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- Creator:
- Nunley, Hayden, Xue, Xufeng, Sun, Yubing, Resto-Irizarry, Agnes M, Yuan, Ye, Yong, Koh Meng Aw, Zheng, Yi, Weng, Shinuo, Shao, Yue, Lubensky, David K, Studer, Lorenz, and Fu, Jianping
- Description:
- Studies of fate patterning during development typically emphasize cell-cell communication via diffusible chemical signals. Recent experiments on stem cell colonies (see Xue et al. Nature Materials 2018), however, suggest that in some cases mechanical stresses, rather than secreted chemicals, enable long-ranged cell-cell interactions that specify positional information and pattern cell fates. The authors of this earlier publication reported a set of in vitro experiments in which uniformly supplied chemical media induced spatially patterned fates in cell colony in a disc geometry. They provided significant evidence that inter-cellular mechanical interactions, as well as mechanical interactions between cells and the substrate, play an important role in this in vitro differentiation process. As part of these experiments, they showed that the concentric width of the outer fate domain is approximately constant as the colony diameter is increased from 300 um to 800 um. In this subsequent publication, we propose a mathematical model for this fate patterning process and explore how the fate pattern depends on substrate stiffness. The experimental images of cell colonies, both for varying cell colony diameter (from Xue et al. Nature Materials 2018) and for varying substrate stiffness (data generated for the publication linked to these data), are provided here. Each example has an image for PAX3 signal (marker for outer fate domain; Paired box gene 3) and an image for DAPI signal (staining nuclei; 4′,6-diamidino-2-phenylindole).
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, Force sensing, and Vertebrate development
- Citation to related publication:
- Nunley H, Xue X, Fu, J, Lubensky, DK. Generation of fate patterns via intercellular forces. BioRxiv 442205 [Preprint]. April 30, 2021 [cited 2025 Feb 20]. Available from: doi: https://doi.org/10.1101/2021.04.30.442205 and Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9
- Discipline:
- Science and Engineering
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- Creator:
- Nunley, Hayden and Lubensky, David K
- Description:
- In a previous study (Xue et al. Nature Materials 2018), the authors showed that a key fate patterning event in vertebrate development can be reproduced in an in vitro stem cell culture. They further showed that this in vitro fate pattern seems to depend on mechanical signals rather than secreted chemical signals. In this follow-up study, a mathematical model of this process is proposed. The code in this deposit is for the simulation of this mathematical model in various cell layer geometries and substrate geometries. These geometries include a 1D cell layer, quasi-1D stripe geometry, disc geometry (all on a very thin substrate or a substrate composed of microposts) as well as a 1D cell layer on a finite-thickness substrate. Our model implies that the width of the outer fate domain varies non-monotonically with substrate stiffness, a prediction that we confirm experimentally.
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, and Force sensing
- Citation to related publication:
- Nunley H, Xue X, Fu, J, Lubensky, DK. Generation of fate patterns via intercellular forces. BioRxiv 442205 [Preprint]. April 30, 2021 [cited 2025 Feb 20]. Available from: doi: https://doi.org/10.1101/2021.04.30.442205, Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9, Banerjee S, Marchetti MC. Substrate rigidity deforms and polarizes active gels. EPL (Europhysics Letters) 96, 28003 (2011). https://doi.org/10.1209/0295-5075/96/28003, Edwards CM, Schwarz US. Force Localization in Contracting Cell Layers, Physical Review Letters 107, 128101 (2011). https://doi.org/10.1103/PhysRevLett.107.128101, and Banerjee S, Marchetti MC. Contractile Stresses in Cohesive Cell Layers on Finite-Thickness Substrates, Physical Review Letters 109, 108101 (2012). https://doi.org/10.1103/PhysRevLett.109.108101
- Discipline:
- Engineering and Science
-
- Creator:
- Nunley, Hayden, Xue, Xufeng, Sun, Yubing, Resto-Irizarry, Agnes M, Yuan, Ye, Yong, Koh Meng Aw, Zheng, Yi, Weng, Shinuo, Shao, Yue, Lubensky, David K, Studer, Lorenz, and Fu, Jianping
- Description:
- In an earlier study (Xue et al. Nature Materials 2018), stem cells differentiated into one of two cell types, neural plate border (NPB) or neural plate (NP), in vitro. This previous study demonstrated that this differentiation is likely mechanics-guided. Part of this demonstration was measurements of the displacement of microposts under the cell layer as the cells differentiate. These measurements suggested that the NPB cells are more contractile than NP cells. In a follow-up study (linked to this dataset), we quantitatively analyzed these data to demonstrate even further that the NPB cells are mechanically different than the NP cells and that the post displacement profile is not explained by a model of a cell layer with uniform mechanical properties. This analysis motivated the mathematical model -- for this cell colony system -- that we proposed and analyzed.
