Article
Physics, Fluids & Plasmas
Fu-Lai Wen
Summary: The folding of epithelial cell sheets is a fundamental process in development. This study uses simulations to show that the physical properties of expanding supracellular contractile rings determine the patterns of epithelial fold formation. These findings have important implications for understanding epithelial folding morphogenesis.
Article
Multidisciplinary Sciences
Tom Brandstaetter, David B. Brueckner, Yu Long Han, Ricard Alert, Ming Guo, Chase P. Broedersz
Summary: Cell migration in rotating spherical tissues exhibits a collective mode with a single-wavelength velocity wave, which is accompanied by a supracellular flow pattern featuring topological defects. This collective migration mode arises from the effect of curvature on the active flocking behavior of cells on a spherical surface.
NATURE COMMUNICATIONS
(2023)
Article
Developmental Biology
Susannah B. P. McLaren, Benjamin J. Steventon
Summary: The internal pressure of the notochord increases its elongation and stiffening, playing a key role in elongating the somitic compartment. Anterior expansion generates a force that displaces notochord cells posteriorly, contributing to the elongation of segmented tissue during posttailbud stages.
Article
Multidisciplinary Sciences
Kenji Nishizawa, Shao-Zhen Lin, Claire Chardes, Jean-Francois Rupprecht, Pierre-Francois Lenne
Summary: Biological tissues acquire reproducible shapes through dynamic cell behaviors, particularly the remodeling of cell-cell contacts. This study developed a technique to manipulate stress patterns on these contacts in the early epithelium of Drosophila embryos and found that Myosin -II activity responds to junction strain rate, facilitating junction shrinkage. These findings provide insights into the efficient deformation of cell-cell contacts in vivo and reveal the mechanosensitive features of their remodeling.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Physics, Multidisciplinary
Muhamet Ibrahimi, Matthias Merkel
Summary: By studying a hydrodynamic model of active polar material, it is found that protein concentration gradients can stabilize active anisotropic deformation, and stability is strongly affected by the coupling way between fluid pressure and protein concentration gradient as well as the control of polarity magnitude.
NEW JOURNAL OF PHYSICS
(2023)
Article
Multidisciplinary Sciences
Yi Peng, Zhengyang Liu, Xiang Cheng
Summary: Our experimental study reveals the dominant role of hydrodynamic interactions in bacterial collective swimming. By triggering bacterial turbulence, we identify two unusual kinetic pathways.
Article
Biochemical Research Methods
Sijie M. Tong, Navreeta K. Singh, Rastko M. Sknepnek, Andrej Kosmrlj
Summary: Epithelial tissues exhibit complex viscoelastic rheological behavior, where cells can actively tune their mechanical properties to change the overall response of the tissue. This study systematically investigated the shear and bulk responses of epithelia in both fluid and solid phases using small oscillatory shear and bulk deformations. The findings suggest that the solid-fluid transition can be controlled by applying pre-deformation to the system.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Mark Skamrahl, Hongtao Pang, Maximilian Ferle, Jannis Gottwald, Angela Ruebeling, Riccardo Maraspini, Alf Honigmann, Tabea A. Oswald, Andreas Janshoff
Summary: This study demonstrates the essential role of ZO proteins in efficient collective cell migration by maintaining tissue fluidity and controlling proliferation. Loss of ZO1 and ZO2 leads to actomyosin remodeling in individual cells, altering their viscoelastic properties and resulting in a tug-of-war between subpopulations with distinct morphological and mechanical properties. Co-cultures of wildtype and dKD cells migrate inefficiently due to differences in contractility rather than adhesion.
