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Theoretical basis for cell deaths
Open accessPublished version of a preprint
Abstract
Understanding deaths and life-death boundaries of cells is a fundamental challenge in biological sciences. In this study, we present a theoretical framework for investigating cell death. We conceptualize cell death as a controllability problem within dynamical systems, and compute the life-death boundary through the development of “stoichiometric rays.” This method utilizes enzyme activity as control parameters, exploiting the inherent property of enzymes to enhance reaction rates without affecting thermodynamic potentials. This approach facilitates the efficient evaluation of the global controllability of models. We demonstrate the utility of our framework using its application to a toy metabolic model, where we delineate the life-death boundary. The formulation of cell death through mathematical principles provides a foundation for the theoretical study of cellular mortality. Published by the American Physical Society 2024
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Citations
Cites
Bacterial Persistence as a Phenotypic Switch
Balaban, N. Q., Merrin, J., Chait, R., Kowalik, L., & Leibler, S. (2004) · Science · doi:10.1126/science.1099390 · Cited by 2,952
Non-linear dynamical control systems
Nijmeijer, H., & van der Schaft, A. J. (1990) · Springer eBooks · doi:10.1007/978-1-4757-2101-0 · Cited by 2,683
Cell death: a review of the major forms of apoptosis, necrosis and autophagy
D'Arcy, M. (2019) · Cell Biology International · doi:10.1002/cbin.11137 · Cited by 2,430
Hopfield, J. J. (1974) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.71.10.4135 · Cited by 1,594
Robustness in simple biochemical networks
Barkai, N., & Leibler, S. (1997) · Nature · doi:10.1038/43199 · Cited by 1,513
The maintenance energy of bacteria in growing cultures
Pirt, S. (1965) · Proceedings of the Royal Society of London. Series B. Biological Sciences · doi:10.1098/rspb.1965.0069 · Cited by 1,466
Definitions and guidelines for research on antibiotic persistence
Balaban, N. Q., Helaine, S., Lewis, K., Ackermann, M., Aldridge, B., Andersson, D. I., Brynildsen, M. P., Bumann, D., Camilli, A., Collins, J. J., et al. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0196-3 · Cited by 1,313
Recent findings on the viable but nonculturable state in pathogenic bacteria.
Oliver, J. (2010) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2009.00200.x · Cited by 1,231
Newton, K., Strasser, A., Kayagaki, N., & Dixit, V. M. (2024) · Cell · doi:10.1016/j.cell.2023.11.044 · Cited by 1,043
Robust Growth of Escherichia coli
Wang, P., Robert, L., Pelletier, J., Dang, W. L., Taddei, F., Wright, A., & Jun, S. (2010) · Current Biology · doi:10.1016/j.cub.2010.04.045 · Cited by 1,014
A guide to cell death pathways
Yuan, J., & Ofengeim, D. (2023) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-023-00689-6 · Cited by 998
The depth of chemical time and the power of enzymes as catalysts.
