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Grob A, Enrico Bena C, Di Blasi R, Pessina D, Sood M, Yunyue Z, Bosia C, Isalan M, Ceroni F. Mammalian cell growth characterisation by a non-invasive plate reader assay. Nat Commun 2024; 15:57. [PMID: 38167870 PMCID: PMC10761699 DOI: 10.1038/s41467-023-44396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
Automated and non-invasive mammalian cell analysis is currently lagging behind due to a lack of methods suitable for a variety of cell lines and applications. Here, we report the development of a high throughput non-invasive method for tracking mammalian cell growth and performance based on plate reader measurements. We show the method to be suitable for both suspension and adhesion cell lines, and we demonstrate it can be adopted when cells are grown under different environmental conditions. We establish that the method is suitable to inform on effective drug treatments to be used depending on the cell line considered, and that it can support characterisation of engineered mammalian cells over time. This work provides the scientific community with an innovative approach to mammalian cell screening, also contributing to the current efforts towards high throughput and automated mammalian cell engineering.
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Affiliation(s)
- Alice Grob
- Department of Chemical Engineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Chiara Enrico Bena
- Italian Institute for Genomic Medicine, Torino, Italy
- Université Paris-Saclay (INRAE), AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Roberto Di Blasi
- Department of Chemical Engineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Daniele Pessina
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Matthew Sood
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Zhou Yunyue
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Carla Bosia
- Italian Institute for Genomic Medicine, Torino, Italy.
- Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy.
| | - Mark Isalan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
- Department of Life Sciences, Imperial College London, London, United Kingdom.
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, London, UK.
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
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del Olmo Lianes I, Yubero P, Gómez-Luengo Á, Nogales J, Espeso DR. Technical upgrade of an open-source liquid handler to support bacterial colony screening. Front Bioeng Biotechnol 2023; 11:1202836. [PMID: 37404684 PMCID: PMC10315574 DOI: 10.3389/fbioe.2023.1202836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 06/07/2023] [Indexed: 07/06/2023] Open
Abstract
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.
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Affiliation(s)
- Irene del Olmo Lianes
- Department of Systems Biology, Centro Nacional de Biotecnología—Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Pablo Yubero
- Department of Systems Biology, Centro Nacional de Biotecnología—Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Álvaro Gómez-Luengo
- Department of Systems Biology, Centro Nacional de Biotecnología—Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy—Consejo Superior de Investigaciones Científicas, SusPlast-CSIC, Madrid, Spain
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología—Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy—Consejo Superior de Investigaciones Científicas, SusPlast-CSIC, Madrid, Spain
| | - David R. Espeso
- Department of Systems Biology, Centro Nacional de Biotecnología—Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Kang DH, Ko SC, Heo YB, Lee HJ, Woo HM. RoboMoClo: A Robotics-Assisted Modular Cloning Framework for Multiple Gene Assembly in Biofoundry. ACS Synth Biol 2022; 11:1336-1348. [PMID: 35167276 DOI: 10.1021/acssynbio.1c00628] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Efficient and versatile DNA assembly frameworks have had an impact on promoting synthetic biology to build complex biological systems. To accelerate system development, laboratory automation (or biofoundry) provides an opportunity to construct organisms and DNA assemblies via computer-aided design. However, a modular cloning (MoClo) system for multiple DNA assemblies limits the biofoundry workflow in terms of simplicity and feasibility by preparing the number of cloning materials such as destination vectors prior to the automation process. Herein, we propose robot-assisted MoClo (RoboMoClo) to accelerate a synthetic biology project with multiple gene expressions at the biofoundry. The architecture of the RoboMoClo framework provides a hybrid strategy of hierarchical gene assembly and iterative gene assembly, and fewer destination vectors compared with other MoClo systems. An industrial bacterium, Corynebacterium glutamicum, was used as a model host for RoboMoClo. After building a biopart library (promoter and terminator; level 0) and evaluating its features (level 1), various transcriptional directions in multiple gene assemblies (level 2) were studied using the RoboMoClo vectors. Among the constructs, the convergent construct exhibited potential transcriptional interference through the collision of RNA polymerases. To study design of experiment-guided lycopene biosynthesis in C. glutamicum (levels 1, 2, and 3), the biofoundry-assisted multiple gene assembly was demonstrated as a proof-of-concept by constructing various sub-pathway units (level 2) and pathway units (level 3) for C. glutamicum. The RoboMoClo framework provides an improved MoClo toolkit for laboratory automation in a synthetic biology application.
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Affiliation(s)
- Dong Hun Kang
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Sung Cheon Ko
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Yu Been Heo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Hyun Jeong Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
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Santos-Aberturas J, Vior NM. Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them. Antibiotics (Basel) 2022; 11:195. [PMID: 35203798 PMCID: PMC8868522 DOI: 10.3390/antibiotics11020195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.
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Affiliation(s)
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich NR7 4UH, UK
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