Article
Cell Biology
Zhiyi Lv, Na Zhang, Xiaozhu Zhang, Joerg Grosshans, Deqing Kong
Summary: Dorsal closure is a prominent morphogenetic process during Drosophila embryogenesis, and the epidermis actively responds and antagonizes the pull from the amnioserosa. Increased microtubules in the epidermis may help bear part of the mechanical force.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biology
Masaya Hagiwara, Hisataka Maruyama, Masakazu Akiyama, Isabel Koh, Fumihito Arai
Summary: The study demonstrates that actively remodeling the cellular microenvironment can modulate the force exerted on cells by ECM, influencing the directionality of collective cell migration and pattern formation. Using microfabrication techniques, optical tweezers, and mathematical models, the research confirms the presence of this mechanism.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Tong Liu, Xianyue Shen, Qingming Ji, Jianlin Xiao, Jianlin Zuo, Zhongli Gao
Summary: This study investigated the displacements and 3D morphological changes of knee menisci under weight-bearing and early flexion conditions in healthy adults using MRI technology. The research revealed that menisci showed different changes in morphological patterns under various flexion angles and external loading conditions, providing a valuable reference for evaluating meniscal integrity.
SCIENTIFIC REPORTS
(2021)
Article
Physics, Fluids & Plasmas
L. H. Miranda-Filho, T. A. Sobral, A. J. F. de Souza, Y. Elskens, Antonio R. de C. Romaguera
Summary: This article discusses the dynamical phase transition in Vicsek systems and investigates their chaotic behavior by computing the largest Lyapunov exponent (LLE). The authors find a chaotic regime for the collective behavior of the self-propelled particles (SPPs) based on the LLE and observe a significant change in the dependence of LLE on applied noise near the known transition points of the Vicsek model.
Article
Cell Biology
Paolo Ronchi, Giulia Mizzon, Pedro Machado, Edoardo D'Imprima, Benedikt T. Best, Lucia Cassella, Sebastian Schnorrenberg, Marta G. Montero, Martin Jechlinger, Anne Ephrussi, Maria Leptin, Julia Mahamid, Yannick Schwab
Summary: Cells are 3D objects, and volume EM is essential for interpreting ultrastructural data accurately. FIB-SEM methods such as focused ion beam are now commonly used, but precise targeting of volumes of interest within large samples remains challenging. This study introduces a workflow for targeting specific cells or subcellular structures with micrometer precision using fluorescence preservation and confocal maps to guide FIB-SEM acquisition, allowing for the discovery of new ultrastructural details.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Physics, Multidisciplinary
Carles Blanch-Mercader, Pau Guillamat, Aurelien Roux, Karsten Kruse
Summary: Research shows that cell monolayers exert compressive stresses at defect centers, leading to localized cell differentiation and formation of three-dimensional shapes in these regions.
PHYSICAL REVIEW LETTERS
(2021)
Article
Biochemical Research Methods
Hyun Gyu Lee, Kyoung J. Lee
Summary: Proper cell-cell adhesiveness can enhance the super-diffusive nature of individual cells and promote cell movement within a dense population. Interestingly, research shows that cell dispersal within a densely packed population differs from free crawling, and this phenomenon can be explained by a simple cellular Potts model.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Physics, Multidisciplinary
David Richard, Geert Kapteijns, Julia A. Giannini, M. Lisa Manning, Edan Lerner
Summary: The study proposes a simple definition of shear transformation zones (STZs) based on the harmonic approximation of a glass's energy, which is shown to be more broadly applicable than previous anharmonic definitions. An open-source library is provided for analyzing low-lying STZs in computer glasses and laboratory materials. The results represent a methodological advancement towards characterizing mechanical disorder in glasses and understanding their yielding behavior.
PHYSICAL REVIEW LETTERS
(2021)
Article
Physics, Multidisciplinary
Steffen Grosser, Jurgen Lippoldt, Linda Oswald, Matthias Merkel, Daniel M. Sussman, Frederic Renner, Pablo Gottheil, Erik W. Morawetz, Thomas Fuhs, Xiaofan Xie, Steve Pawlizak, Anatol W. Fritsch, Benjamin Wolf, Lars-Christian Horn, Susanne Briest, Bahriye Aktas, M. Lisa Manning, Josef A. Kas
Summary: The morphology of tissues, cells, and nuclei changes during tumor progression, with cancer cell motility correlating to a fluidization of tumor tissue. The degree of tissue fluidity in 3D is found to correlate with elongated cell and nucleus shapes. Two active states of matter, amorphous glasslike and disordered fluid, are observed in solid tumors, with cell and nucleus shape potentially serving as markers for metastatic potential in personalized cancer treatment.
