Team:Stanford-Brown

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<h2>Project Descriptions:</h2>
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<B>BioWires -</B> We seek to use recent advances in nucleic acid chemistry to replace hydrogen bonds between mismatched DNA bases with cations. A chelation event has been described for mismatched pyrimidines, and we have selected a C-Ag+-C bond for silver's uniquely powerful conductivity. We will rigorously test the structural and thermodynamic properties of this bonding system. Our hope is to show that silver chelation by cytosine mismatches is able to enhance the conductivity of DNA. By engineering cytosine mismatches into synthetic oligonucleotide duplexes, we seek to establish a reliable platform for nanowire and nanodevice assembly. We will design and test various nucleic acid secondary structures, and hope to ultimately produce a DNA-based nanowire system that is conductive enough to be used in microchip design and other bioengineering applications.
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<span id="abs-title" style="margin-top:-30px;"><a href="/Team:Stanford-Brown/Team/Apply">JOIN US IN 2014! CLICK HERE!</a></span>
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            <span id="abs-title">ABSTRACT</span>
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Communication is an integral part of life as we know it. This summer, we pursued four synthetic biology projects with the goal of improving communication across different mediums. On the atomic level, our <b>BioWires</B> project has created silver-incorporating DNA strands to use as nanowires, which could improve the cost and effectiveness of electronics. Our <b>CRISPR</B> project worked on a system for passing DNA regulatory messages between cells, in effect creating transmissible vaccines. We also extrapolated proteins from the past to better understand early life on Earth for our <B>De-Extinction</B> project. Finally, we built a sucrose biosensor in <I>B. subtilis</I> that will be launched on the <b>EuCROPIS</B> satellite  into low-Earth orbit. <br><br>
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<big><B>We are the Stanford-Brown iGEM team, and we're connecting life on Earth to help us prepare for life beyond it.</B></big>
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<B>Bacterial Immunity -</B> Recently, the bacterial immune system protein Cas9 was adapted to activate or repress arbitrary genes. We combine Cas9 transcriptional regulation with horizontal gene transfer for two purposes: vaccination and DNA-based communication. We adapt Cas9 as a vaccine by transferring the system into pathogenic bacteria, in which it inactivates disease-causing genes without killing the cell. Because the approach avoids strong selective pressure, we believe it will circumvent the resistance mechanisms that have rendered many antibiotics therapeutically useless. We also adapt Cas9 to read and respond to DNA messages transferred into the cell. The system functions as a switch capable of uniquely responding to millions of possible messages, exponentially more than provided by existing chemical communication systems.
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            <div style="margin-top:15px; text-align:center; font-weight: 600; font-size: 18px;">ACHIEVEMENTS</div>
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                <li> <a href="/Team:Stanford-Brown/Projects/BioWires">Demonstrated silver-ion incorporation in the DNA double-helix </a></li>
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                <li> <a href="/Team:Stanford-Brown/Projects/EuCROPIS">Worked with NASA and the German Space agency to develop BioBrick constructs for the EuCROPIS Satellite Mission</a></li>
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                <li> <a href="/Team:Stanford-Brown/Projects/CRISPR">Isolated and bricked components of two CRISPR-Cas systems</a></li>
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                <li> <a href="/Team:Stanford-Brown/Projects/De-Extinction">Designed and modeled ancestral proteins to understand early conditions of earth</a></li>
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<li> <a href="/Team:Stanford-Brown/Projects/De-Extinction#Evolutionary_Modeling">Collaborated with Dr. Rich Lenski to use 25 years of evolutionary data to model and text bioinformatics software </li>
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                <li> <a href="/Team:Stanford-Brown/Projects/HumanPractices">Authored reports on the the ethics of de-extinction and the iGEM workflow </a></li>
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                <li> <a href="https://2013.igem.org/Team:UC_Davis/Database/Initial_Population">Collaborated with team UC Davis to characterize promoter strengths</a></li>
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<li> <a href="https://2013.igem.org/Edinburgh_University">Consulted with Team Edinburgh on <i>B. subtilis</i> methods and protocols </li>
