcription factor, we aim to design biocompatible transistor-like elements. Our ultimate goal is to make cells smarters by assembling these transistors into logic gates that are both chainable and parallelizable in a homogenous logic framework.</p>
                      <h2>Thinking Binary</h2>
-                     <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>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”). Modern computers represent all forms of information using strings of the same 0s and 1s (also named “Bits”). The processing of bits is handled by logical transistors - which can be seen as electronically controllable switches. Elementary logic operation are performed using cleverly assembled transistors. Such assemblies are named “logic gates”. Gates are the bricks with which complex behaviour is produced.</p>
-                     <h2>A Biological Computer</h2>
+                     <h2>Biological computers</h2>
-                     <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>Since the early 2000’s, multiple synthetic biological gates have been built, revolutionizing our ability to dictate the way organisms react to stimuli. Their applications range from intelligent biosensors to cellular therapeutics with improved in vivo targeting and curing.<br>
-                     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). <br>
+                    Unfortunately, the development of programmable cells has been hampered by difficulties in the multiplication and chaining of logic elements. This has hindered the complexification of bio-circuits as well as the automation and flexibility of their design.<br>
-                     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>
+                    To overcome these limitations, an ideal in vivo logic element should be modular, reusable, and orthogonal - i.e avoiding unwanted cross-talk with its host organism as well as other elements of the engineered circuit.</p>
-                    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>
+                     <h2>Cas9 Logic Gates</h2>
+                    <p>Cas9 (CRISPR associated protein 9) is an RNA-guided DNA endonuclease that targets and cleave any DNA sequence complementary to its guide RNA (gRNA). Our project will be based upon a derivative of this technology : catalytically “dead” Cas9 (dCas9) that lack the ability to cleave DNA. When fused to a RNA polymerase (RNAP) recruiting element (e.g. the omega subunit of RNAP in E. Coli or VP64 in eukaryotes), chimeric dCas9 can act as a  programmable transcription activator. In addition, activating dCas9 may also act as a DNA transcription inhibitor: depending on its gRNA-determined binding site, it has been shown in yeasts to sterically hinder RNAP recruitment to promoter sequences.<br>
+                     Exploiting dCas9-omega/VP64’s ambivalence, we propose the creation of gRNA-controlled switch-like elements analogous to transistors. The state of the switch would be solely dependent on the position of dCas9 relative to the promoter. The content of the gRNA-targeted sequences might therefore be designed such that each transistor is orthogonal to other logic elements. Using gRNA to make what could be seen as “biological wires”,  we also hope to achieve chainability of the transistors and thus complexification of bio-circuits.</p>
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