Wolfenden, R., & Snider, M. (2001) · Accounts of Chemical Research · doi:10.1021/ar000058i · Cited by 823
Foundations of Chemical Reaction Network Theory
Feinberg, M. (2019) · Applied Mathematical Sciences · doi:10.1007/978-3-030-03858-8 · Cited by 467
Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction
Li, F., Yuan, L., Lu, H., Li, G., Chen, Y., Engqvist, M. K. M., Kerkhoven, E. J., & Nielsen, J. (2022) · Nature Catalysis · doi:10.1038/s41929-022-00798-z · Cited by 466
Structural Sources of Robustness in Biochemical Reaction Networks
Shinar, G., & Feinberg, M. (2010) · Science · doi:10.1126/science.1183372 · Cited by 413
Diversity and complexity of cell death: a historical review
Park, W., Wei, S., Kim, B., Kim, B., Bae, S., Chae, Y. C., Ryu, D., & Ha, K. (2023) · Experimental & Molecular Medicine · doi:10.1038/s12276-023-01078-x · Cited by 375
Die for the community: an overview of programmed cell death in bacteria
Allocati, N., Masulli, M., Ilio, C. D., & Laurenzi, V. D. (2015) · Cell Death and Disease · doi:10.1038/cddis.2014.570 · Cited by 293
The role of metabolism in bacterial persistence
Amato, S. M., Fazen, C. H., Henry, T. C., Mok, W. W. K., Orman, M. A., Sandvik, E. L., Volzing, K., & Brynildsen, M. P. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00070 · Cited by 269
Extreme slow growth as alternative strategy to survive deep starvation in bacteria
Gray, D. A., Dugar, G., Gamba, P., Strahl, H., Jonker, M. J., & Hamoen, L. W. (2019) · Nature Communications · doi:10.1038/s41467-019-08719-8 · Cited by 248
Input–output robustness in simple bacterial signaling systems
Shinar, G., Milo, R., Martínez, M. R., & Alon, U. S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706792104 · Cited by 193
Fundamental behaviors emerge from simulations of a living minimal cell
Thornburg, Z. R., Bianchi, D. M., Brier, T. A., Gilbert, B. R., Earnest, E. E., Melo, M. C. R., Safronova, N., Sáenz, J. P., Cook, A. T., Wise, K. S., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.025 · Cited by 165
Persistence: mechanisms for triggering and enhancing phenotypic variability
Balaban, N. (2011) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2011.10.001 · Cited by 156
Biselli, E., Schink, S., & Gerland, U. (2020) · Molecular Systems Biology · doi:10.15252/msb.202010070 · Cited by 117
Death Rate of E. coli during Starvation Is Set by Maintenance Cost and Biomass Recycling
Schink, S. J., Biselli, E., Ammar, C., & Gerland, U. (2019) · Cell Systems · doi:10.1016/j.cels.2019.06.003 · Cited by 102
Global Controllability of Linear Systems with Positive Controls
Saperstone, S. (1973) · doi:10.1137/0311034 · Cited by 86
Choudhury, S., Moret, M., Salvy, P., Weilandt, D. R., Hatzimanikatis, V., & Miskovic, L. (2022) · Nature Machine Intelligence · doi:10.1038/s42256-022-00519-y · Cited by 80
Bacterial persistence: Fundamentals and clinical importance
Jung, S., Ryu, C., & Kim, J. (2019) · The Journal of Microbiology · doi:10.1007/s12275-019-9218-0 · Cited by 79
Dynamic modelling of cell death during biofilm development.
Fagerlind, M., Webb, J., Barraud, N., Mcdougald, D., Jansson, A., Nilsson, P., Harlén, M., Kjelleberg, S., & Rice, S. (2012) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2011.10.007 · Cited by 61
Gouy, S., Ferron, G., Glehen, O., Bayar, A., Marchal, F., Pomel, C., Quénet, F., Bereder, J., Deley, M. L., & Morice, P. (2016) · Gynecologic Oncology · doi:10.1016/j.ygyno.2016.05.032 · Cited by 58
Aging, mortality, and the fast growth trade-off of Schizosaccharomyces pombe
Nakaoka, H., & Wakamoto, Y. (2017) · bioRxiv · doi:10.1371/journal.pbio.2001109 · Cited by 56
'Viable But Non-Culturable Cells' are Dead.
