Article
Chemistry, Analytical
Yanrong Wen, Ge Ge, Dan Xie, Zhen Liu
Summary: A comprehensive analytical platform is lacking for tracking and quantifying cell migration behaviors and molecular dynamics at the single-cell level. In this study, an integrated single living cell analysis platform was developed to address this limitation. It enables long-term observation of migration behavioral phenotypes in single cells and simultaneous analysis of signaling proteins and complexes, providing insights into the molecular mechanism and phenotypes in cell migration.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Zenia Motiwala, Anand S. Sandholu, Durba Sengupta, Kiran Kulkarni
Summary: The Ras superfamily of GTPases regulate critical cellular processes by shuttling between GTP-bound ON and GDP-bound OFF states. A unique wavelet coherence (WC) analysis-based approach shows that the structural changes in switch regions could be mapped onto the wavelet coherence phase couplings (WPCs). Disentanglement of WPCs in oncogenic GTPases shows how breakdown of structural allostery leads to their aberrant function.
Article
Multidisciplinary Sciences
Fernando Anjos-Afonso, Florian Buettner, Syed A. Mian, Hefin Rhys, Jimena Perez-Lloret, Manuel Garcia-Albornoz, Namrata Rastogi, Linda Ariza-McNaughton, Dominique Bonnet
Summary: This study reveals an uncharacterized population of human CD34(+) HSCs, referred to as EPCR+ HSCs, which exhibit high repopulation and self-renewal abilities. Their unique transcriptomic wiring, associated with gene modules related to differentiated cell lineages, allows them to exhibit multilineage lineage output.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Dakota Y. Hawkins, Daniel T. Zuch, James Huth, Nahomie Rodriguez-Sastre, Kelley R. McCutcheon, Abigail Glick, Alexandra T. Lion, Christopher F. Thomas, Abigail E. Descoteaux, William Evan Johnson, Cynthia A. Bradham
Summary: In this study, a novel unsupervised algorithm called ICAT is proposed, which can accurately identify and resolve cell states in single-cell RNA sequencing experiments, especially in perturbation experiments, where cell states need to be matched and population substructure needs to be removed. Through validation using simulated and real datasets, it is shown that ICAT outperforms current integration workflows and is robust to various conditions. Empirical validation in a developmental model demonstrates that only ICAT can identify perturbation-unique cellular responses.
Article
Multidisciplinary Sciences
Zhenzhen Liang, Zhouqing Luo, Weimin Zhang, Kang Yu, Hui Wang, Binan Geng, Qing Yang, Zuoyu Ni, Cheng Zeng, Yihui Zheng, Chunyuan Li, Shihui Yang, Yingxin Ma, Junbiao Dai
Summary: The relationship between gene sequence and function is important for both fundamental and practical reasons. This study systematically refactored yeast essential genes to explore the plasticity of gene sequences and identify the logic behind encoding and regulation. Further understanding of gene sequence choice can guide the design of genes in various applications.
Article
Mathematics, Interdisciplinary Applications
Xiaoxue Han, Jianbin Chen, Jianfeng Yang, Minqian Liu
Summary: In this paper, a new pattern called the individual word length pattern (IWLP) is proposed to measure the aliasing between the effect assigned to a column of the design matrix and effects involving other factors. The IWLP criterion is extended from regular fractional factorial (FF) designs to fractional factorial split-plot (FFSP) designs. The authors further propose combined word length patterns (CwWLP and CsWLP) to select good designs for different cases based on the potential important factors being in whole-plot or sub-plot.
JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY
(2023)
Article
Multidisciplinary Sciences
Lucy L. W. Owen, Thomas H. Chang, Jeremy R. Manning
Summary: The coordinated patterns of brain activity reflect cognitive processes, showing a fractal-like hierarchy during story listening. High-order dynamic correlations in neural activity patterns reflect different subgraphs of the brain's functional connectome, with complex thoughts reflected in higher-order patterns of dynamic network interactions throughout the brain.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Alexandre Martins, Carlos Contreras-Martel, Manon Janet-Maitre, Mayara M. Miyachiro, Leandro F. Estrozi, Daniel Maragno Trindade, Caique C. Malospirito, Fernanda Rodrigues-Costa, Lionel Imbert, Viviana Job, Guy Schoehn, Ina Attree, Andrea Dessen
Summary: The elongasome, or Rod system, is a protein complex that controls cell wall formation in rod-shaped bacteria. MreC, a membrane-associated component of the elongasome, interacts with the cytoskeletal element MreB and regulates cell wall biosynthesis enzymes through self-association, contributing to the regulation of elongasome activity.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Penghong Chen, Shijie Tang, Ming Li, Dezhi Wang, Caixiang Chen, Yiqun Qiu, Zhuoqun Fang, Haoruo Zhang, Hangqi Gao, Haiyan Weng, Kailun Hu, Jian Lin, Qingxia Lin, Yi Tan, Shirong Li, Jinghua Chen, Liangwan Chen, Xiaosong Chen
Summary: This study systematically analyzed the characteristics of Wharton's jelly mesenchymal stem cells (WJ-MSCs) using single-cell and spatial transcriptome sequencing. Four subpopulations of WJ-MSCs were identified, and their transcriptomes, cellular heterogeneity, and cell-state trajectories were characterized. The biofunctional-type MSCs showed promising wound repair properties. Additionally, it was found that a specific subpopulation derived from the fetal segment of the umbilical cord might have potential as an ideal therapeutic agent for wound healing.
Article
Chemistry, Multidisciplinary
Xun Chen, Min-Yeh Tsai, Peter G. Wolynes
Summary: Accurate reading of genetic information during transcription is crucial for gene expression. Proteins can recognize DNA sequences through direct readout (specific interactions between amino acid residues and nucleotide bases) or indirect readout (DNA sequence elements cooperating to localize transcription factors). In this study, a protein-DNA model is used to investigate the sequence specificity of the binding of PU.1 protein to DNA. It is found that the binding specificity of PU.1 is achieved through a nonspecific electrostatically driven DNA mechanism.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Cell Biology
Paolo Armando Gagliardi, Benjamin Graedel, Marc-Antoine Jacques, Lucien Hinderling, Pascal Ender, Andrew R. Cohen, Gerald Kastberger, Olivier Pertz, Maciej Dobrzynski
Summary: This article introduces a computational method called ARCOS for the detection and quantification of collective signaling in cell collectives. The method is demonstrated on cell and organism collectives with space-time correlations of varying scales. The study reveals the importance of intercellular signaling for the functionality and adaptation of cell collectives to environmental challenges.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Tapsi Kumar, Kevin Nee, Runmin Wei, Siyuan He, Quy H. Nguyen, Shanshan Bai, Kerrigan Blake, Maren Pein, Yanwen Gong, Emi Sei, Min Hu, Anna K. Casasent, Aatish Thennavan, Jianzhuo Li, Tuan Tran, Ken Chen, Benedikt Nilges, Nachiket Kashikar, Oliver Braubach, Bassem Ben Cheikh, Nadya Nikulina, Hui Chen, Mediget Teshome, Brian Menegaz, Huma Javaid, Chandandeep Nagi, Jessica Montalvan, Tatyana Lev, Sharmila Mallya, Delia F. Tifrea, Robert Edwards, Erin Lin, Ritesh Parajuli, Summer Hanson, Sebastian Winocour, Alastair Thompson, Bora Lim, Devon A. Lawson, Kai Kessenbrock, Nicholas Navin
Summary: By studying the adult human breast tissue at a single-cell and spatial level, we constructed a comprehensive Human Breast Cell Atlas, identifying 12 major cell types and 58 biological cell states. Our findings reveal a rich ecosystem of tissue-resident immune cells, as well as molecular differences between ductal and lobular regions. These data serve as a reference for studying mammary biology and diseases like breast cancer.
Article
Plant Sciences
Tomoyuki Furuya, Haruka Shinkawa, Masataka Kajikawa, Ryuichi Nishihama, Takayuki Kohchi, Hideya Fukuzawa, Hirokazu Tsukaya
Summary: DYRK family, particularly the plant-specific DYRKPs subgroup, plays crucial roles in the morphogenesis of plants, with MpDYRKP in Marchantia polymorpha contributing significantly to orderly tissue morphogenesis by regulating cell shape.
