Article
Cell Biology
Xiaowei Sun, Yujie Liu, Shuheng Zhou, Li Wang, Jinzi Wei, Rui Hua, Zhongyang Shen, Sei Yoshida
Summary: Circular dorsal ruffles (CDRs) are membrane ruffles induced by growth factors (GF) on the dorsal surfaces of cells, which activate AKT protein kinase. This study identified the presence of CDRs in the hepatocellular carcinoma Hep3B cell line and investigated their role in modulating the AKT pathway.
CELL COMMUNICATION AND SIGNALING
(2022)
Article
Cell Biology
Rui Hua, Jinzi Wei, Mauricio Torres, Yuxin He, Yanan Li, Xiaowei Sun, Li Wang, Ken Inoki, Sei Yoshida
Summary: Using ultrahigh-resolution scanning electron microscopy, we have discovered the expression of Circular Dorsal Ruffles (CDRs) in glomerular podocytes. These CDRs function as precursors for macropinocytosis, and through biochemical and imaging analyses, we have found that they play a role in the AKT-mTORC1 growth factor signaling pathway. Targeting CDR formation could potentially be a therapeutic approach for podocyte diseases caused by aberrant mTORC1 activation.
JOURNAL OF CELLULAR PHYSIOLOGY
(2023)
Article
Cell Biology
Pai Li, Ze Zhang, Yiying Tong, Bardees M. Foda, Brad Day
Summary: Li and Zhang et al. introduce Implicit Laplacian of Enhanced Edge (ILEE), an algorithm and toolbox for unbiased, quantitative, and cytoskeletal image analysis. ILEE solves historical challenges and improves the accuracy, stability, and robustness of cytoskeletal quantification, as well as extending the number of quantifiable cytoskeletal features.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Mathematics, Interdisciplinary Applications
Nicolas E. Muzzio, Claudio M. Horowitz, Omar Azzaroni, Sergio E. Moya, Miguel A. Pasquale
Summary: The study showed that the flux of cells at the cell colony border region is controlled by ridge-patterned substrates, and the cell colony displacement velocity is influenced by the orientation of the ridges with respect to the colony contour. Adjusting the tilt angle s can alter the morphological characteristics and velocity of the cell colony front.
CHAOS SOLITONS & FRACTALS
(2021)
Article
Physics, Applied
Zi-Dong Zhang, Cheng Cheng, Si-Yuan Yu, Ming-Hui Lu, Yan-Feng Chen
Summary: The paper introduces an elastic topological insulator based on atomically thin 2D materials, which can achieve topological edge states and corner states of elastic waves, accompanied by functional components. These components, such as waveguides, splitters, and resonators for elastic waves, are frequency tunable due to the electromechanical sensitivity of 2D materials.
PHYSICAL REVIEW APPLIED
(2021)
Article
Materials Science, Multidisciplinary
Zhao-Yang Dong, Wei Wang, Zhao-Long Gu, Jian-Xin Li
Summary: In this study, we use entanglement entropy analysis to quantitatively identify the confinement and deconfinement of spinons in the spin excitations of quantum magnets. We observe the transition of spinons from deconfinement to confinement with the increase of Hubbard interaction, and the fractionalization of the Higgs mode into four degenerate spinons. This work extends our understanding of the deconfinement of spinons and their coexistence with magnons in quantum magnets.
Article
Nanoscience & Nanotechnology
B. W. Xie, F. Z. Ding, H. J. Shang, D. X. Huang, T. G. Li, Q. Zou, H. W. Gu
Summary: Patterned piezoelectric films as inter-digital transducer (PP-IDT) structures on diamond substrates have been studied for their increased working frequency, electromechanical coupling, and quality factor. By considering each patterned piezoelectric IDT bar as a longitudinal bulk acoustic wave vibrating source, researchers investigated how the BAW excites and couples with the surface acoustic wave on the surface of diamond substrates. The developed delta-function model combined with electric impedance theory was used to calculate resonance frequency and corresponding piezoelectric IDT thickness, with results validating the developed model for PP-IDT structures.
