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                    <h1>Bio LOGIC</h1>
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                    <h2>Logic Orthogonal gRNA Implemented Circuits</h2>
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                        <!--<a class="navbar-brand" href="https://2015.igem.org/Team:EPF_Lausanne">Bio Logic</a>-->
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                    <p>Engineering transcriptional logic gates to program cellular behavior remains an important challenge for synthetic biology. Currently, genetic circuits reproducing digital logic are limited in scalability and robustness by output discrepancies and crosstalk between transcriptional pathways. We propose to address these issues using RNA-guided dCas9 fused to a transcription activation domain as a programmable transcription factor.</p>
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                    <h3>Read More</h3>
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                          <p>Discover the ideas behind our project, from boolean logic to the the complete explanation of a biologic logic gate.</p>
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                          <p>Having a robust system is the key when devising new concepts. It enables testing in silico before ordering the expensive parts...</p>
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                    <h3>Biologic Orthogonal GRNA-Implemented Circuit</h3>
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                  <a href="https://2015.igem.org/Team:EPF_Lausanne/Achivements/Vivo">
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                    <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>
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                     <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>
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                    <h2>In Vivo</h2>
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                      <p>Our achievements in the wet-lab, the result of a summer in the cold labrooms.</p>
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                    <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>
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                     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>
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                    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>
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                    <h2>Cas9 Logic Gates</h2>
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                    <p>Cas9 (CRISPR associated protein 9) is an RNA-guided DNA endonuclease that targets and cleaves 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>
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                     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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Latest revision as of 21:38, 31 August 2015

EPFL 2015 iGEM bioLogic Logic Orthogonal gRNA Implemented Circuits EPFL 2015 iGEM bioLogic Logic Orthogonal gRNA Implemented Circuits

Bio LOGIC

Logic Orthogonal gRNA Implemented Circuits

Engineering transcriptional logic gates to program cellular behavior remains an important challenge for synthetic biology. Currently, genetic circuits reproducing digital logic are limited in scalability and robustness by output discrepancies and crosstalk between transcriptional pathways. We propose to address these issues using RNA-guided dCas9 fused to a transcription activation domain as a programmable transcription factor.

Read More

Project

Background

Discover the ideas behind our project, from boolean logic to the the complete explanation of a biologic logic gate.

Description

Understand our project in the smallest details and explore the world of CRISPR-dCas9 with us.

Applications

Need a biosensor? Want a bacteria that can depollute a lake? Here are a few examples of how you could apply our technology for your own designs.

Modeling

Having a robust system is the key when devising new concepts. It enables testing in silico before ordering the expensive parts...

Achievements

In Vivo

Our achievements in the wet-lab, the result of a summer in the cold labrooms.

In silico

What we were able to do using the computer.

Judging

The criterias that we fulfilled for the different medals.

Parts

iGEM is all about Biobricks. Here is our contribution to this expanding library.

Policy and Practices

Ethics

Is working on the genome ethically correct? We tried to answer to this question.

Safety

Doing safe work with small organisms can be dangerous. Here is what we did to protect ourselves and the environment.

Human Practices

We do good ! Don't listen to the mass media.

Notebook

E. coli

See how we planned our summer and how it went for the E.coli team.

Yeast

Even if we used a beer icon Yeasts are not all about beer, discover how we experimented with this tough organism.

Protocols

These are the protocols that you need if you want to redo our work.

Team

Meet us!

Brief description of who is who and for what (s)he is renowned.

Timeline

How did our summer go?

Aknowledgements

We are thankfull to all the people that helped us.

Attributions

What you do is what you get.
EPFL 2015 iGEM bioLogic Logic Orthogonal gRNA Implemented Circuits

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