Article
Chemistry, Physical
Shao-Zhen Lin, Matthias Merkel, Jean-Francois Rupprecht
Summary: Vertex models describe tissue as tilings of polygons, with tissue dynamics resulting from a balance between isotropic stresses and tensions associated with cell-cell interfaces. However, it is less clear how to describe anisotropic stresses arising from the bulk of cells. Two recent publications proposed different schemes to implement bulk anisotropic stresses in vertex models, and their results led to significantly different tissue dynamics.
EUROPEAN PHYSICAL JOURNAL E
(2022)
Article
Physics, Multidisciplinary
O. K. Damavandi, M. L. Manning, J. M. Schwarz
Summary: This study proposes an effective medium theory for random regular spring networks with purely geometrical disorder to predict their stiffness through the distribution of tensions. The study finds a linear dependence of stiffness on strain in the rigid phase and a nontrivial dependence on both the mean and standard deviation of the tension distribution. Although the theory does not accurately predict shear modulus due to spatial heterogeneities, it serves as an ideal starting point for experimentalists to quantify the mechanics of such networks.
Article
Multidisciplinary Sciences
Varda F. Hagh, Sidney R. Nagel, Andrea J. Liu, M. Lisa Manning, Eric Corwin
Summary: The introduction of transient degrees of freedom can lead to stable jammed packings with deep energy minima, and different choices for the added degrees of freedom can result in different training outcomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biophysics
E. Lawson-Keister, M. L. Manning
Summary: Studied the potential mechanisms for collective chemotaxis in cellular monolayers, and found that advection, contact inhibition of locomotion, and heterotypic interfacial tension can all drive collective chemotaxis. The scaling behavior of cluster motion was well captured by simple analytic theories.
BIOPHYSICAL JOURNAL
(2022)
Article
Physics, Multidisciplinary
Muhamet Ibrahimi, Matthias Merkel
Summary: By studying a hydrodynamic model of active polar material, it is found that protein concentration gradients can stabilize active anisotropic deformation, and stability is strongly affected by the coupling way between fluid pressure and protein concentration gradient as well as the control of polarity magnitude.
NEW JOURNAL OF PHYSICS
(2023)
Article
Physics, Multidisciplinary
Shao-Zhen Lin, Matthias Merkel, Jean-Francois Rupprecht
Summary: Cells can adjust their intracellular architecture based on overall shape, and this study investigates the rheological implications of such coupling in a minimal model of dense cellular material. Increasing the active mechanical stress leads to transitions from a hexagonal crystal motif to a solid with anisotropic cells, followed by a re-entrant transition to a regime with finite hexatic order and shear modulus. Further increasing activity results in spontaneous tissue flows and topological defects, consistent with active nematic theory and observations in epithelial tissue experiments.
PHYSICAL REVIEW LETTERS
(2023)
Article
Physics, Multidisciplinary
M. Lisa Manning
Summary: The field of soft matter physics has expanded rapidly in recent decades, revealing the importance of entropy, elasticity, and geometry in understanding various materials and systems. Similarly, the fields of biological physics and the physics of living systems have gained recognition as independent areas of study, aided by tools from molecular and cell biology and optical physics. This Essay explores two future challenges at the intersection of these two fields: the characterization of emergent behavior and the manipulation of highly deformable active objects. Progress in these areas holds the potential for creating adaptive smart materials and advancing our understanding of biological function, particularly in the fight against disease.
PHYSICAL REVIEW LETTERS
(2023)
Article
Chemistry, Physical
Cheng-Tai Lee, Matthias Merkel
Summary: This study numerically investigates the elastic behavior of spring networks and predicts the scaling behavior related to rigidity transition. The results indicate that the predictions apply to various classes of spring networks and there is a linear scaling relationship between shear modulus and stress.
Article
Chemistry, Physical
Simon Gsell, Matthias Merkel
Summary: Phase separation plays a key role in the spatial organization of multicomponent mixtures, and is observed in animal embryos and stem cell aggregates. This study uses numerical simulations to investigate the interplay between different phases in deformable systems and finds that under specific conditions, highly elongated droplets can form, which are mechanically close to equilibrium.