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, Force sensing, and Vertebrate development
- Citation to related publication:
- Hayden Nunley, Xufeng Xue, Jianping Fu, David K. Lubensky bioRxiv 2021.04.30.442205; doi: https://doi.org/10.1101/2021.04.30.442205 and Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9
- Discipline:
- Engineering and Science
-
- Creator:
- Nunley, Hayden, Xue, Xufeng, Fu, Jianping, and Lubensky, David K
- Description:
- In an earlier publication (Xue et al. Nature Materials 2018), the authors reported a set of in vitro experiments in which uniformly supplied chemical media induced spatially patterned fates in cell colony in a disc geometry. They provided significant evidence that inter-cellular mechanical interactions, as well as mechanical interactions between cells and the substrate, play an important role in this in vitro differentiation process. In this subsequent publication, we propose a mathematical model for this fate patterning process and explore how the fate pattern depends on substrate stiffness. One ingredient of this mathematical model is that the cells at the very edge of the colony (lacking adherens junctions on one side) are geometrically different than the rest (by occupying a larger area on the micropattern). These images of DAPI (staining nuclei) and ECad (at adherens junctions) for colonies during early cell differentiation demonstrate this difference. Corresponding code for analysis is included.
- Keyword:
- Biomechanics, Cell mechanics, and Developmental pattern formation
- Citation to related publication:
- Nunley H, Xue X, Fu, J, Lubensky, DK. Generation of fate patterns via intercellular forces. BioRxiv 442205 [Preprint]. April 30, 2021 [cited 2025 Feb 20]. Available from: doi: https://doi.org/10.1101/2021.04.30.442205 and Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9
- Discipline:
- Engineering and Science
-
- Creator:
- Nunley, Hayden, Xue, Xufeng, Sun, Yubing, Resto-Irizarry, Agnes M, Yuan, Ye, Yong, Koh Meng Aw, Zheng, Yi, Weng, Shinuo, Shao, Yue, Studer, Lorenz, Fu, Jianping, and Lubensky, David K
- Description:
- In an earlier study (Xue et al. Nature Materials 2018), stem cells differentiated into one of two cell types, neural plate border (NPB) or neural plate (NP), in vitro with the NP forming a central circular domain. This previous study demonstrated that this differentiation is likely mechanics-guided. Part of this demonstration was measurements of the displacement of microposts under the cell layer as the cells differentiate. These measurements suggested that the NPB cells are more contractile than NP cells (see Dataset of cell layers on micro-patterned substrates compost of posts). The authors of the 2018 study and of a follow-up study further explored how the size of the NPB domain depends on experimental conditions (see Dataset of stem cell colonies differentiating in neural induction medium and code for analysis of resulting fate pattern). To further understand what factors could be driving NPB formation, we estimated cell area at the colony edge (see Dataset on cell areas and nuclear densities in differentiating stem cell colonies). This analysis inspired a mathematical model of mechanical patterning: fate affects cell contractility, and pressure in the cell layer biases fate. Cells at the colony edge, more contractile than cells at the center, seed a pattern that propagates via force transmission. We simulated the model in various cell geometries and for different substrates (see Code for simulating NP/NPB fate patterning in stem cell colonies). Strikingly, our model implies that the width of the outer fate domain varies non-monotonically with substrate stiffness, a prediction that we confirm experimentally. Our findings thus support the idea that mechanical stress can mediate patterning in the complete absence of chemical morphogens, even in non-motile cell layers, thus expanding the repertoire of possible roles for mechanical signals in development and morphogenesis.
