title: Quantitative estimation of activity and quality for collections of functional genetic elements.
abstract: 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.
authors.affiliation: BIOFAB International Open Facility Advancing Biotechnology, Emeryville, California, USA.
authors.forename: Vivek K
authors.initials: VK
authors.lastname: Mutalik
authors.forename: Joao C
authors.initials: JC
authors.lastname: Guimaraes
authors.forename: Guillaume
authors.initials: G
authors.lastname: Cambray
authors.forename: Quynh-Anh
authors.initials: QA
authors.lastname: Mai
authors.forename: Marc Juul
authors.initials: MJ
authors.lastname: Christoffersen
authors.forename: Lance
authors.initials: L
authors.lastname: Martin
authors.forename: Ayumi
authors.initials: A
authors.lastname: Yu
authors.forename: Colin
authors.initials: C
authors.lastname: Lam
authors.forename: Cesar
authors.initials: C
authors.lastname: Rodriguez
authors.forename: Gaymon
authors.initials: G
authors.lastname: Bennett
authors.forename: Jay D
authors.initials: JD
authors.lastname: Keasling
authors.forename: Drew
authors.initials: D
authors.lastname: Endy
authors.forename: Adam P
authors.initials: AP
authors.lastname: Arkin
mesh_terms: D000818:Animals; D001426:Bacterial Proteins; D057005:Bioengineering / Q000379:methods*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology; D015723:Gene Library; D010442:Peptide Chain Initiation, Translational; D010448:Peptide Initiation Factors / Q000378:metabolism*; D039662:Prokaryotic Initiation Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D010448:Peptide Initiation Factors; D039662:Prokaryotic Initiation Factors