JOURNAL OF PLANT RESEARCH
(2021)
Article
Computer Science, Software Engineering
Ying Yu, Tzu-Chieh Kurt Hong, Athanassios Economou, Glaucio H. Paulino
Summary: Origami, as a paper folding art, has promising applications in science and engineering. Shape grammars and Shape Machine offer an automated solution for origami pattern generation by applying shape rewriting rules to create unique patterns.
COMPUTER-AIDED DESIGN
(2021)
Article
Engineering, Civil
Daizheng Hou, Yafu Zhou, Jing Lian
Summary: This paper proposes a robustly integrated design method to address the limited integrated design level of plug-in fuel cell electric buses (PFCEB). The method involves using Taguchi robust design (TRD) to find robust design parameters, analyzing the mechanism of action between components and the evaluation index, and considering noise in the component matching design. Simulation results demonstrate the effectiveness of the proposed methods, and show that the energy economy of the proposed adaptive Pontryagin's Minimum Principle (A-PMP) based energy management strategy is better than rule-based control.
IEEE TRANSACTIONS ON INTELLIGENT TRANSPORTATION SYSTEMS
(2023)
Article
Developmental Biology
Margherita Perillo, S. Zachary Swartz, Gary M. Wessel
Summary: A conserved post-translational mechanism of germ cell specification is identified in two echinoderm species. This mechanism involves the degradation of Vasa protein in future somatic cells by the E3-ubiquitin-ligase Gustavus. Despite the divergence in germ cell specification mechanisms between these species, the regulation of Vasa by Gustavus is conserved. This study suggests an ancestral and evolutionarily transposable role of Gustavus-mediated Vasa regulation in primordial germ cell formation.
DEVELOPMENTAL BIOLOGY
(2022)
Article
Physics, Multidisciplinary
Borislav Polovnikov, Patrick Wilke, Erwin Frey
Summary: This study reveals two different processes in the diffusive epidemic process, namely the subdiffusive propagation of infection clusters and the diffusive fluctuations in the healthy population. It sheds new light on the theoretical classification of the system.
PHYSICAL REVIEW LETTERS
(2022)
Article
Multidisciplinary Sciences
Florian M. Gartner, Isabella R. Graf, Erwin Frey
Summary: The time complexity of nonequilibrium self-assembly processes is characterized and different assembly scenarios are identified with distinct degrees of complexity. Optimal control strategies are determined. An efficient irreversible scheme for artificial self-assembly of nanostructures is proposed.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Laeschki Wurthner, Fridtjof Brauns, Grzegorz Pawlik, Jacob Halatek, Jacob Kerssemakers, Cees Dekker, Erwin Frey
Summary: Self-organized pattern formation is crucial in biological processes. This study introduces a semi-phenomenological approach based on mass conservation, allowing the reconstruction of pattern information from large-scale dynamics. The approach is demonstrated using the Min system, which produces multiscale patterns in a spatially heterogeneous geometry.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Alfredo Sciortino, Lukas J. Neumann, Timo Krueger, Ivan Maryshev, Tetsuhiko F. Teshima, Bernhard Wolfrum, Erwin Frey, Andreas R. Bausch
Summary: This study demonstrates the use of passive nematic materials to control the pattern formation process of active fluids by introducing and controlling defects. It shows that defects in the passive material can guide the flow of active microtubules and lead to the formation of macroscopic polar patterns, opening up new possibilities for shaping active materials using passive defects.
Article
Multidisciplinary Sciences
Sabrina Meindlhumer, Fridtjof Brauns, Jernej Rudi Finzgar, Jacob Kerssemakers, Cees Dekker, Erwin Frey
Summary: Meindlhumer et al. have conducted a combined theoretical and experimental study on how the propagation direction of Min protein patterns can be changed by a bulk flow of solution. They demonstrate that the direction of in vitro Min protein patterns can be controlled by hydrodynamic flow, with downstream propagation for low concentration ratios of MinE:MinD, upstream propagation for large ratios, and multistability in between. Their study reveals the potential of using flow to probe molecular features and constrain mathematical models for pattern formation systems.