Article
Engineering, Civil
Kristel C. Meza-Fajardo, Apostolos S. Papageorgiou
Summary: The Mexico City basin is an extreme example of an alluvial geological structure that induces long duration and large amplification on ground motions. Surface waves are the dominant component of the seismic wavefield within the basin. This study presents an analysis of surface waves generated by thrust- and normal-faulting events in the basin, using a technique based on ground motion polarization.
EARTHQUAKE ENGINEERING & STRUCTURAL DYNAMICS
(2023)
Article
Biochemical Research Methods
Yu-Le Wu, Philipp Hoess, Aline Tschanz, Ulf Matti, Markus Mund, Jonas Ries
Summary: Quantitative data analysis is crucial for extracting biological insights from the coordinates of single fluorophores in a single-molecule localization microscopy (SMLM) workflow. LocMoFit, an open-source framework, is introduced to fit an arbitrary model to localization coordinates, extract meaningful parameters, and select suitable models. It enables the analysis of complex, heterogeneous, and dynamic structures, and has been demonstrated in assembling multi-protein distribution maps, calculating single-particle averages, and performing time-resolved reconstruction of dynamic processes from static snapshots. Extensive simulation and visualization routines validate the robustness of LocMoFit, and tutorials are provided to enhance users' extraction of information from SMLM data.
Article
Biochemical Research Methods
Yu-Le Wu, Philipp Hoess, Aline Tschanz, Ulf Matti, Markus Mund, Jonas Ries
Summary: This paper presents an open-source framework called LocMoFit for fitting arbitrary models to localization coordinates. The framework has significant potential for analyzing complex, heterogeneous, and dynamic structures, and can be used for assembling protein distribution maps, calculating single-particle averages, and performing time-resolved analysis of highly dynamic processes.
Article
Biochemistry & Molecular Biology
Judith E. Lutton, Helena L. E. Coker, Peggy Paschke, Christopher J. Munn, Jason S. King, Till Bretschneider, Robert R. Kay
Summary: This study reveals the underlying principles of macropinocytic cup formation and closure in Dictyostelium amoebae using light-sheet microscopy. Cups are formed by recruiting PIP3 domains and a specialized F-actin scaffold, and they close through inward or outward actin polymerization and membrane stretching and delamination when cup expansion stalls. This research is important for understanding intracellular fluid engulfment processes.
Article
Multidisciplinary Sciences
Hui Zhang, Eric B. Dammer, Duc M. Duong, Diana Danelia, Nicholas T. Seyfried, David S. Yu
Summary: This study used a proteomic approach to investigate the acetylation effects of SIRT2 and identified a large number of acetylation sites and substrates. The results revealed that SIRT2 regulates protein networks in diverse pathways, including carbon metabolism, glycolysis, and RNA transport.
SCIENTIFIC REPORTS
(2022)
Article
Mechanics
David Barreiro-Villaverde, Anne Gosset, Marcos Lema, Miguel Alfonso Mendez
Summary: In this article, the stability of a thin liquid film dragged by a vertical substrate moving against gravity is investigated in the context of coating processes. The receptivity of the film to three-dimensional disturbances is discussed using Direct Numerical Simulations, an in-house non-linear Integral Boundary Layer film model, and Linear Stability Analysis. The results show that transverse modulations can be beneficial for damping two-dimensional waves in air-knife and slot-die coating processes.
Article
Biophysics
Mary Ecke, Jana Prassler, Gunther Gerisch
Summary: Circular actin waves propagate on the membrane of Dictyostelium cells, separating an inner domain rich in PIP3 and an external domain decorated with PTEN. The inner domain increases while the external domain decreases during wave propagation. Beyond a size limit, the inner domain breaks into an inner and an external domain.
