Conserved nucleocytoplasmic density homeostasis drives cellular organization across euraryotes
Abin Biswas,
Omar Muñoz,
Kyoohyun Kim,
Carsten Hoege,
Benjamin M. Lorton,
Rainer Nikolay,
Matthew L. Kraushar,
David Shechter,
Jochen Guck, et al.
Nature Communications
16
7597
(2025)
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The confinement of macromolecules has profound implications for cellular biochemistry. It generates environments with specific physical properties affecting diffusion, macromolecular crowding, and reaction rates. Yet, it remains unknown how intracellular density distributions emerge and affect cellular physiology. Here, we show that the nucleus is less dense than the cytoplasm and that living systems establish a conserved density ratio between these compartments due to a pressure balance across the nuclear envelope. Nuclear transport establishes a specific nuclear proteome that exerts a colloid osmotic pressure, which, assisted by chromatin pressure, increases nuclear volume. During C. elegans development, the nuclear-to-cytoplasmic density ratio is robustly maintained even when nuclear-to-cytoplasmic volume ratios change. We show that loss of density homeostasis correlates with altered cell functions like senescence and propose density distributions as key markers in pathophysiology. In summary, this study reveals a homeostatic coupling of macromolecular densities that drives cellular organization and function.
Nonequilibrium Structure and Relaxation in Active Microemulsions
Rakesh Chatterjee,
Hui-Shun Kuan,
Frank Jülicher,
Vasily Zaburdaev
Microphase separation is common in active biological systems as exemplified by the separation of RNA- and DNA-rich phases in the cell nucleus driven by the transcriptional activity of polymerase enzymes acting similarly to amphiphiles in a microemulsion. Here we propose an analytically tractable model of an active microemulsion to investigate how the activity affects its structure and relaxation dynamics. Continuum theory derived from a lattice model exhibits two distinct regimes of the relaxation dynamics and is linked to the broken detailed balance due to intermittent activity of the amphiphiles.
Cell state-specific cytoplasmic density controls spindle architecture and scaling
Nature Cell Biology
27
959-971
(2025)
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Mitotic spindles are dynamically intertwined with the cytoplasm they assemble in. How the physicochemical properties of the cytoplasm affect spindle architecture and size remains largely unknown. Using quantitative biochemistry in combination with adaptive feedback microscopy, we investigated mitotic cell and spindle morphology during neural differentiation of embryonic stem cells. While tubulin biochemistry and microtubule dynamics remained unchanged, spindles changed their scaling behaviour; in differentiating cells, spindles were considerably smaller than those in equally sized undifferentiated stem cells. Integrating quantitative phase imaging, biophysical perturbations and theory, we found that as cells differentiated, their cytoplasm became more dilute. The concomitant decrease in free tubulin activated CPAP (centrosomal P4.1-associated protein) to enhance the centrosomal nucleation capacity. As a consequence, in differentiating cells, microtubule mass shifted towards spindle poles at the expense of the spindle bulk, explaining the differentiation-associated switch in spindle architecture. This study shows that cell state-specific cytoplasmic density tunes mitotic spindle architecture. Thus, we reveal physical properties of the cytoplasm as a major determinant in organelle size control.
Cellular morphodynamics as quantifiers for functional states of resident tissue macrophages in vivo
Miriam Schnitzerlein,
Eric Greto,
Anja Wegner,
Anna Möller,
Oliver Aust,
Oumaima Ben Brahim,
David B. Blumenthal,
Vasily Zaburdaev,
Stefan Uderhardt, et al.
