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Technical upgrade of an open-source liquid handler to support bacterial colony screening
The optimization of genetically engineered biological constructs is a key step to deliver high-impact biotechnological applications. The use of high-throughput DNA assembly methods allows the construction of enough genotypic variants to successfully cover the target design space. This, however, enta...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10315574/ https://www.ncbi.nlm.nih.gov/pubmed/37404684 http://dx.doi.org/10.3389/fbioe.2023.1202836 |
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author | del Olmo Lianes, Irene Yubero, Pablo Gómez-Luengo, Álvaro Nogales, Juan Espeso, David R. |
author_facet | del Olmo Lianes, Irene Yubero, Pablo Gómez-Luengo, Álvaro Nogales, Juan Espeso, David R. |
author_sort | del Olmo Lianes, Irene |
collection | PubMed |
description | The optimization of genetically engineered biological constructs is a key step to deliver high-impact biotechnological applications. The use of high-throughput DNA assembly methods allows the construction of enough genotypic variants to successfully cover the target design space. This, however, entails extra workload for researchers during the screening stage of candidate variants. Despite the existence of commercial colony pickers, their high price excludes small research laboratories and budget-adjusted institutions from accessing such extensive screening capability. In this work we present COPICK, a technical solution to automatize colony picking in an open-source liquid handler Opentrons OT-2. COPICK relies on a mounted camera to capture images of regular Petri dishes and detect microbial colonies for automated screening. COPICK’s software can then automatically select the best colonies according to different criteria (size, color and fluorescence) and execute a protocol to pick them for further analysis. Benchmark tests performed for E. coli and P. putida colonies delivers a raw picking performance over pickable colonies of 82% with an accuracy of 73.4% at an estimated rate of 240 colonies/h. These results validate the utility of COPICK, and highlight the importance of ongoing technical improvements in open-source laboratory equipment to support smaller research teams. |
format | Online Article Text |
id | pubmed-10315574 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-103155742023-07-04 Technical upgrade of an open-source liquid handler to support bacterial colony screening del Olmo Lianes, Irene Yubero, Pablo Gómez-Luengo, Álvaro Nogales, Juan Espeso, David R. Front Bioeng Biotechnol Bioengineering and Biotechnology The optimization of genetically engineered biological constructs is a key step to deliver high-impact biotechnological applications. The use of high-throughput DNA assembly methods allows the construction of enough genotypic variants to successfully cover the target design space. This, however, entails extra workload for researchers during the screening stage of candidate variants. Despite the existence of commercial colony pickers, their high price excludes small research laboratories and budget-adjusted institutions from accessing such extensive screening capability. In this work we present COPICK, a technical solution to automatize colony picking in an open-source liquid handler Opentrons OT-2. COPICK relies on a mounted camera to capture images of regular Petri dishes and detect microbial colonies for automated screening. COPICK’s software can then automatically select the best colonies according to different criteria (size, color and fluorescence) and execute a protocol to pick them for further analysis. Benchmark tests performed for E. coli and P. putida colonies delivers a raw picking performance over pickable colonies of 82% with an accuracy of 73.4% at an estimated rate of 240 colonies/h. These results validate the utility of COPICK, and highlight the importance of ongoing technical improvements in open-source laboratory equipment to support smaller research teams. Frontiers Media S.A. 2023-06-19 /pmc/articles/PMC10315574/ /pubmed/37404684 http://dx.doi.org/10.3389/fbioe.2023.1202836 Text en Copyright © 2023 del Olmo Lianes, Yubero, Gómez-Luengo, Nogales and Espeso. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Bioengineering and Biotechnology del Olmo Lianes, Irene Yubero, Pablo Gómez-Luengo, Álvaro Nogales, Juan Espeso, David R. Technical upgrade of an open-source liquid handler to support bacterial colony screening |
title | Technical upgrade of an open-source liquid handler to support bacterial colony screening |
title_full | Technical upgrade of an open-source liquid handler to support bacterial colony screening |
title_fullStr | Technical upgrade of an open-source liquid handler to support bacterial colony screening |
title_full_unstemmed | Technical upgrade of an open-source liquid handler to support bacterial colony screening |
title_short | Technical upgrade of an open-source liquid handler to support bacterial colony screening |
title_sort | technical upgrade of an open-source liquid handler to support bacterial colony screening |
topic | Bioengineering and Biotechnology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10315574/ https://www.ncbi.nlm.nih.gov/pubmed/37404684 http://dx.doi.org/10.3389/fbioe.2023.1202836 |
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