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-	<B>De-Extinction -</B>Death is not permanent; everything on this Earth leaves some kind of mark from which we can learn. Take the Latin language, for example. It is a dead language, but is still studied because it helps us understand the origins of our own language. The De-Extinction project performs such a function. Like the Rosetta Stone, reconstructing ancestral versions of proteins will help us understand the modern biological language. 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 at Michigan State University, and we are including a bioethics section in our project to address the moral uncertainties that arise from the idea that, one day, we may be able to reverse the extinction of entire organisms.	+	<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 at Michigan State University, and we are including a bioethics section in our project 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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Revision as of 22:59, 9 August 2013

Stanford-Brown iGEM

Project Descriptions:

BioWires - We seek to utilize recent advances in nucleic acid chemistry to replace hydrogen bonds between mismatched DNA bases with cations. A kelation 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 kelation 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 - Over half of bacteria species contain a CRISPR immune system capable of sequence-specific surveillance and targeting. Recently, the CRISPR gene 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 at Michigan State University, and we are including a bioethics section in our project to address the moral uncertainties that arise from the idea that, one day, we may be able to reverse the extinction of entire organisms. I'm A Badass Caption: I can haz links, style or anything that is valid markup :)