Article
Chemistry, Physical
Ethan Stanifer, M. Lisa Manning
Summary: Under applied shear strain, particles in granular and amorphous materials undergo localized deformations, forming avalanches. The dynamics during these avalanches have been studied using numerical simulations and persistent homology methods. It has been found that bursts of localized deformations occur at identified localized excitations using the linear spectrum. This new framework provides insights for understanding avalanche statistics in glasses and granular matter.
Article
Physics, Fluids & Plasmas
Ojan Khatib Damavandi, Varda F. Hagh, Christian D. Santangelo, M. Lisa Manning
Summary: This paper discusses the calculation method of energetic rigidity and applies it to examples in two dimensions. Underconstrained spring networks and vertex models require second-order rigidity to predict their rigidity, while overconstrained spherical jammed packings can be calculated using first-order constraint counting. Aspherical jammed packings are jammed at hypostaticity and require a modified constraint counting.
Article
Physics, Fluids & Plasmas
Ojan Khatib Damavandi, Varda F. Hagh, Christian D. Santangelo, M. Lisa Manning
Summary: Rigidity plays a crucial role in the integrity and function of various physical and biological systems. This paper introduces the concept of energetic rigidity, which is a more practical notion of rigidity compared to commonly used rigidity tests. The formalism of energetic rigidity not only unifies our understanding of mechanical stability but also opens up new avenues for material design.
Article
Chemistry, Physical
Takaki Yamamoto, Daniel M. Sussman, Tatsuo Shibata, M. Lisa Manning
Summary: This study investigates how spatiotemporally heterogeneous forces affect the dynamical and mechanical properties of confluent tissue. The authors find that the long-time diffusion constant describing cell rearrangements depends non-monotonically on the persistence time, while increasing monotonically with the amplitude of the fluctuating tension.
Review
Cell Biology
Alyssa Kearly, Andrew D. L. Nelson, Aleksandra Skirycz, Monika Chodasiewicz
Summary: Stress Granules (SGs) and Processing-bodies (P-bodies) are important biomolecular condensates that play crucial roles in maintaining mRNA balance and regulating stress responses. They are composed of proteins and RNAs involved in translation, protein folding, and energy metabolism.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
P. Lemonnier, T. Lawson
Summary: Stomatal conductance plays a crucial role in determining CO2 uptake and water loss in plants, affecting overall water status and productivity. However, the signals coordinating mesophyll demands for CO2, the role of chloroplasts in stomatal function, and other GC metabolic processes in stomatal function remain poorly understood.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Matteo Gionfriddo, Timothy Rhodes, Spencer M. Whitney
Summary: Rubisco is a key enzyme that facilitates the entry of CO2 into the biosphere, but its catalytic properties are slow and error-prone. More effective Rubisco variants have been discovered in certain algae, offering the potential to significantly improve crop productivity. However, incompatibilities in protein folding have hindered the transplantation of these variants into plants. Directed evolution is now being explored to enhance Rubisco catalysis.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Vittoria Clapero, Stephanie Arrivault, Mark Stitt
Summary: The Calvin-Benson cycle has undergone massive selection and co-evolution with carbon-concentrating mechanisms due to changing environmental factors. Metabolite profiling reveals species-specific variations in the operation of the cycle, indicating the influence of different modes of photosynthesis. Connectivity analysis identifies constraints and driving factors for cross-species diversity in the cycle.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Sukhbir Kaur, David D. Roberts
Summary: Thrombospondin-1 modulates cell behavior by interacting with components of the extracellular matrix and cell surface receptors. Its release and expression are influenced by injuries and various diseases, while its sustained presence in the extracellular space is regulated by receptor-mediated clearance. Thrombospondin-1 plays important roles in immune responses.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Richard P. Tucker, Josephine C. Adams
Summary: Thrombospondins (TSPs) play diverse roles in animals and have been found to belong to a superfamily that includes different subgroups such as mega-TSPs, sushi-TSPs, and poriferan-TSPs. Invertebrates encode a greater diversity of TSP superfamily members than vertebrates.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
James Petrik, Sylvia Lauks, Bianca Garlisi, Jack Lawler