PLOS Computational Biology
21
e1011859
(2025)
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Resident tissue macrophages (RTMs) are essential for tissue homeostasis. Their diverse functions, from monitoring interstitial fluids to clearing cellular debris, are accompanied by characteristic morphological changes that reflect their functional status. While current knowledge of macrophage behaviour comes primarily from in vitro studies, their dynamic behavior in vivo is fundamentally different, necessitating a more physiologically relevant approach to their understanding. In this study, we employed intravital imaging to generate dynamic data from peritoneal RTMs in mice under various conditions and developed a comprehensive image processing pipeline to quantify RTM morphodynamics over time, defining human-interpretable cell size and shape features. These features allowed for the quantitative and qualitative differentiation of cell populations in various functional states, including pro- and anti-inflammatory activation and endosomal dysfunction. The study revealed that under steady-state conditions, RTMs exhibit a wide range of morphodynamical phenotypes, constituting a naïve morphospace of behavioral motifs. Upon challenge, morphodynamic patterns changed uniformly at the population level but predominantly within the constraints of this naïve morphospace. Notably, aged animals displayed a markedly shifted naïve morphospace, indicating drastically different behavioral patterns compared to their young counterparts. The developed method also proved valuable in optimizing explanted tissue setups, bringing RTM behavior closer to the physiological native state. Our versatile approach thus provides novel insights into the dynamic behavior of bona fide macrophages in vivo, enabling the distinction between physiological and pathological cell states and the assessment of functional tissue age on a population level.
Hierarchical Heterogeneities in Spatio-Temporal Dynamics of the Cytoplasm
Understanding of the dynamics inherent to biological matter is crucial for illuminating the physical mechanisms underlying cellular processes. In this study, we employ bright-field differential dynamic microscopy (DDM) to investigate density fluctuations inherent in a cell-free model of eukaryotic cytoplasm. Our measurements reveal subdiffusive fractional Brownian motion and non-Gaussian displacement distributions, highlighting cytoplasmic heterogeneity. We introduce an empirical model that combines fractional Brownian motion with an inverse Gaussian distribution of diffusivities to describe the observed non-Gaussianity. Validated through Monte Carlo simulations, this model allows us to estimate the fractional diffusivity and exponent effectively. By altering macromolecular composition, the addition of energy, and assembly of a cytoskeleton, we identify three independent mechanisms that result in similar fractional exponents yet distinct diffusivities. We find that energy addition leads to non-stationary dynamics, in contrast to the stationary behavior observed under passive conditions. Presence of microtubules introduces a secondary dynamical timescale, which we describe using a two-state fractional Brownian motion model to differentiate between cytosolic and microtubule network associated contributions. Our findings demonstrate the effectiveness of DDM as a label-free tool for quantifying viscoelastic and heterogeneous properties of the cytoplasm and provide insights into how physical and biochemical factors, including cytoskeletal organization, govern subcellular dynamics.
Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges
Suyen Solange Espinoza Miranda,
Gorkhmaz Abbaszade,
Wolfgang R. Hess,
Knut Drescher,
Antoine-Emmanuel Saliba,
Vasily Zaburdaev,
Liraz Chai,
Klaus Dreisewerd,
Alexander Grünberger, et al.
Microbiology and Molecular Biology Reviews
89
e00138-24
(2025)
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The development of multicellularity represents a key evolutionary transition that is crucial for the emergence of complex life forms. Although multicellularity has traditionally been studied in eukaryotes, it originates in prokaryotes. Coordinated aggregation of individual cells within the confines of a colony results in emerging, higher-level functions that benefit the population as a whole. During colony differentiation, an almost infinite number of ecological and physiological population-forming forces are at work, creating complex, intricate colony structures with divergent functions. Understanding the assembly and dynamics of such populations requires resolving individual cells or cell groups within such macroscopic structures. Addressing how each cell contributes to the collective action requires pushing the resolution boundaries of key technologies that will be presented in this review. In particular, single-cell techniques provide powerful tools for studying bacterial multicellularity with unprecedented spatial and temporal resolution. These advancements include novel microscopic techniques, mass spectrometry imaging, flow cytometry, spatial transcriptomics, single-bacteria RNA sequencing, and the integration of spatiotemporal transcriptomics with microscopy, alongside advanced microfluidic cultivation systems. This review encourages exploring the synergistic potential of the new technologies in the study of bacterial multicellularity, with a particular focus on individuals in differentiated bacterial biofilms (colonies). It highlights how resolving population structures at the single-cell level and understanding their respective functions can elucidate the overarching functions of bacterial multicellular populations.
Kontakt
Abteilung Immunophysik Prof. Vasily Zaburdaev Principal Investigator
Max-Planck-Zentrum für Physik und Medizin Kussmaulallee 2 Raum 02.116 91054 Erlangen 09131 8284 102