BIOPHYSICAL JOURNAL
(2023)
Article
Mechanics
Paul Clavin, Raul Hernandez Sanchez, Bruno Denet
Summary: The critical dynamics of supersonic combustion waves in the context of direct initiation of detonation in a spherical geometry are studied through an asymptotic analysis. Analysis includes factors such as unsteadiness, curvature, and the gradient of the burnt-gas flow. The phenomenon is explained by the dynamics of the sonic point inside the inert rarefaction wave behind the reaction zone, with a critical slowdown leading to detonation failure if the rate of decay is too strong. Successful detonation initiation involves understanding the trajectories in both fully unsteady problems and self-similar CJ solutions in the long-time limit.
JOURNAL OF FLUID MECHANICS
(2021)
Article
Physics, Multidisciplinary
Raj Kumar Sadhu, Samo Penic, Ales Iglic, Nir S. Gov
Summary: The study reveals that a high concentration of curved proteins can increase cell spreading by reducing bending energy penalty, especially in the low bare vesicle-substrate adhesion regime. Curved proteins inducing protrusive forces help cells form sheet-like lamellipodia structures.
EUROPEAN PHYSICAL JOURNAL PLUS
(2021)
Article
Biochemistry & Molecular Biology
Harikrishnan Rajendran, Amir Haluts, Nir S. Gov, Ofer Feinerman
Summary: Social groups often need to overcome differences in individual interests and knowledge to reach consensus decisions. In the case of emigrating ant colonies, cohesive emigration is achieved only by intermediate-sized colonies, and individuals are willing to concede their potential benefit to promote social consensus.
Article
Multidisciplinary Sciences
Vivek H. Sridhar, Liang Li, Dan Gorbonos, Mate Nagy, Bianca R. Schell, Timothy Sorochkin, Nir S. Gov, Iain D. Couzin
Summary: The study reveals that animals make multichoice decisions by breaking them into a series of binary decisions in space-time, with spontaneous and abrupt critical transitions occurring during the process. This happens across different taxa and ecological contexts, demonstrating fundamental geometric principles underlying animal decision-making.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Amir Haluts, Sylvia F. Garza Reyes, Dan Gorbonos, Robert Ian Etheredge, Alex Jordan, Nir S. Gov
Summary: Competition among animals for resources is common at all levels of life. It is often resolved through contests, where outcomes depend on decision-making by individuals. By studying simple systems, a theoretical framework can be constructed to understand animal contest behaviors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Correction
Physics, Multidisciplinary
Raj Kumar Sadhu, Samo Penic, Ales Iglic, Nir S. Gov
EUROPEAN PHYSICAL JOURNAL PLUS
(2022)
Article
Multidisciplinary Sciences
Adel Al Jord, Gaelle Letort, Soline Chanet, Feng-Ching Tsai, Christophe Antoniewski, Adrien Eichmuller, Christelle Da Silva, Jean-Rene Huynh, Nir S. Gov, Raphael Voituriez, Marie-Emilie Terret, Marie-Helene Verlhac
Summary: Cells can regulate the function of nuclear condensates through the use of cytoplasmic forces generated by cytoskeletal motors. This finding has implications for understanding and studying diseases associated with nuclear condensates.
NATURE COMMUNICATIONS
(2022)
Article
Physics, Multidisciplinary
Rituparno Mandal, Saroj Kumar Nandi, Chandan Dasgupta, Peter Sollich, Nir S. Gov
Summary: This study simulated the behavior of active glass and found that the activity parameters have an impact on the relaxation time of the structural arrangement. In the case of high activity, the extended model predicts qualitative changes.
JOURNAL OF PHYSICS COMMUNICATIONS
(2022)
Article
Cell Biology
Darren Chen Pei Wong, Catherine Qiurong Pan, Shi Yin Er, T. Thivakar, Tan Zi Yi Rachel, Sock Hong Seah, Pei Jou Chua, Tingting Jiang, Ti Weng Chew, Parthiv Kant Chaudhuri, Somsubhro Mukherjee, Agus Salim, Thike Aye Aye, Cheng Gee Koh, Chwee Teck Lim, Puay Hoon Tan, Boon Huat Bay, Anne J. Ridley, Boon Chuan Low
Summary: ARHGAP8/BPGAP1 plays a crucial role in cell motility and cancer metastasis by recruiting Vav1 to activate Rac1 and inhibiting RhoA activity to synchronize Rac1 and Rho signaling pathways.
