iGEM 2010 General Update and Project Ideas

iGEM 2010 iGEM 2010 registration is open Recruitment and forming a Team Saftey Lab Training on Saturdays Synthetic Biology bootcamp, 1st week of summer Informal Lectures Funding Publicity / Outreach EOH Biobricks Public Engagement Symposium Surveys Undergraduate Research Symposium IBE Conference March 4-6

Advisor Involvement Weekly meetings over the summer Critique ideas Recommend papers Informal Lectures during the beginning of summer Ex: How to build primers

General Project Goals Gold!   It'd be nice to build off of the sRNA we've already been working with. The ultimate goal should involve some concrete humanitarian application Keep the different category prizes in mind when deciding on a project.

Project Ideas Make a decoder More with logic gates Maz proofing   Make a decoder More with logic gates Maz proofing  Test the Tools Team's Program Gene Silencing through sRNAs

Decoder and Logic Gates Take the Decoder to the next level by having it respond to toxins and produce either a reporter or anti-toxin. This would give us the opportunity to have a really humanitarian application   Create a system with different logic gates Have a system loop back on itself Submit specific logic gates for future teams to use

Test the Tools Team Project Create and test one of the pathways that their program

mazEF Programming Cell Death Toxin-Antitoxin system mazE antitoxin mazF toxin Responds to stresses specific antibiotics EDF (Extracellular Death Factor) Quorum sensing molecules   

Gene silencing in Prokaryotes Prokaryotes as machines Issues Gene silencing in Prokaryotes Prokaryotes as machines

Issues: Gene Silencing in Prokaryotes RNAi has proven to be extremely useful in eukaryotes. It has applications in just about every field of biology, medicine, and more. No standardized non-invasive artificial gene silencing exists for prokaryotes.

Issues: Prokaryotes as Machines ~50% of dry cell mass is protein. Peptide Synthesis is the most taxing on cellular resources. If proteins are not the output or desired product, using other means of performing the same function will make the machine more efficient and conservative.

Artificial RNA-RNA Regulation sRNA Model Endogenously used as regulators in response to cellular stress Target Specificity Degradation of Transcript Irreversible Transient, Dynamic Recent Characterizations Structure Function Origin Associated Proteins Performance

Artificial RNA-RNA Regulation Transcript Stability and Regulation Construct high stability transcripts Construct strong RNA regulators Sites of Strong Regulation RBS Stem-loop of Instrinsic Terminator A/U rich regions

Artificial RNA-RNA Regulation Gene Silencing as Genetic Tools Plasmid Construct MegaPrimer P1 P2 Target Specificity Hfq Binding Intrinsic Terminator High Copy #