Quantitative estimation of activity and quality for collections of functional genetic elements

Mutalik, Vivek K; Guimaraes, Joao C; Cambray, Guillaume; Mai, Quynh-Anh; Christoffersen, Marc Juul; Martin, Lance; Yu, Ayumi; Lam, Colin; Rodriguez, Cesar; Bennett, Gaymon; Keasling, Jay D; Endy, Drew; Arkin, Adam P
April 2013
Nature Methods;Apr2013, Vol. 10 Issue 4, p347
Academic Journal
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.


Related Articles

  • Development of a Reference Standard of Escherichia coli DNA for Residual DNA Determination in China. Wang, Lan; Rao, Chunming; Gao, Kai; Li, Yonghong; Fu, Zhihao; Bi, Hua; Wang, Junzhi // PLoS ONE;Sep2013, Vol. 8 Issue 9, p1 

    This collaborative study developed the first national Escherichia coli (E. coli) DNA reference standard for standardizing quantitative residual DNA assay methods, fluorescence dye (PicoGreen) and quantitative PCR (q-PCR), which were widely employed to measure residual DNA contents of...

  • Two Tales of Prokaryotic Genomic Diversity: Escherichia coli and Halophiles. Pašić, Lejla; Ambrožič Avguštin, Jerneja; Starčič Erjavec, Marjanca; Herzog-Velikonja, Blagajana; Podlesek, Zdravko; Žgur-Bertok, Darja // Food Technology & Biotechnology;Apr-Jun2014, Vol. 52 Issue 2, p158 

    Prokaryotes are generally characterized by vast genomic diversity that has been shaped by mutations, horizontal gene transfer, bacteriocins and phage predation. Enormous genetic diversity has developed as a result of stresses imposed in harsh environments and the ability of microorganisms to...

  • Established Microbial Colonies Can Survive Type VI Secretion Assault. Borenstein, David Bruce; Ringel, Peter; Basler, Marek; Wingreen, Ned S. // PLoS Computational Biology;10/20/2015, Vol. 11 Issue 10, p1 

    Type VI secretion (T6S) is a cell-to-cell injection system that can be used as a microbial weapon. T6S kills vulnerable cells, and is present in close to 25% of sequenced Gram-negative bacteria. To examine the ecological role of T6S among bacteria, we competed self-immune T6S+ cells and...

  • The mysterious orphans of Mycoplasmataceae. Tatarinova, Tatiana V.; Lysnyansky, Inna; Nikolsky, Yuri V.; Bolshoy, Alexander // Biology Direct;1/8/2016, Vol. 11, p1 

    Background: The length of a protein sequence is largely determined by its function. In certain species, it may be also affected by additional factors, such as growth temperature or acidity. In 2002, it was shown that in the bacterium Escherichia coli and in the archaeon Archaeoglobus fulgidus,...

  • Solving proteins' sticky problem. Bradley, David // New Scientist;3/25/95, Vol. 145 Issue 1970, p19 

    Reports on the discovery of a solution to the clumping of bioengineered proteins in the bacterium Escherichia coli. Use of proteins for drugs; Tests on the enzymes carbonic anhydrase and citrate synthase.

  • Viability of free and encapsulated Escherichia coli overexpressing cyclopentanone monooxygenase monitored during model Baeyer-Villiger biooxidation by confocal laser scanning microscopy. Schenkmayerová, Andrea; Bučko, Marek; Gemeiner, Peter; Chorvát, Dušan; Lacík, Igor // Biotechnology Letters;Feb2012, Vol. 34 Issue 2, p309 

    Baeyer-Villiger biooxidation of 4-methylcyclohexanone-5-methyloxepane-2-one catalysed by recombinant Escherichia coli overexpressing cyclopentanone monooxygenase encapsulated in polyelectrolyte complex capsules was used to investigate effect of substrate conversion on the viability of cells....

  • Quantitative frame analysis and the annotation of GC-rich (and other) prokaryotic genomes. An application to Anaeromyxobacter dehalogenans. Oden, Steve; Brocchieri, Luciano // Bioinformatics;10/15/2015, Vol. 31 Issue 20, p3254 

    Motivation: Graphical representations of contrasts in GC usage among codon frame positions (frame analysis) provide evidence of genes missing from the annotations of prokaryotic genomes of high GC content but the qualitative approach of visual frame analysis prevents its applicability on a...

  • Cloning, Expression, and In Vitro Functional Activity Assay of phiC31 Integrase cDNA in Escherichia coli. Sekhavati, Mohammad Hadi; Tahmoorespur, Mojtaba; Ghaedi, Kamran; Dormiani, Kianoush; Reza Nassiri, Mohammad; Khazaie, Yahya; Foruzanfar, Mahboubeh; Hosseini, Morteza; Hossein Nasr Esfahani, Mohammad // Cell Journal (Yakhteh);Winter2013, Vol. 14 Issue 4, p264 

    Objective: The aim of present study was cloning and expression of phiC31 integrase cDNA in a bacterial expression vector. Thus, an intra molecular assay vector was applied to show in vitro activity of recombinant protein. Materials and Methods: In this experimental study, phiC31 cDNA was...

  • Enhanced 5-methylcytosine detection in singlemolecule, real-time sequencing via Tet1 oxidation. Clark, Tyson A.; Lu, Xingyu; Luong, Khai; Dai, Qing; Boitano, Matthew; Turner, Stephen W.; He, Chuan; Korlach, Jonas // BMC Biology;2013, Vol. 11 Issue 1, p1 

    Background: DNA methylation serves as an important epigenetic mark in both eukaryotic and prokaryotic organisms. In eukaryotes, the most common epigenetic mark is 5-methylcytosine, whereas prokaryotes can have 6-methyladenine, 4-methylcytosine, or 5-methylcytosine. Single-molecule, real-time...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics