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Mechanically-driven growth and competition in a Voronoi model of tissues

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arXiv 2024年

作者： Brézin, Louis Korolev, Kirill S. Department of Physics Graduate Program in Bioinformatics Biological Design Center Boston University BostonMA02215 United States

The mechanisms leading cells to acquire a fitness advantage and establish themselves in a population are paramount to understanding the development and growth of cancer. Although there are many works that study separately either the evolutionary dynamics or the mechanics of cancer, little has been done to couple evolutionary dynamics to mechanics. To address this question, we study a confluent model of tissue using a Self-Propelled Voronoi (SPV) model with stochastic growth rates that depend on the mechanical variables of the system. The SPV model is an out-of-equilibrium model of tissue derived from an energy functional that has a jamming/unjamming transition between solid-like and liquid-like states. By considering several scenarios of mutants invading a resident population in both phases, we determine the range of parameters that confer a fitness advantage and show that the preferred area and perimeter are the most relevant ones. We find that the liquid-like state is more resistant to invasion and show that the outcome of the competition can be determined from the simulation of a non-growing mixture. Moreover, a mean-field approximation can accurately predict the fate of a mutation affecting mechanical properties of a cell. Our results can be used to infer evolutionary dynamics from tissue images, understand cancer-suppressing effects of tissue mechanics, and even search for mechanics-based therapies. © 2024, CC BY.

关键词： Tissue

New sector morphologies emerge from anisotropic colony growth

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arXiv 2024年

作者： Swartz, Daniel W. Lee, Hyunseok Kardar, Mehran Korolev, Kirill S. Department of Physics Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics Graduate Program in Bioinformatics and Biological Design Center Boston University BostonMA02215 United States

Competition during range expansions is of great interest from both practical and theoretical view points. Experimentally, range expansions are often studied in homogeneous Petri dishes, which lack spatial anisotropy that might be present in realistic populations. Here, we analyze a model of anisotropic growth, based on coupled Kardar-Parisi-Zhang and Fisher-Kolmogorov-Petrovsky-Piskunov equations that describe surface growth and lateral competition. Compared to a previous study of isotropic growth, anisotropy relaxes a constraint between parameters of the model. We completely characterize spatial patterns and invasion velocities in this generalized model. In particular, we find that strong anisotropy results in a distinct morphology of spatial invasion with a kink in the displaced strain ahead of the boundary between the strains. This morphology of the out-competed strain is similar to a shock wave and serves as a signature of anisotropic growth. Copyright © 2024, The Authors. All rights reserved.

关键词： Strain

Competition on the edge of an expanding population

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arXiv 2023年

In growing populations, the fate of mutations depends on their competitive ability against the ancestor and their ability to colonize new territory. Here we present a theory that integrates both aspects of mutant fitness by coupling the classic description of one-dimensional competition (Fisher equation) to the minimal model of front shape (KPZ equation). We solved these equations and found three regimes, which are controlled solely by the expansion rates, solely by the competitive abilities, or by both. Collectively, our results provide a simple framework to study spatial competition. Copyright © 2023, The Authors. All rights reserved.

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Computational design of serine hydrolases

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Science (New York, N.Y.) 2025年第6744期388卷 eadu2454页

作者： Lauko, Anna Pellock, Samuel J. Sumida, Kiera H. Anishchenko, Ivan Juergens, David Ahern, Woody Jeung, Jihun Shida, Alexander F. Hunt, Andrew Kalvet, Indrek Norn, Christoffer Humphreys, Ian R. Jamieson, Cooper Krishna, Rohith Kipnis, Yakov Kang, Alex Brackenbrough, Evans Bera, Asim K. Sankaran, Banumathi Houk, K.N. Baker, David Department of Biochemistry University of Washington Seattle WA United States Institute for Protein Design University of Washington Seattle WA United States Graduate Program in Biological Physics Structure and Design University of Washington Seattle WA United States Department of Chemistry University of Washington Seattle WA United States Graduate Program in Molecular Engineering University of Washington Seattle WA United States Paul G. Allen School of Computer Science and Engineering University of Washington Seattle WA United States Medical Scientist Training Program University of Washington Seattle WA United States Howard Hughes Medical Institute University of Washington Seattle WA United States Department of Chemistry and Biochemistry University of California Los Angeles CA United States

The design of enzymes with complex active sites that mediate multistep reactions remains an outstanding challenge. With serine hydrolases as a model system, we combined the generative capabilities of RFdiffusion with an ensemble generation method for assessing active site preorganization at each step in the reaction to design enzymes starting from minimal active site descriptions. Experimental characterization revealed catalytic efficiencies (kcat/Km) up to 2.2 × 105 M-1 s-1 and crystal structures that closely match the design models (Cα root mean square deviations <1 angstrom). Selection for structural compatibility across the reaction coordinate enabled identification of new catalysts remove with five different folds distinct from those of natural serine hydrolases. Our de novo approach provides insight into the geometric basis of catalysis and a roadmap for designing enzymes that catalyze multistep transformations.

