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Revision as of 23:09, 15 August 2017
NOISE Parts
In deciding which parts to submit to the iGEM Registry we focused on three main aspects. First: ensuring our project is as reproducible and extensible as possible. To that end we have submitted all of new composite fluorescent protein parts that we constructed during the project. Measurement & Modeling We measured noise in fluorescence data for dual-integrated sets of CFP and YFP under three promoters: BBa_R0010, BBa_R0011, and BBa_R0051. We also developed an analytic model of the impact of plasmid copy number fluctuations on transcriptional noise, which revealed that intrinsic noise cannot be accurately measured from reporters on the pSB1X3 plasmid series. Human practices Our Human Practices effort was a multi-faceted outreach approach to science literacy, focusing specifically on spreading a basic understanding of synthetic biology to the general public. We collaborated with numerous organizations to host nine educational Synthetic Biology workshops for the public (from first graders to adults!) and to implement our educational 24-activity Synthetic Biology booklet into schools worldwide, to further sustain our efforts for years to come. Collaboration W&M iGEM met and exceeded iGEM's collaboration requirements by collaborating with other researchers in four main ways: creating a pen pal program to connect teams with similar projects, participating in the interlab measurement study, interviewing the general public to provide data to future teams about how to communicate synthetic biology, and collaborating on individual research projects with iGEM teams from University of Georgia, University of Maryland, and Cambridge. 2015 Jamboree Results Undergraduate Grand Prize Winner ReferencesCharacterization of promoter-driven transcriptional noise in E. coli
Second: Making genome integration as straightforward as possible for iGEM teams. In order to accomplish this goal we designed, tested, and validated a new integrator cassette that allows simple genome integration using 3A or Gibson Assembly.
Third: Increasing the number of tools available for promoter-mediated regulation in synthetic biology. We created and validated an E. coli codon optimized dCas9 variant and a suite of gRNAs to target the most commonly used promoters in iGEM. 
Best in Track: Measurement
Best Education & Public Engagement
Best Presentation
Nominee: Best Mathematical Model
A fundamental goal of synthetic biology is to create a modular genetic basis for control over circuit behavior properties. While much progress has been made in achieving this objective for properties such as gene expression strength, where well-characterized ribosome binding sites (RBSs) can be conveniently swapped within a genetic part, there is much to be desired in altering gene expression speed. Currently, no such robust mechanism of speed control exists. We intend to provide a means to tune the speed of gene expression in transcriptional circuits, where a pre-characterized genetic part can be inserted into a gene to alter its expression in a predictable way.
Based on multiple well-cited claims in literature, a strong relationship can be asserted between gene expression speed and the rate of protein degradation. Using a basic mathematical model of gene expression, one can derive that the speed of gene expression, defined as the time it takes for its protein product to reach half of its steady-state concentration, is a function of the protein’s degradation rate. This reveals that tuning protein degradation rate is essential to controlling gene expression, thus amenable to an approach involving protein degradation tags. Degradation tags are used endogenously to identify misfolded proteins, and different tags have unique protease-binding affinities which confer various degradation rates on the tagged proteins.
In 2008, the Sauer lab at MIT reported that Mycoplasma florum’s Lon protease system was orthogonal to the endogenous protein degradation machinery in E. coli. As of now, mf-Lon degradation tags exist only as isolated sequences on the BioBrick Registry. We intend to build a suite of BioBrick parts in the form of [mf-Lon tag] - [Stop Codon] - [Double Terminator] that can be swapped in to directly modulate protein degradation rate just as RBS and promoter sequences can be swapped to modify protein production. This would drastically increase the accessibility of mf-Lon tags and enable other teams to easily amplify their desired protein sequence by simply cloning it into our construct. Should the relationship between gene expression speed and protein degradation rate exist robustly, we will be providing the first modular genetic basis of speed control, fulfilling a core aspiration of synthetic biology to have every gene expression and circuit property accessible at the genetic level.
