Biofab

Articles

Precise and Reliable Gene Expression via Standard Transcription and Translation Initiation Elements Vivek K Mutalik, Joao C Guimaraes, Guillaume Cambray, Colin Lam, Marc Juul Christoffersen, Quynh-Anh Mai, Andrew B Tran, Morgan Paull, Jay D Keasling, Adam P Arkin & Drew Endy An inability to reliably predict quantitative behaviors for novel combinations of genetic elements limits the rational engineering of biological systems. We developed an expression cassette architecture for genetic elements controlling transcription and translation initiation in Escherichia coli: transcription elements encode a common mRNA start, and translation elements use an overlapping genetic motif found in many natural systems. We engineered libraries of constitutive and repressor-regulated promoters along with translation initiation elements following these definitions. We measured activity distributions for each library and selected elements that collectively resulted in expression across a 1,000-fold observed dynamic range. We studied all combinations of curated elements, demonstrating that arbitrary genes are reliably expressed to within twofold relative target expression windows with ~93% reliability. We expect the genetic element definitions validated here can be collectively expanded to create collections of public-domain standard biological parts that support reliable forward engineering of gene expression at genome scales. browse data for article download data in csv format

Quantitative Estimation of Activity and Quality for Collections of Functional Genetic Elements Vivek K Mutalik, Joao C. Guimaraesa, Guillaume Cambray, Quynh-Anh Mai, Marc Juul Christoffersen, Lance Martin, Ayumi Yu, Colin Lam, Cesar Rodriguez, Gaymon Bennett, Jay D Keasling, Drew Endy, Adam P. Arkin. The practice of engineering biology now depends on the ad hoc reuse of genetic elements whose precise activities vary across changing contexts. Methods are lacking for researchers to affordably coordinate the quantification and analysis of part performance across varied environments, as needed to identify, evaluate and improve problematic part types. We developed an easy-to-use analysis of variance (ANOVA) framework for quantifying the performance of genetic elements. For proof of concept, we assembled and analyzed combinations of prokaryotic transcription and translation initiation elements in Escherichia coli. We determined how estimation of part activity relates to the number of unique element combinations tested, and we show how to estimate expected ensemble-wide part activity from just one or two measurements. We propose a new statistic, biomolecular part 'quality', for tracking quantitative variation in part performance across changing contexts. browse data for article download data in csv format

Measurement and modeling of intrinsic transcription terminators Guillaume Cambray, Joao C. Guimaraes,Vivek K. Mutalik, Colin Lam, Quynh-Anh Mai, Tim Thimmaiah, James M. Carothers, Adam P. Arkin and Drew Endy The reliable forward engineering of genetic systems remains limited by the ad hoc reuse of many types of basic genetic elements. Although a few intrinsic prokaryotic transcription terminators are used routinely, termination efficiencies have not been studied systematically. Here, we developed and validated a genetic architecture that enables reliable measurement of termination efficiencies. We then assembled a collection of 61 natural and synthetic terminators that collectively encode termination efficiencies across an ∼800-fold dynamic range within Escherichia coli. We simulated co-transcriptional RNA folding dynamics to identify competing secondary structures that might interfere with terminator folding kinetics or impact termination activity. We found that structures extending beyond the core terminator stem are likely to increase terminator activity. By excluding terminators encoding such context-confounding elements, we were able to develop a linear sequence-function model that can be used to estimate termination efficiencies (r = 0.9, n = 31) better than models trained on all terminators (r = 0.67, n = 54). The resulting systematically measured collection of terminators should improve the engineering of synthetic genetic systems and also advance quantitative modeling of transcription termination. Terminators and Termination efficiency (.xls)

Data Access Client

The Data Access Client is the human-centered interface of the BIOFAB's electronic datasheets. It is a rich internet application (RIA) that provides user-friendly access to the design and performance of BIOFAB parts and constructs. Click Here to Start the Data Access Client Version 2.0 alpha Released on 9-23-2011 This is a stable release of the application. The data and information gathered with this version are correct, but are being curated and enhanced.

Gene Designer

DNA2.0's Gene Designer is a free computer-aided design (CAD) tool that is able to directly import BIOFAB part design and performance. Click Here to Download Gene Designer

Data Analysis and Simulation Tools

You are able to import BIOFAB part design and performance into popular data analysis and simulation tools like R, MATLAB, and Mathematica. Example Click Here to Download an Example Mathematica Notebook If you do not own a copy of Mathematica, you can view the example notebook using the Wolfram CDF Player which can be downloaded free of charge. Click here to get information about the Wolfram CDF Player.

Data Access Web Service

The Data Access Web Service is the application interface (API) of the BIOFAB's electronic datasheets. It is a RESTful web service that provides the design and performance of BIOFAB parts and constructs. The data and information are in machine-readable formats. Version 2.0 alpha Released on 10-11-2011 This is a stable release of the application. The data and information gathered with this version are correct, but are being curated and enhanced. Documentation

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BIOFAB @ GitHub