Robotic search for optimal cell culture in regenerative medicine

Kanda, Genki N.; Tsuzuki, Taku; Terada, Makoto; Sakai, Noriko; Motozawa, Naohiro; Masuda, Tomohiro; Nishida, Mitsuhiro; Watanabe, Chihaya T; Higashi, Tatsuki; Horiguchi, Shuhei A.; Kudo, Takeo; Kamei, Motohisa; Sunagawa, Genshiro A.; Matsukuma, Kenji; Sakurada, Takeshi; Ozawa, Yosuke; Takahashi, Masayo; Takahashi, Koichi; Natsume, Tohru

doi:10.7554/elife.77007

Cited by 42 publications

(15 citation statements)

References 37 publications

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“…By utilizing GSCAS find common ancestor strains and MTM to minimize total manipulations, the proposed method can effectively reduce the working load of large‐scale parallel strain construction in biofoundry. The methods presented in this paper are in the upstream and complimentary to existing relative down‐stream algorithms, such as equipment scheduling [ 20 ] and Bayesian/machine learning algorithms for fine‐tuning promoter/RBS strength [ 6 ] and optimizing culture medium, [ 21 ] We believe that integrating GSCAS/MTM and other methods in biofoundry practice can significantly reduce cost, time and man‐power involved in large scale strain developments, thereby contributing to the acceleration of the DBTL cycle for strain development.…”

Section: Discussionmentioning

confidence: 99%

Designing gene manipulation schedules for high throughput parallel construction of objective strains

Cai,

Liao,

Mao

et al. 2023

Biotechnology Journal

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Recent advances in biofoundries have enabled the construction of a large quantity of strains in parallel, accelerating the design‐build‐test‐learn (DBTL) cycles for strain development. However, the construction of a large number of strains by iterative gene manipulation is still time‐consuming and costly, posing a challenge for the development of commercial strains. Common gene manipulations among different objective strains open up the possibility of reducing cost and time for strain construction in biofoundries by optimizing genetic manipulation schedules. A method is introduced consisting of two complementary algorithms for designing optimal parent‐children manipulation schedules for strain construction: greedy search of common ancestor strains (GSCAS) and minimizing total manipulations (MTM). By reusing common ancestor strains, the number of strains to be constructed can be effectively reduced, resulting in a tree‐like structure of descendants instead of linear lineages for each strain. The GSCAS algorithm can quickly find common ancestor strains and clusters them together based on their genetic makeup, and the MTM algorithm subsequently minimize the genetic manipulations required, resulting in a further reduction in the total number of genetic manipulations. The effectiveness of our method is demonstrated through a case study of 94 target strains, where GSCAS reduces an average of 36% of the total gene manipulations, and MTM reduces an additional 10%. The performance of both algorithms is robust among case studies with different average occurrences of gene manipulations across objective strains. Our method potentially improves cost efficiency and accelerate the development of commercial strains significantly. The implementation of the methods can be freely accessed via https://gscas‐mtm.biodesign.ac.cn/

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Section: Discussionmentioning

confidence: 99%

Designing gene manipulation schedules for high throughput parallel construction of objective strains

Cai,

Liao,

Mao

et al. 2023

Biotechnology Journal

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“…While the transfection efficiency of 10 to 15% allows us to visually isolate a single cell and observe its entire structure without being overlapped by other surrounding cells, it also means that a limited number of cells can be observed per experiment, resulting in low throughput. However, this limitation can be overcome by incorporating laboratory automation, which is becoming increasingly available, into our analysis system ( 41 , 42 ). By automating the analysis and observing more cells, we believe that the difference between without and with stretch will become more visible even in single-cell analysis and that the distribution will eventually converge to a histogram similar to the one obtained from the multicell-scale analysis (Fig.…”

Section: Discussionmentioning

confidence: 99%

Spatiotemporal single-cell tracking analysis in 3D tissues to reveal heterogeneous cellular response to mechanical stimuli

Kasahara,

Muramatsu,

Kurashina

et al. 2023

Sci. Adv.

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Mechanical stimuli have been recognized as important for tissue maturation, homeostasis and constructing engineered three-dimensional (3D) tissues. However, we know little about the cellular mechanical response in tissues that could be considerably heterogeneous and spatiotemporally dynamic due to the complex structure of tissues. Here, we report a spatiotemporal single-cell tracking analysis of in vitro 3D tissues under mechanical stretch, to reveal the heterogeneous cellular behavior by using a developed stretch and optical live imaging system. The system could affect the cellular orientation and directly measure the distance of cells in in vitro 3D myoblast tissues (3DMTs) at the single-cell level. Moreover, we observed the spatiotemporal heterogeneous cellular locomotion and shape changes under mechanical stretch in 3DMTs. This single-cell tracking analysis can become a principal method to investigate the heterogeneous cellular response in tissues and provide insights that conventional analyses have not yet offered.

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“…Exciting examples in biology include autonomous experimentation for genome engineering, [172][173][174] and optimal growth of cell cultures. 175 Si et al 173 and HamediRad et al 174 utilize iBioFab, a delocalized biofoundry which is similar to the concept of delocalized experimentation with cloud labs. iBioFab can produce one gene sequence for <3 USD, so it is inexpensive from the user's perspective.…”

Section: Frugal Twins In Biologymentioning

confidence: 99%

Review of low-cost self-driving laboratories in chemistry and materials science: the “frugal twin” concept

Lo,

Baird,

Schrier

et al. 2024

Digital Discovery

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Robotic search for optimal cell culture in regenerative medicine

Cited by 42 publications

References 37 publications

Designing gene manipulation schedules for high throughput parallel construction of objective strains

Designing gene manipulation schedules for high throughput parallel construction of objective strains

Spatiotemporal single-cell tracking analysis in 3D tissues to reveal heterogeneous cellular response to mechanical stimuli

Review of low-cost self-driving laboratories in chemistry and materials science: the “frugal twin” concept

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