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Correction to: Multistate and functional protein design using RoseTTAFold sequence space diffusion (Nature Biotechnology, (2024), 10.1038/s41587-024-02395-w)

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Nature Biotechnology 2024年

作者： Lisanza, Sidney Lyayuga Gershon, Jacob Merle Tipps, Samuel W. K. Sims, Jeremiah Nelson Arnoldt, Lucas Hendel, Samuel J. Simma, Miriam K. Liu, Ge Yase, Muna Wu, Hongwei Tharp, Claire D. Li, Xinting Kang, Alex Brackenbrough, Evans Bera, Asim K. Gerben, Stacey Wittmann, Bruce J. McShan, Andrew C. Baker, David Department of Biochemistry University of Washington SeattleWA United States Institute for Protein Design University of Washington SeattleWA United States Graduate Program in Biological Physics Structure and Design University of Washington SeattleWA United States Department of Molecular Engineering University of Washington SeattleWA United States Molecular & amp Cellular Biology Medical Scientist Training Program University of Washington SeattleWA United States Faculty of Engineering Sciences Heidelberg University Heidelberg Germany School of Chemistry and Biochemistry Georgia Institute of Technology AtlantaGA United States Office of the Chief Scientific Officer Microsoft RedmondWA United States Howard Hughes Medical Institute University of Washington SeattleWA United States

Correction to: Nature Biotechnologyhttps://***/10.1038/s41587-024-02395-w, published online 25 September 2024. In the version of the article initially published, in the key to Fig. 2f the colors were swapped and have now been amended so that "W guidance" is purple and "Unconditional" is grey. In Fig. 5a, the color of "Child B" has been corrected from pink to purple, and in Fig. 5d, "β-helix" has now been amended to "β-sheet". These corrections have been made to the HTML and PDF versions of the article. © The Author(s) 2024.

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1 Slow expanders invade by forming dented fronts in microbial 2 colonies

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arXiv 2021年

作者： Lee, Hyunseok Gore, Jeff Korolev, Kirill S. Physics of Living Systems Group Department of Physics Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics Graduate Program in Bioinformatics Biological Design Center Boston University BostonMA02215 United States

Most organisms grow in space, whether they are viruses spreading within a host tissue or invasive species colonizing a new continent. Evolution typically selects for higher expansion rates during spatial growth, but it has been suggested that slower expanders can take over under certain conditions. Here, we report an experimental observation of such population dynamics. We demonstrate that the slower mutants win not only when the two types are intermixed at the front but also when they are spatially segregated into sectors. The latter was thought to be impossible because previous studies focused exclusively on the global competitions mediated by expansion velocities but overlooked the local competitions at sector boundaries. We developed a theory of sector geometry that accounts for both local and global competitions and describes all possible sector shapes. In particular, the theory predicted that a slower, but more competitive, mutant forms a dented V-shaped sector as it takes over the expansion front. Such sectors were indeed observed experimentally and their shapes matched up quantitatively with the theory. In simulations, we further explored several mechanism that could provide slow expanders with a local competitive advantage and showed that they are all well-described by our theory. Taken together, our results shed light on previously unexplored outcomes of spatial competition and establish a universal framework to understand evolutionary and ecological dynamics in expanding populations. © 2021, CC BY-NC-ND.

