Characterization of Gene Circuit Parts Based on Multiobjective Optimization by Using Standard Calibrated Measurements.
DNA
bioinformatics
fluorescence
gene technology
synthetic biology
Journal
Chembiochem : a European journal of chemical biology
ISSN: 1439-7633
Titre abrégé: Chembiochem
Pays: Germany
ID NLM: 100937360
Informations de publication
Date de publication:
15 10 2019
15 10 2019
Historique:
received:
27
04
2019
revised:
12
06
2019
pubmed:
4
7
2019
medline:
10
9
2020
entrez:
4
7
2019
Statut:
ppublish
Résumé
Standardization and characterization of biological parts is necessary for the further development of bottom-up synthetic biology. Herein, an easy-to-use methodology that embodies both a calibration procedure and a multiobjective optimization approach is proposed to characterize biological parts. The calibration procedure generates values for specific fluorescence per cell expressed as standard units of molecules of equivalent fluorescein per particle. The use of absolute standard units enhances the characterization of model parameters for biological parts by bringing measurements and estimations results from different sources into a common domain, so they can be integrated and compared faithfully. The multiobjective optimization procedure exploits these concepts by estimating the values of the model parameters, which represent biological parts of interest, while considering a varied range of experimental and circuit contexts. Thus, multiobjective optimization provides a robust characterization of them. The proposed calibration and characterization methodology can be used as a guide for good practices in dry and wet laboratories; thus allowing not only portability between models, but is also useful for generating libraries of tested and well-characterized biological parts.
Identifiants
pubmed: 31269324
doi: 10.1002/cbic.201900272
doi:
Substances chimiques
Bacterial Proteins
0
DNA, Bacterial
0
Fluorescent Dyes
0
Fluorescein
TPY09G7XIR
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2653-2665Subventions
Organisme : MINECO/AEI EU
ID : DPI2017-82896- C2-1-R
Pays : International
Informations de copyright
© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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