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, Force Sensing, and Vertebrate development
- Discipline:
- Science
4Works -
- Creator:
- Howard, Cecilia M., Sheldon, Nathan D., Loveall, Zachary, Keating, Katarina A., Hong, Jungpyo, Smith, Selena Y., and Passey, Benjamin H.
- Description:
- This study uses an array of stratigraphic, morphological, and geochemical tools to investigate lateral and temporal variability in environmental records preserved by microbialites during a global hothouse environment. It also inverts tools for reconstructing environmental conditions to elucidate ancient microbial processes. Key Points: - The Green River Basin, WY, USA preserves lacustrine microbialites deposited during the Early Eocene Climatic Optimum, a period of high CO2 and temperatures - Morphological and geochemical analyses of these microbialites preserve variable local, regional, and global environmental conditions - Measurements of environmental conditions can be inverted to understand ancient microbial processes, which could be used to inform modeling of microbial influences on carbon cycling and Abstract: The Green River Basin, WY, USA, contains extensive lacustrine microbialite beds that formed during the hothouse Early Eocene Climatic Optimum (53–49 Ma). The records of biological, chemical, and physical processes preserved in these microbialites can inform our understanding of terrestrial conditions in this warm climate, but separating the competing signals of local, regional and global changes is difficult. Studies focusing on individual localities may miss spatial drivers of differences in microbialites. In this study, we used stratigraphic, morphological, and geochemical techniques to study microbialites deposited in the Green River Basin across three million years spanning the peak of the EECO, including samples from two beds covering 13–25 km of lateral extent. These samples cover a broad set of lake conditions as well as local differences such as spring deposits. We found that these microbialites preserved a mixture of conditions such as global hothouse temperatures, regional shifts in lake level, and local variability from sediment and water sources. Morphological and elemental variability were driven primarily by local and regional conditions such as stream, spring, and clastic inputs and water depth. Isotopic data preserved these local and regional changes as well as evidence of global hothouse conditions. Comparison of past [CO2] estimates to reconstructions using organic and inorganic carbon isotopes with clumped isotope-derived temperatures provides evidence for low to moderate microbial growth rates in these microbialite building communities, demonstrating that environmental tools can be inverted to better understand ancient microbial processes. A diverse toolkit was necessary to isolate the individual controls on microbialite records, and comparing across both space and time enabled us to identify local drivers that lead to significant differences from the expected regional signal.
- Keyword:
- Geosciences, Paleoclimate, Microbialite, Stromatolite, Eocene, Paleolake, and Green River Basin
- Citation to related publication:
- Howard, C.M. (2025). Unraveling Records of Time and Environment in Microbial Ecosystems from the Archean to Today (Ph.D. Dissertation). University of Michigan. and Howard, C.M., et al. (in prep). Disentangling Morphological and Chemical Records of Climate, Hydrology, and Diagenesis in Microbialites from the Eocene Green River Basin, WY, USA.
- Discipline:
- Science
-
- Creator:
- Phillips, Chrystian D, DeFazio, R. Anthony, and Moenter, Suzanne M.
