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Tsai K, Zhou Z, Yang J, Xu Z, Xu S, Zandi R, Hao N, Chen W, Alber M. Study of Impacts of Two Types of Cellular Aging on the Yeast Bud Morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582376. [PMID: 38464259 PMCID: PMC10925247 DOI: 10.1101/2024.02.29.582376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Understanding the mechanisms of cellular aging processes is crucial for attempting to extend organismal lifespan and for studying age-related degenerative diseases. Yeast cells divide through budding, providing a classical biological model for studying cellular aging. With their powerful genetics, relatively short lifespan and well-established signaling pathways also found in animals, yeast cells offer valuable insights into the aging process. Recent experiments suggested the existence of two aging modes in yeast characterized by nucleolar and mitochondrial declines, respectively. In this study, by analyzing experimental data it was shown that cells evolving into those two aging modes behave differently when they are young. While buds grow linearly in both modes, cells that consistently generate spherical buds throughout their lifespan demonstrate greater efficacy in controlling bud size and growth rate at young ages. A three-dimensional chemical-mechanical model was developed and used to suggest and test hypothesized mechanisms of bud morphogenesis during aging. Experimentally calibrated simulations showed that tubular bud shape in one aging mode could be generated by locally inserting new materials at the bud tip guided by the polarized Cdc42 signal during the early stage of budding. Furthermore, the aspect ratio of the tubular bud could be stabilized during the late stage, as observed in experiments, through a reduction on the new cell surface material insertion or an expansion of the polarization site. Thus model simulations suggest the maintenance of new cell surface material insertion or chemical signal polarization could be weakened due to cellular aging in yeast and other cell types.
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Affiliation(s)
- Kevin Tsai
- Department of Mathematics, University of California, Riverside, CA, United States of America
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, CA, United States of America
| | - Zhen Zhou
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, CA, United States of America
| | - Jiadong Yang
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, United States of America
| | - Zhiliang Xu
- Applied and Computational Mathematics and Statistics Department, University of Notre Dame, Notre Dame, IN, United States of America
| | - Shixin Xu
- Duke Kunshan University, Kunshan, Jiangsu, China
| | - Roya Zandi
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, CA, United States of America
- Department of Physics and Astronomy, University of California, Riverside, CA, United States of America
- Biophysics Graduate Program, University of California, Riverside, CA, United States of America
| | - Nan Hao
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, CA, United States of America
| | - Weitao Chen
- Department of Mathematics, University of California, Riverside, CA, United States of America
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, CA, United States of America
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, United States of America
- Biophysics Graduate Program, University of California, Riverside, CA, United States of America
| | - Mark Alber
- Department of Mathematics, University of California, Riverside, CA, United States of America
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, CA, United States of America
- Department of Bioengineering, University of California, Riverside, CA, United States of America
- Biophysics Graduate Program, University of California, Riverside, CA, United States of America
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Zhu C, Lee CT, Rangamani P. Mem3DG: Modeling membrane mechanochemical dynamics in 3D using discrete differential geometry. BIOPHYSICAL REPORTS 2022; 2:100062. [PMID: 36157269 PMCID: PMC9495267 DOI: 10.1016/j.bpr.2022.100062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022]
Abstract
Biomembranes adopt varying morphologies that are vital to cellular functions. Many studies use computational modeling to understand how various mechanochemical factors contribute to membrane shape transformations. Compared with approximation-based methods (e.g., finite element method [FEM]), the class of discrete mesh models offers greater flexibility to simulate complex physics and shapes in three dimensions; its formulation produces an efficient algorithm while maintaining coordinate-free geometric descriptions. However, ambiguities in geometric definitions in the discrete context have led to a lack of consensus on which discrete mesh model is theoretically and numerically optimal; a bijective relationship between the terms contributing to both the energy and forces from the discrete and smooth geometric theories remains to be established. We address this and present an extensible framework, Mem3DG, for modeling 3D mechanochemical dynamics of membranes based on discrete differential geometry (DDG) on triangulated meshes. The formalism of DDG resolves the inconsistency and provides a unifying perspective on how to relate the smooth and discrete energy and forces. To demonstrate, Mem3DG is used to model a sequence of examples with increasing mechanochemical complexity: recovering classical shape transformations such as 1) biconcave disk, dumbbell, and unduloid; and 2) spherical bud on spherical, flat-patch membrane; investigating how the coupling of membrane mechanics with protein mobility jointly affects phase and shape transformation. As high-resolution 3D imaging of membrane ultrastructure becomes more readily available, we envision Mem3DG to be applied as an end-to-end tool to simulate realistic cell geometry under user-specified mechanochemical conditions.
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Affiliation(s)
- Cuncheng Zhu
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla CA 92093
| | - Christopher T. Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla CA 92093
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla CA 92093
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Abstract
A strain gradient was created by punching a hole in the center of a stretched elastic polydimethylsiloxane membrane to determine the effect of different strains on cultured human keratocytes (HK). In this study, two stretching methods were used: continuous stretching and cyclic stretching. Continuous stretching is relatively static, while acyclic stretching is relatively dynamic. These methods, respectively, represented the effects of high intraocular pressure and rubbing of the eyes on corneal cells. Image processing codes were developed to observe the effects of stress concentration, shear stress, continuous stretching, and cyclic stretching on HKs. The results demonstrate that stretching and shear stress are not conducive to the proliferation of corneal cells and instead cause cell death. A 10% strain had greater inhibitory effects than a 3% strain on cell proliferation. Cell survival rates for continuous stretching (static) were higher than those for cyclic stretching (dynamic). The stretching experiment revealed that cyclic stretching has a greater inhibitory effect on the growth and proliferation of corneal cells than continuous stretching. Accordingly, it shows that cyclic loading is more harmful than high intraocular pressure (static loading) to corneal cells.
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MacLean AL, Nie Q. The diverse landscape of modeling in single-cell biology. Phys Biol 2021; 18. [PMID: 34283805 DOI: 10.1088/1478-3975/ac0b7f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 06/15/2021] [Indexed: 11/12/2022]
Affiliation(s)
- Adam L MacLean
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, United States of America
| | - Qing Nie
- Department of Mathematics, Department of Developmental and Cell Biology, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, United States of America
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