Summary: Many cancers start with a small nest of transformed cells that can remain dormant. Thrombospondin-1 (TSP-1) initially promotes dormancy by suppressing angiogenesis, but over time, factors promoting angiogenesis become dominant and recruit various cells to form a complex tumor microenvironment. TSPs play a role in the proliferation, migration, and invasion of cells in the tumor microenvironment, as well as influencing the immune characteristics and phenotype of tumor-associated macrophages.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Hana Fakim, Christine Vande Velde
Summary: There has been increasing attention to the role of phase-separated biomolecular condensates, specifically stress granules, in neurodegenerative diseases like ALS. ALS-associated mutations in genes involved in stress granule assembly have been found, and stress granule proteins have been detected in pathological inclusions in ALS patient neurons. However, protein components of stress granules are also present in other physiological biomolecular condensates, which have not been adequately discussed in relation to ALS. This review explores the functions of TDP-43 and FUS in physiological condensates occurring in the nucleus and neurites beyond stress granules, and discusses the impact of ALS-linked mutations on their ability to phase separate and perform their functions in stress-independent biomolecular condensates.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Alexander Lin, Yogambha Ramaswamy, Ashish Misra
Summary: Smooth muscle cells, endothelial cells, and macrophages in blood vessels display remarkable heterogeneity, and their developmental origins may influence their plasticity. Unbiased single cell whole transcriptome analysis techniques are revolutionizing the understanding of cellular diversity and plasticity, providing insights for therapeutic research.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Elton P. Hudson
Summary: The Calvin Benson cycle plays a crucial role in the ecological and biotechnological aspects of bacteria. Recent studies have shed light on the regulation of this cycle in bacteria, with post-transcriptional and post-translational regulation being important in phototrophic bacteria, and transcriptional regulation being prominent in chemolithoautotrophic bacteria. Understanding the regulation of the Calvin Benson cycle has implications for enhancing CO2 fixation and improving the synthesis of desired products. Non-canonical cycles may offer potential benefits for industrial applications.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Xin-Guang Zhu, Haim Treves, Honglong Zhao
Summary: This paper discusses the major regulatory mechanisms over the Calvin Benson Cycle (CBC) that maintain homeostasis of metabolite levels. These mechanisms include redox regulation of enzymes, metabolite regulations (especially allosteric regulations), and balanced activities of enzymes. These regulatory mechanisms are crucial for maintaining high flux and photosynthetic efficiency in CBC.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Hunter C. Herriage, Yi-Ting Huang, Brian R. Calvi
Summary: Apoptosis prevents the inappropriate acquisition of extra copies of the genome, known as polyploidy, but the polyploid state can suppress apoptosis. The mechanisms linking apoptosis and polyploid cell cycles are still largely unknown, and studying the regulation of apoptosis in development and cancer could lead to more effective therapies.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Daniel Campbell, Steven Zuryn
Summary: Mitochondrial dynamics play a crucial role in regulating cellular and organismal homeostasis, impacting various aspects of an organism's healthspan. By studying the nematode Caenorhabditis elegans, a comprehensive understanding of the impact of mitochondrial dynamics on homeostasis over a lifetime can be obtained.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Diba Borgmann, Henning Fenselau
Summary: Maintaining blood glucose at an appropriate physiological level requires coordination of multiple organs and tissues, with the vagus nerve playing a key role in central control. Recent studies have revealed the cellular identity, neuroanatomical organization, and functional contributions of vagal neurons in the regulation of systemic glucose metabolism. These findings provide new insights into the precise roles of vagal neurons in coordinating glucose levels and offer potential avenues for treating glucose metabolism disorders.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Tatiana C. Coverdell, Stephen B. G. Abbott, John N. Campbell
Summary: In this article, we review how genetic technology and single-cell genomics are revealing the organizational principles of the efferent vagus in unprecedented detail.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