MOLECULAR BIOLOGY OF THE CELL
(2023)
Article
Chemistry, Physical
Raj Kumar Sadhu, Sarah R. Barger, Samo Penic, Ales Iglic, Mira Krendel, Nils C. Gauthier, Nir S. Gov
Summary: Phagocytosis is the process of cells engulfing large particles, and the presence of curved proteins and the recruitment of cytoskeletal forces can enhance this process. Our model provides a mechanism for the self-organization of the actin cytoskeleton at the phagocytic cup, leading to faster engulfment.
Article
Multidisciplinary Sciences
Jeremy Joon Ho Goh, Corinna Jie Hui Goh, Qian Wei Lim, Songjing Zhang, Cheng-Gee Koh, Keng-Hwee Chiam
Summary: Breast cancer cell lines are valuable tools for studying cancer biology, but their relevance to clinical breast cancer is unclear. By comparing gene expression profiles of tumorigenic MCF7 and non-tumorigenic MCF10A cells in 2D and 3D cultures, this study found that the genes and gene sets distinguishing MCF7 from MCF10A were different from those distinguishing luminal A breast cancer from normal tissue. These findings suggest that MCF7 and MCF10A cell lines may have limitations in modeling cancer-related processes in clinical luminal A breast tumors.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Apratim Mukherjee, Jonathan Emanuel Ron, Hooi Ting Hu, Tamako Nishimura, Kyoko Hanawa-Suetsugu, Bahareh Behkam, Yuko Mimori-Kiyosue, Nir Shachna Gov, Shiro Suetsugu, Amrinder Singh Nain
Summary: This study investigates the role of IRSp53 as a regulator of membrane curvature during cell migration on single, suspended 1D fibers. IRSp53 depletion reduces actin stress fibers, protrusive activity, and contractility, leading to uncoupling of the nucleus from cellular movements. The findings demonstrate the unique role of IRSp53 in controlling cell migration in 3D.
Article
Biology
Songjing Zhang, Lor Huai Chong, Jessie Yong Xing Woon, Theng Xuan Chua, Elsie Cheruba, Ai Kia Yip, Hoi-Yeung Li, Keng-Hwee Chiam, Cheng-Gee Koh
Summary: Zyxin regulates mouse embryonic stem cell differentiation by integrating mechanical cues through actin stress fibres and focal adhesions and biochemical cues through YAP signalling. Crosstalk between mechanical and biochemical cues in embryonic development is not extensively investigated.
COMMUNICATIONS BIOLOGY
(2023)
Review
Developmental Biology
Lior Atia, Jeffrey J. Fredberg, Nir S. Gov, Adrian F. Pegoraro
Summary: Recent evidence supports the transition of multicellular tissue from a jammed phase to an unjammed phase, impacting tissue homeostasis and developmental dynamics. The gradual departure from a jammed phase may enable controlled malleability required in development.
CELLS & DEVELOPMENT
(2021)
Article
Mathematics, Interdisciplinary Applications
Oran Ayalon, Yigal Sternklar, Ehud Fonio, Amos Korman, Nir S. Gov, Ofer Feinerman
Summary: Cooperative transport of large food loads by Paratrechina longicornis ants involves repeated decision-making processes, with carried loads exhibiting biased random walk behavior. This behavior reflects an emergent version of the psychophysical Weber's law. The variable step size of the carried loads expands the scope of the Evidence Accumulation model from isolated to sequential decisions.
FRONTIERS IN APPLIED MATHEMATICS AND STATISTICS
(2021)
Article
Biophysics
Inge M. N. Wortel, Ioana Niculescu, P. Martijn Kolijn, Nir S. Gov, Rob J. de Boer, Johannes Textor
Summary: Cell migration is diverse, but a universal coupling between speed and persistence exists. An existing cellular Potts model shows how cell shape dynamics and local protrusion dynamics play a role in reproducing this speed-persistence coupling.
BIOPHYSICAL JOURNAL
(2021)