NATURE COMMUNICATIONS
(2023)
Article
Nanoscience & Nanotechnology
Alexandru Bacanu, James F. Pelletier, Yoon Jung, Nikta Fakhri
Summary: In living systems, molecular interactions form multiscale structures that mediate processes in a close relationship between structure and function. However, their dynamics remain poorly characterized due to a lack of methods to quantify non-equilibrium activity. By measuring time-reversal asymmetry encoded in conformational dynamics of carbon nanotubes, we characterize the multiscale dynamics of non-equilibrium activity and relate it to physical parameters. Our analysis provides a general tool to characterize non-equilibrium activity in high-dimensional spaces.
NATURE NANOTECHNOLOGY
(2023)
Article
Physics, Multidisciplinary
Meifang Fu, Tom Burkart, Ivan Maryshev, Henri G. Franquelim, Adrian Merino-Salomon, Maria Reverte-Lopez, Erwin Frey, Petra Schwille
Summary: Through a mechanochemical feedback loop involving Min proteins of Escherichia coli, liposomes start to move, which may help to design motile artificial cells.
Article
Physics, Multidisciplinary
Leonardo Demarchi, Andriy Goychuk, Ivan Maryshev, Erwin Frey
Summary: Enzyme-enriched condensates can regulate the distribution of their substrates and induce enzyme fluxes through feedback interactions. Weak feedback leads to condensate movement towards the center of a confined domain, while above a threshold, self-propulsion and oscillatory dynamics occur. Enzyme-driven fluxes can also result in interrupted coarsening and condensate division, leading to equidistant positioning.
PHYSICAL REVIEW LETTERS
(2023)
Article
Multidisciplinary Sciences
Zihang Wang, M. Cristina Marchetti, Fridtjof Brauns
Summary: Orientational order, encoded in anisotropic fields, is important in organism development. The study focuses on the freshwater polyp Hydra and its muscle fiber orientation defects. A minimal model is introduced to study the interaction between muscle fiber orientation, morphogen gradients, and body shape. The model successfully reproduces experimentally observed reorganization of orientational order on curved surfaces mimicking Hydra's morphologies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Mechanics
Freddy A. Cisneros, Nikta Fakhri, Jordan M. Horowitz
Summary: We propose and investigate a method for identifying timescales of dissipation in nonequilibrium steady states modeled as discrete-state Markov jump processes. The method is based on how the irreversibility, measured by the statistical breaking of time-reversal symmetry, varies under temporal coarse-graining. We observe a sigmoidal-like shape of the irreversibility as a function of the coarse-graining time, which allows us to develop a method for estimating the dissipative time scale from time-series data.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2023)
Article
Physics, Fluids & Plasmas
Laeschkir Wuerthner, Andriy Goychuk, Erwin Frey
Summary: Intracellular protein patterns play a crucial role in regulating important cellular processes and their dynamics are influenced by changes in cell shape. To understand the underlying mechanisms, a conceptual model for cell polarity on a dynamic one-dimensional manifold is explored. The dynamics of the membrane shape induce pattern-forming instabilities and can also suppress pattern formation and shift existing patterns.
Article
Chemistry, Physical
Timo Krueger, Ivan Maryshev, Erwin Frey
Summary: Topological defects play a central role in the formation and organization of various biological systems. In this paper, agent-based simulations are used to study phase-separated active nematics and the formation of -1/2 defects. The authors investigate the morphology and characteristics of these defects, as well as observe and characterize lateral arc-like structures separating from nematic bands. The study also introduces a hydrodynamic theory that explains the emergence of defects and arcs.
Article
Physics, Fluids & Plasmas
Tom Burkart, Jan Willeke, Erwin Frey
Summary: This article investigates how periodic temporal environmental variation can affect the composition and biodiversity of an ecosystem. By using a population dynamics model and timescale separation, the study shows that the impact of environmental changes on species coexistence and stability depends on the timescale of the changes.
Review
Physics, Applied
Tom Burkart, Manon C. Wigbers, Laeschkir Wurthner, Erwin Frey
Summary: Proteins play a crucial role in controlling various vital functions in living cells. Understanding the formation of protein patterns inside cells is essential for comprehending information processing in biological systems.
NATURE REVIEWS PHYSICS
(2022)