Team:Stanford-Brown

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<h2>Please bear with us! Page is still under construction</h2>
 
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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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<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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<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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<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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            <span id="abs-title" style="margin-top:-30px;"><a href="/Team:Stanford-Brown/AboutUs/Recruiting">COME JOIN US IN 2013! CLICK HERE!</a></span>
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            <span id="abs-title">ABSTRACT</span>
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                Astrobiology revolves around three central questions: "Where do we come from?", "Where are we going?", and "Are we alone?"  The Stanford-Brown iGEM team explored synthetic biology's untapped potential to address these questions. To approach the second question, the Hell Cell subgroup developed BioBricks that allow a cell to survive harsh extraterrestrial conditions. Such a toolset could create a space-ready synthetic organism to perform useful functions off-world. For example, the Biomining branch attempted to engineer bacteria to recycle used electronics by degenerating silica and extracting metal ions <i>in situ</i>. The Venus Life subproject grappled with the third key astrobiological question by exploring Carl Sagan's theory that life could exist in Venusian clouds. To this end, Venus Life designed a cell-cycle reporter to test for growth in aerosol within an adapted Millikan apparatus. Through this triad of projects, Stanford-Brown iGEM aims to illuminate synthetic biology's value as a tool for astrobiology.
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            <div style="margin-top:15px; text-align:center; font-weight: 600; font-size: 18px;">ACCOMPLISHMENTS</div>
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                <li> <a href="#"> Introduced Synthetic Biology as a tool for Astrobiology </a></li>
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                <li> <a href="#">Top 16 at iGEM World Competition </a></li>
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                <li> <a href="#">Best Natural BioBrick at Americas West Regionals </a></li>
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                <li> <a href="/Team:Stanford-Brown/HellCell/Introduction">Isolated parts that improve resistance to extreme conditions in <i>Escherichia coli</i></a></li>
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                <li> <a href="/Team:Stanford-Brown/VenusLife/Biosensing">Developed two cell-cycle dependent promoters for use as remote biosensors </a></li>
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                <li> <a href="/Team:Stanford-Brown/Biomining/Harvesting">Improved part BBa_K133038 by standardizing ligation into flagella and engineered the <i>E. coli</i> flagellum to extract metals <i>in situ</i></a></li>
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                <li> <a href="/Team:Stanford-Brown/VenusLife/Modeling">Modeled bacterial growth in the Venusian atmosphere </a></li>
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                <li> <a href="/Team:Stanford-Brown/HumanPractices/Introduction">Wrote Guides to Bioethics and Gene Patent Law </a></li>
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                <li> <a href="http://www.wired.com/wiredscience/2012/08/engineering-bacteria-for-mars/">Featured in Wired Magazine and Cal Academy of Sciences </a></li>
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                <li> <a href="http://www.facebook.com/IgemMemes">Created and maintained iGEM memes </a></li>
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          <div class="feature"><a href="https://2012.igem.org/Team:Stanford-Brown/HellCell/Introduction"><img src="https://static.igem.org/mediawiki/2012/5/5a/HellCell.png" width="281"/></a>
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            <p class="brief">Surviving in the harsh conditions of space is not easy for an organism.  Extreme temperatures, desiccation, and pressures are only some of the problems an intrepid bacterium might face on its journey.  We successfully strengthened our organisms with some of these abilities––desiccation and extreme basicity--in preparation for a journey into space!
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          <div class="feature"><a href="https://2012.igem.org/Team:Stanford-Brown/VenusLife/Introduction"><img src="https://static.igem.org/mediawiki/2012/d/dc/Venus.png" width="281"/></a>
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            <p class="brief">The surface of Venus is a harsh and unforgiving environment.  However, research suggests that there may be layers of its atmosphere that are more temperate.  To prepare for tests to see if organisms can survive in the clouds of Venus, we successfully developed cell-cycle dependent reporters to tell us when our cells are happy and dividing!
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          <div class="feature"><a href="https://2012.igem.org/Team:Stanford-Brown/Biomining/Introduction"><img src="https://static.igem.org/mediawiki/2012/6/60/Biomining.png" width="281" /></a>
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            <p class="brief">If we are to colonize space, we are going to need rare metals for materials. But bringing heavy duty equipment for traditional mining is not very viable at all! Bacteria and other biological organisms can be used to extract rare metals from sediment. Bacteria could mine asteroids and do all the work for us, and we equipped their flagella with the tools to do so!
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Revision as of 00:15, 20 September 2013

COME JOIN US IN 2013! CLICK HERE! ABSTRACT

Astrobiology revolves around three central questions: "Where do we come from?", "Where are we going?", and "Are we alone?" The Stanford-Brown iGEM team explored synthetic biology's untapped potential to address these questions. To approach the second question, the Hell Cell subgroup developed BioBricks that allow a cell to survive harsh extraterrestrial conditions. Such a toolset could create a space-ready synthetic organism to perform useful functions off-world. For example, the Biomining branch attempted to engineer bacteria to recycle used electronics by degenerating silica and extracting metal ions in situ. The Venus Life subproject grappled with the third key astrobiological question by exploring Carl Sagan's theory that life could exist in Venusian clouds. To this end, Venus Life designed a cell-cycle reporter to test for growth in aerosol within an adapted Millikan apparatus. Through this triad of projects, Stanford-Brown iGEM aims to illuminate synthetic biology's value as a tool for astrobiology.

ACCOMPLISHMENTS

Surviving in the harsh conditions of space is not easy for an organism. Extreme temperatures, desiccation, and pressures are only some of the problems an intrepid bacterium might face on its journey. We successfully strengthened our organisms with some of these abilities––desiccation and extreme basicity--in preparation for a journey into space!

The surface of Venus is a harsh and unforgiving environment. However, research suggests that there may be layers of its atmosphere that are more temperate. To prepare for tests to see if organisms can survive in the clouds of Venus, we successfully developed cell-cycle dependent reporters to tell us when our cells are happy and dividing!

If we are to colonize space, we are going to need rare metals for materials. But bringing heavy duty equipment for traditional mining is not very viable at all! Bacteria and other biological organisms can be used to extract rare metals from sediment. Bacteria could mine asteroids and do all the work for us, and we equipped their flagella with the tools to do so!

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