- Description:
- Supplemental tables containing the statistical analysis for the manuscript "Sex and time of day alter the interactions between hypothalamic glia and the neural circuits controlling reproduction"
- Discipline:
- Science
-
- Creator:
- Raymond, Matt, Elvati, Paolo, Saldinger, Jacob C, Lin, Jonathan, Shi, Xuetao, and Violi, Angela
- Description:
- Nanoparticles (NPs) formed in nonthermal plasmas (NTPs) can have unique properties and applications. However, modeling their growth in these environments presents significant challenges due to the non-equilibrium nature of NTPs, making them computationally expensive to describe. In this work, we address the challenges associated with accelerating the estimation of parameters needed for these models. Specifically, we explore how different machine learning models can be tailored to improve prediction outcomes. We apply these methods to reactive classical molecular dynamics data, which capture the processes associated with colliding silane fragments in NTPs. These reactions exemplify processes where qualitative trends are clear, but their quantification is challenging, hard to generalize, and requires time-consuming simulations. Our results demonstrate that good prediction performance can be achieved when appropriate loss functions are implemented and correct invariances are imposed. While the diversity of molecules used in the training set is critical for accurate prediction, our findings indicate that only a fraction (15-25%) of the energy and temperature sampling is required to achieve high levels of accuracy. This suggests a substantial reduction in computational effort is possible for similar systems.
- Keyword:
- machine learning, molecular dynamics, nanoparticle, nonthermal plasma, silane, and sticking coefficient
- Citation to related publication:
- Raymond, M., Elvati, P., Saldinger, J. C., Lin, J., Shi, X., & Violi, A. (2025). Machine learning models for Si nanoparticle growth in nonthermal plasma. Plasma Sources Science and Technology. https://doi.org/10.1088/1361-6595/adbae1 and https://arxiv.org/abs/2501.00003
- Discipline:
- Science
-
- Creator:
- Wang, Danhao and Mi, Zetian
- Description:
- Wurtzite ferroelectrics possess transformative potential for next-generation microelectronics. A comprehensive understanding of their ferroelectric properties and domain energetics is crucial for tailoring their ferroelectric characteristics and exploiting their functional properties in practical devices. Despite burgeoning interest, the exact configurations, and electronic structures of domain walls in wurtzite ferroelectrics remain elusive. In this work, we elucidate the atomic configurations and electronic properties of electric-field-induced domain walls in ferroelectric ScGaN. By combining transmission electron microscopy and theoretical calculations, a novel charged domain wall with a buckled two-dimensional hexagonal phase is revealed. Density functional theory calculations confirm that such domain wall structures further give rise to unprecedented mid-gap states within the forbidden band. Quantitative analysis unveils a universal charge-compensation mechanism stabilizing antipolar domain walls in ferroelectric materials, wherein the polarization discontinuity at the 180º domain wall is compensated by the unbonded valence electrons. Furthermore, the reconfigurable conductivity of these domain walls is experimentally demonstrated, showcasing their potential for ultra-scaled device applications. Our findings represent a pivotal advancement in understanding the structural and electronic properties of wurtzite ferroelectric domain walls and lay the groundwork for fundamental physics studies and device applications.
- Keyword:
- Charged domain walls, Scanning transmission electron microscopy, and Density functional theory calculations
- Discipline:
- Science
-
- Creator:
- Brinkmeier, Michelle L, Wang, Su Qing, Pittman, Hannah, Cheung, Leonard Y, and Prasov, Lev
- Description:
- MYRF is a gene that regulates the development and function of the retinal pigmented epithelium (RPE), which play an important role in maintaining photoreceptor structure and function. Mutations in patients have been implicated in eye size disorders, particularly causing a small, but structurally normal eye. We have utilized a molecular technique, single cell RNA sequencing, to investigate how loss of Myrf specifically in the RPE in a mouse model impacts downstream gene expression at three developmental timepoints and used this information to define the role of Myrf in development. Our work identified key cytoskeletal structural genes specific to the RPE, Ermn and Upk3b, and a gene important for the cell survival, Sox10, as critical targets of Myrf. In addition, we have identified and confirmed that the TGFbeta signaling pathway is dysregulated when Myrf is lost during development. This pathway is particularly relevant in RPE health and eye growth. Our electron microscopy and histologic analyses also confirm a defect in RPE structure and function. We place MYRF within a hierarchy of genes involved in RPE development and introduce novel candidate genes for further study as retinal degeneration and nanophthalmos candidate genes.
- Keyword:
- ERMN, MYRF, Hypopigmentation, TMEM98, SOX10, Retinal Pigment Epithelium (RPE), and Retinal degeneration
- Discipline:
- Science