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<li> <a href="https://2013.igem.org/Team:Stanford-Brown/Team/Outreach#Teaching_a_BioEngineering_Bootcamp">Instructed high school seniors in the basics of synthetic biology and how to build an iGEM team </li>
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<li> <a href="https://2013.igem.org/Team:Stanford-Brown/Team/Outreach#Bay_Area_and_NYC_Maker_Faires">Demonstrated SynBio and iGEM to the public at Maker Faire in SF and NYC </li>
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<li> <a href="http://www.facebook.com/IgemMemes">Curated iGEM memes with additional social outreach via Instagram and Twitter </li>
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<li> <a href="https://2013.igem.org/Team:Stanford-Brown/Team/Outreach#Podcasts_and_Memes">Produced iGEM podcast to discuss SynBio topics </li>
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            <p class="brief">Atomic Communication
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<B>De-Extinction -</B> Like the Rosetta Stone, reconstructing ancestral versions of proteins will help us understand modern biology. Consider the amino acid alphabet. CysE, the protein that makes cysteine, contains cysteine in its structure, producing a chicken-and-egg problem. We hypothesize that there must have existed a version of CysE that did not contain cysteine in early life. By reconstructing ancestral versions of CysE and similar amino acid forming protein HisC, we will understand more about early life and its evolution. We hope not only to improve our understanding of evolution, but also to create applicative value. For this part of our project, we are focusing on CasA. An ancestral reconstruction of the modern CasA gene may give us insight into the mechanism of the CASCADE sequence. It may also demonstrate that ancient proteins were more thermostable or more resistant to acidity. We hope this will allow us to expand the functionality of the CRISPR system as it relates to our other projects. The technical aspects of De-Extinction are centered on the use of bioinformatics software to gather data on existing sequences for our genes and construct phylogenetic trees. We constructed a likelihood tree to determine which evolutionary substitution model we should use, and then worked backwards to construct the ancestral sequence, while also using software to model our protein and hypothesize how the active sites have changed over the years. We are further demonstrating the accuracy of our methods by working with Dr. Rich Lenski from Michigan State University, and we are including a bioethics section to address the moral uncertainties that arise from the idea that, one day, we may be able to reverse the extinction of entire organisms.
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            <p class="brief">Cellular Communication
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            <p class="brief">Temporal Communication
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<B>EuCROPIS -</B> In 2011, the Brown-Stanford iGEM team engineered photosynthetic and nitrogen-fixing cyanobacteria to secrete sucrose, a project that they entitled PowerCell. The project was designed to address the problem of in-situ resource utilization when attempting to terraform Mars, since the secreted sucrose can be used as an energy source for other organisms. The goal of the EuCROPIS project is to validate PowerCell by building a chromogenic biosensor in <I>Bacillus subtilis</I>. <I>B. subtilis</I> forms endospores in nutrient-depleted conditions and undergoes germination when exposed to sugars. As a result, we plan to characterize various sporulation and germination reporters with a series of chromoproteins in varying colors, so that we can validate PowerCell's activity by watching <I>B. subtilis</I> change colors in a high altitude helium balloon and, in 2016, as a part of the EuCROPIS satellite mission.
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            <p class="brief">Spatial Communication
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Latest revision as of 04:12, 16 November 2013

JOIN US IN 2014! CLICK HERE!
ABSTRACT

Communication is an integral part of life as we know it. This summer, we pursued four synthetic biology projects with the goal of improving communication across different mediums. On the atomic level, our BioWires project has created silver-incorporating DNA strands to use as nanowires, which could improve the cost and effectiveness of electronics. Our CRISPR project worked on a system for passing DNA regulatory messages between cells, in effect creating transmissible vaccines. We also extrapolated proteins from the past to better understand early life on Earth for our De-Extinction project. Finally, we built a sucrose biosensor in B. subtilis that will be launched on the EuCROPIS satellite into low-Earth orbit.

We are the Stanford-Brown iGEM team, and we're connecting life on Earth to help us prepare for life beyond it.

ACHIEVEMENTS

Atomic Communication

Cellular Communication

Temporal Communication

Spatial Communication

Retrieved from "http://2013.igem.org/Team:Stanford-Brown"