Quantifying the Performance of Micro-Compartmentalized Directed Evolution Protocols
| Autor: | Adèle Dramé-Maigné, Iaroslava Golovkova, Anton S. Zadorin, Yannick Rondelez |
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| Přispěvatelé: | Centre National de la Recherche Scientifique (CNRS) |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
[SDV.BIO]Life Sciences [q-bio]/Biotechnology self-selection Computer science media_common.quotation_subject enrichment factor Machine learning computer.software_genre 01 natural sciences Measure (mathematics) General Biochemistry Genetics and Molecular Biology Article 03 medical and health sciences Quality (business) Fraction (mathematics) directed evolution lcsh:Science Ecology Evolution Behavior and Systematics Selection (genetic algorithm) ComputingMilieux_MISCELLANEOUS media_common Protocol (science) 010405 organic chemistry business.industry Paleontology Contrast (statistics) Directed evolution 0104 chemical sciences 030104 developmental biology Space and Planetary Science Metric (mathematics) lcsh:Q Artificial intelligence business computer |
| Zdroj: | Life Life, MDPI, 2020, 10 (2), pp.17. ⟨10.3390/life10020017⟩ Life, Vol 10, Iss 2, p 17 (2020) Volume 10 Issue 2 |
| ISSN: | 2075-1729 |
| DOI: | 10.3390/life10020017⟩ |
| Popis: | High-throughput, in vitro approaches for the evolution of enzymes rely on a random micro-encapsulation to link phenotypes to genotypes, followed by screening or selection steps. In order to optimise these approaches, or compare one to another, one needs a measure of their performance at extracting the best variants of a library. Here, we introduce a new metric, the Selection Quality Index (SQI), which can be computed from a simple mock experiment, performed with a known initial fraction of active variants. In contrast to previous approaches, our index integrates the effect of random co-encapsulation, and comes with a straightforward experimental interpretation. We further show how this new metric can be used to extract general protocol efficiency trends or reveal hidden selection mechanisms such as a counterintuitive form of beneficial poisoning in the compartmentalized self-replication protocol. |
| Databáze: | OpenAIRE |
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