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The e80boot project

Welcome to E80Boot, the home of the Stanford BIOE 80 project to design, document, synthesize, and test essential genes for a new synthetic organism. The technology for printing DNA is advancing rapidly, and has now matured to the point that undergraduates can design and print complete sets of the ~500 genes needed for life. We will then pool the DNAs, transcribe and translate them, and use omics technologies to measure which proteins are being produced in the test tube. This project will introduce our students to DNA fabrication, cell metabolism, the central dogma, and interdependencies among sets of genes.

Note that this is strictly an in vitro project, with no DNA replication (or living cells). If you are curious about safety and ethics, please see Safety_and_Ethics. Indeed, a major goal of our project is to explore the implications of the dramatically increased availability of DNA- (and genome-) printing, which will benefit medicine, energy, manufacturing, climate, and nutrition, but also brings with it the potential for misuse. Our goal is to facilitate a broader debate about these issues, so that the larger community as well as scientists, industry, and policy makers can converge on the most prudent ways forward.

High level technical overview

Approximately 500 genes are needed for life in a rich growth medium. Our class will design, document, and synthesize these genes. The genes will then be combined in one test tube, which will also contain an in vitro transcription/translation mix. Each cDNA will have a T7 promoter and an E. coli promoter, and therefore, when everything is mixed, mRNAs will be generated which will then be translated into proteins. Finally, we will use mass spectrometry to measure the presence (and accumulation) of these proteins in the test tube. We have many basic questions:

  • 1. Which fraction of the ~500 genes will be transcribed/translated into proteins in this in vitro (aka 'cell free expression') setting?
  • 2. Are some pathways and functional categories disproportionally represented in the proteins that are/are not expressed?
  • 3. Can we find evidence for function of these pathways, e.g. by monitoring certain basic metabolites. For example, will integrated metabolic functions (e.g. central metabolism, the tricarboxylic acid cycle, and oxidative phosphorylation) 'boot' correctly in the cell free system? Extra reading: Cell-Free Synthetic Biology: Thinking Outside the Cell.
  • 4. Will there be evidence of de novo templated transcription and translation based on components encoded by our ~500 gene set?

For a more detailed description of the project, see File:BIOE80 Final Project 2017.pdf.

Basic instructions for adding a new page / gene

  • Create an account (see "Create account" on the top right of the screen) - should be very fast and simple.
  • Pick your gene name - use the JCVI locus identifier (such as MMSYN1_0264) given to the gene in the JCVI-Syn3.0 genome if it is a JCVI gene, or use the EcoCyc E. coli gene accession number (such as EG10893).
    • You may have been assigned the same gene as someone else (check the spreadsheet). If this is the case, add your SUID to the gene page name. For example, MMSYN1_xxxx_jstanford.
  • Follow the instructions given on Gene Specification Instructions. Or, if you want to dive right in, create a new gene spec sheet by entering your gene name below and clicking 'Create page':
  • You can either directly write MediaWiki code, or, if you are not familiar with that, you can use the little Menu Bar (which looks like this Menu.png) above the text field to add images, links, change formatting, etc. Happy gene hunting and editing! If your gene has a function that is not yet listed in the Function/Gene List on the left, just add a new category.

Upcoming Community Events

The Stanford Biological Interdisciplinary Open Maker Environment (BIOME) student society is an open space for anyone to do bioengineering and biology inspired projects. They are currently organizing Stanford's first biohackathon which will take place on May 5-6.