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The Taguchi Method is a statistical way to analyze a set of parameters, for example which promoter to use with a gene of interest, and determines a set of experiments to determine which combination of the parameters gives the most robust system to outside noise such as E. coli strain. Optimization of protein expression is done by introducing multiple shine dalgarno sequences into cistrons containing the gene of interest.
Finally, collaboration among teams allowed for a new standardized form of submitting characterization of parts to the Parts Registry. These combined help move the field of synthetic biology one step closer to being able to successfully prove that biology can in fact be engineered.
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Brief overview of the goals for the summer
This year the Purdue 2013 team has been working on a project titled Back to the Basics of Synthetic Biology. The main goals of this summer were to focus on why the iGEM competition originally started, what the goals of iGEM are, and what are the next steps required to bring the field of synthetic biology and the promise that this field holds to an industrial application.
To do this we looked how difficult it currently is to design robust genetic circuits, the lack of a standard in how data is provided for the characterization of each BioBrick part, and the unreliability of expression of proteins. Finally, we focused our attention on how improving these three aspects of synthetic biology will take this field one step closer to being a field of science with applications in industry. This required delving into the safety and hazards of working with synthetic biology at industrial scales.
Hopefully our work will provide the means necessary to carry past and future iGEM projects to worldwide applications with means to solve some of the greater grand challenges our world faces today.
Overview Content
Characterization Standard
Synthetic biology is a rapidly growing field of science that promises to revolutionize almost every part of our technology. However, one of the biggest drawbacks to synthetic biology compared to other fields is the lack of standardization within the field. Some of this can be attributed to the nature of the field itself; biological systems are much harder to control than electrical or mechanical ones.
A good portion of the problem though, comes from how the genetic parts are characterized and presented. The iGEM competition has sought for many years to create a “Registry of Standardized Parts” so that iGEM teams and other researchers can submit and use genetic parts that have been proven to work and function. While creating and characterizing new parts and devices to be added to the registry are important, if the information needed to use that part is not communicated efficiently, the parts themselves are useless. This year, the Purdue iGEM team set out to solve this problem by creating a definitive characterization standard for the registry. By talking and collaborating with over fifty other iGEM teams around the world, we have developed a way to standardize how characterization data is submitted and presented in the registry.
This system encompasses an easy, template-based system to enter data of a part into the iGEM registry. Once implemented, our solution will revolutionize the Registry of Standardized Parts and add some much-needed standardization to the field of synthetic biology.
Robustness of Genetic Circuits
In nature, organisms’ genes are robust to the point that the organism persistently reproduces under different external and internal conditions. Synthetic robustness within the field of synthetic biology is a hurdle yet to be crossed. Taguchi method is introduced to reduce variation in gene circuits through robust design of experiment. Three promoters combined with three ribosomal binding sites and three terminators are combined in a series of 27 different circuits each consisting of a promoter followed by an RBS followed by GFP and finished with a terminator.
Taguchi method uses orthogonal arrays to organize the parameters and tests for pairs of combinations of factors to gather data with minimum experiments in order to reduce cost and time. The particular gene of interest is GFP, thus, expression level of fluorescence is used as criteria to predict the most robust combination with least variance.
Bicistronic design
Despite having progressed extensively in the field of synthetic biology in terms of DNA synthesis, analysis and transplanting, we still cannot reliably, quantitatively measure expression of new genetic constructs. We engineered an expression cassette to control transcription and translation initiation which can be reused in new genetic contexts. The Bicistronic design(BCD) consists of two Shine-Dalgarno sequences in its translation element which when combined with indiscriminate gene of interests are known to reliably express within twofold of the relative target expression window.
