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Team:Stanford-Brown
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Revision as of 00:06, 10 August 2013
Project Descriptions:
BioWires - We seek to utilize 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 utilized in microchip design and other bioengineering applications.Bacterial Immunity - 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.
De-Extinction - 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.
EuCROPIS - 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 Bacillus subtilis. B. subtilis 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 B. subtilis change colors in a high altitude helium balloon and, in 2016, as a part of the EuCROPIS satellite mission.
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Team
Who are we?
Data Page
Click here to see a summary of all our data collected so far!
Notebook
Here is a record of our summer's work. We also want to thank everybody who helped us along the way!
The Concept
The concept
Human Practices
Human Practices
Initiative
Initiative
Interviews
Interviews
Design Considerations
Design Considerations
Killswitch
Kill Switch
Safety
Safety
Community Outreach
Community Outreach
Project #1
Project #1
Detecting
Project #1 Detection
Reporting
Project #1 Reporting
Modelling
Modelling for Project #1
Prototyping
Prototyping for Project #1
Project #2
Project #2
Decarboxylation
Project #2
Catechol Degradation
Project #2
Flux-Variability Analysis
Project #2
Bioreactor
Project #2
Upgrading
Project #2