关键词： Competition

BPS2025 - Structural and functional characterization of integrin α5-targeting antibodies for anti-angiogenic therapy

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Biophysical Journal 2025年第3期124卷 12a-12a页

作者： Adam Nguyen Joel B. Heim Gabriele Cordara Matthew C. Chan Hedda Johannesen Cristine Charlesworth Ming Li Caleigh M. Azumaya Benjamin Madden Ute Krengel Alexander Meves Melody G. Campbell Basic Sciences Fred Hutchinson Cancer Center Seattle WA USA Biological Physics Structure and Design Graduate Program University of Washington Seattle WA USA Department of Dermatology Mayo Clinic Rochester MN USA Department of Chemistry University of Oslo Oslo Norway Medical Genome and Proteomics Core Mayo Clinic Rochester MN USA

Effects of sodium alginate-poly(acrylic acid) cross-linked hydrogel beads on soil conditioner in the absence and presence of phosphate and carbonate ions

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Case Studies in Chemical and Environmental Engineering 2024年 9卷

作者： Hidayat, Endar Sarbani, Nur Maisarah Mohamad Lahiri, Sudip Kumar Samitsu, Sadaki Yonemura, Seiichiro Mitoma, Yoshiharu Harada, Hiroyuki Graduate School of Comprehensive Scientific Research Program in Biological System Sciences Prefectural University of Hiroshima Shobara 727-0023 Japan Department of Life System Science Faculty of Bioresources Science Prefectural University of Hiroshima Shobara 727-0023 Japan Data-driven Polymer Design Group Research Center for Macromolecules and Biomaterials National Institute for Materials Science 1−2−1 Sengen Tsukuba 305-0047 Japan Department of Mechanical & Industrial Engineering University of Toronto Toronto M5S 3G8 ON Canada Faculty of Allied Health Sciences Chettinad Hospital and Research Institute Chettinad Academy of Research and Education Tamil Nadu Kelambakkam 603103 India

Hydrogel beads, composed of polymers, possess the ability to absorb substantial quantities of water simultaneously and gradually release it in dry conditions. In this work, hydrogel beads were synthesized using sodium alginate (S-Alg) and poly (acrylic acid) (P-Acc), either in the absence or presence of phosphate (PO₄ ³⁻) (S-Alg/P-Acc@PO₄ ³⁻) and carbonate (CO₃ ²⁻) anionic ions (S-Alg/P-Acc@CO₃ ²⁻). Subsequently, these beads were crosslinked with Ca²⁺ ions. The scanning electron microscopy (SEM) images demonstrated that the presence of anionic ions has an impact on the structure of the hydrogel beads and enhances porosity expansion while concurrently reducing the concentration of carboxyl (COOH) groups. The hydrogel beads exhibited a great swelling behavior, with S-Alg/P-Acc@CO₃ ²⁻ capable of absorbing up to 73.5 % of water in acidic conditions, but decreased under neutral and basic conditions. Soil water loss (SWL) experiments confirmed the ability of hydrogel beads to retain water in the soil. Additionally, observations of soil characteristics after a 14-day treatment revealed no significant difference in pH and C/N ratio (P-value <0.05). However, soil's available Fe and N–NO₃ ^- significantly reduced (P-value <0.05) while substantially promoting soil N–NH₄ ⁺, available phosphorus (P), cation exchange capacity (CEC), soil organic carbon (SOC), and exchangeable cation (Ca²⁺, K⁺ and Mg²⁺). The presence of hydroxyl (-OH) and –COOH groups was found to be crucial for enhancing soil properties. © 2024 The Authors

关键词： Anionic ions Hydrogel beads Poly (acrylic acid) Sodium alginate Soil characteristics Soil water retention Swelling

Ecological landscapes guide the assembly of optimal microbial communities

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arXiv 2021年

作者： George, Ashish B. Korolev, Kirill S. Department of Physics Boston University BostonMA02215 United States Biological Design Center Boston University BostonMA02215 United States Carl R. Woese Institute for Genomic Biology Department of Plant Biology University of Illinois at Urbana-Champaign UrbanaIL61801 United States Graduate Program in Bioinformatics Boston University BostonMA02215 United States

Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with the number of species, and so an exhaustive search cannot be performed even for a dozen species. A heuristic search that improves community function by adding or removing one species at a time is more practical, but it is unknown whether this strategy can discover an optimal or nearly optimal community. Using consumer-resource models with and without cross-feeding, we investigate how the efficacy of search depends on the distribution of resources, niche overlap, cross-feeding, and other aspects of community ecology. We show that search efficacy is determined by the ruggedness of the appropriately-defined ecological landscape. We identify specific ruggedness measures that are both predictive of search performance and robust to noise and low sampling density. The feasibility of our approach is demonstrated using experimental data from a soil microbial community. Overall, our results establish the conditions necessary for the success of the heuristic search and provide concrete design principles for building high-performing microbial consortia. © 2021, CC BY-NC-ND.

关键词： Microorganisms