Song, S., & Wood, T. (2021) · Environmental Microbiology · doi:10.1111/1462-2920.15463 · Cited by 54
Erebosis, a new cell death mechanism during homeostatic turnover of gut enterocytes
Ciesielski, H. M., Nishida, H., Takano, T., Fukuhara, A., Otani, T., Ikegawa, Y., Okada, M., Nishimura, T., Furuse, M., & Yoo, S. K. (2022) · PLoS Biology · doi:10.1371/journal.pbio.3001586 · Cited by 32
Microbial life in slow and stopped lanes
Walker, R., Sanabria, V. C., & Youk, H. (2023) · Trends in Microbiology · doi:10.1016/j.tim.2023.11.014 · Cited by 29
Death and the Afterlife in Japanese Buddhism
Stone, J. (1998) · doi:10.21313/hawaii/9780824832049.001.0001 · Cited by 28
Survival dynamics of starving bacteria are determined by ion homeostasis that maintains plasmolysis
Schink, S. J., Polk, M., Athaide, E., Mukherjee, A., Ammar, C., Liu, X., Oh, S., Chang, Y., & Basan, M. (2024) · Nature Physics · doi:10.1038/s41567-024-02511-2 · Cited by 27
Bacterial killing and the dimensions of bacterial death
Wu, R., Li, C., Li, J., Sjollema, J., Geertsema-Doornbusch, G. I., de Haan-Visser, H. W., Dijkstra, E. S. C., Ren, Y., Zhang, Z., Liu, J., et al. (2024) · npj Biofilms and Microbiomes · doi:10.1038/s41522-024-00559-9 · Cited by 25
Dormancy‐to‐death transition in yeast spores occurs due to gradual loss of gene‐expressing ability
Maire, T., Allertz, T., Betjes, M. A., & Youk, H. (2019) · bioRxiv · doi:10.15252/msb.20199245 · Cited by 19
Global controllability of chemical reactions
Drexler, D., & Tóth, J. (2015) · Journal of Mathematical Chemistry · doi:10.1007/s10910-016-0626-7 · Cited by 18
Slowest possible replicative life at frigid temperatures for yeast
Trip, D. S. L., Maire, T., & Youk, H. (2022) · Nature Communications · doi:10.1038/s41467-022-35151-2 · Cited by 16
Flagged first, then by citations
Research works printed but not linked: 16
- A. Casolari, 2018, Physiological Models in Microbiology
- 10.7554/eLife.20340 · DOI
- 10.1128/AEM.01527-09 · DOI
- 10.1103/PhysRevResearch.2.013372 · DOI
- 10.15252/msb.20209478 · DOI
- 10.1101/2021.10.28.466227 · DOI
- 10.1007/BF02010671 · DOI
- H. C. Berg, 2004, E. coli in Motion
- 10.1103/PhysRevResearch.4.043223 · DOI
- 10.1023/A:1019150014783 · DOI
- 10.1016/0959-1524(92)85003-F · DOI
- P. W. Atkins, 2023, Atkins' Physical Chemistry
- A. Cornish-Bowden, 2013, Fundamentals of Enzyme Kinetics
- J.-M. Coron, 2007, Control and Nonlinearity
- 10.1016/S0140-6736(03)15171-9 · DOI
- E. Schrödinger, 1944, What Is Life? The Physical Aspect of the Living Cell and Mind
Cited by
Sorted by citations
Embodied Autonomous Intelligence: A Historical Perspective
Yoshida, N. (2026) · IOP Conference Series Materials Science and Engineering · doi:10.1088/1757-899x/1343/1/012011
Metadata
- Authors
- Himeoka, Y., Horiguchi, S. A., & Kobayashi, T. J.
- Affiliations
- Universal Biology Institute, The University of Tokyo (JP)
- Kanazawa University (JP)
- Institute of Industrial Science, The University of Tokyo (JP)
- Corresponding author
- Himeoka, Yusuke
- Venue
- Physical Review Research
- Publisher
- American Physical Society (APS)
- Published
- 2024-11-27
- Volume
- 6
- Issue
- 4
- ISSN
- 2643-1564 (ISSN-L)
- OpenAlex
- W4404757745
- Cited by
- 5
- References
- 39
- Citations by year
- 2026: 3 · 2025: 2
- FWCI
- 0.68
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Physical Review Research (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- arXiv (Cornell University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- arXiv (Cornell University) (cc-by)
- Funders
- Japan Society for the Promotion of Science (JP22K15069, JP22H05403, JP24H01118, 24K00542, 19H05799, JP21J21415)
- Japan Science and Technology Agency (JPMJCR2011, JPMJCR1927, JPMJGX23B4)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Cell death mechanisms and regulation
- Physical Sciences › Mathematics › Modeling and Simulation › Mathematical Biology Tumor Growth
- Keywords
- cell death, controllability, dynamical systems, enzyme activity, metabolic modeling, global controllability, thermodynamic potential
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