Physical biology最新文献

The tubular network-forming slime moldPhysarum polycephalumis able to maintain long-scale contraction patterns driven by an actomyosin cortex. The resulting shuttle streaming in the network is crucial for the organism to respond to external stimuli and reorganize its body mass giving rise to complex behaviors. However, the chemical basis of the self-organized flow pattern is not fully understood. Here, we present ratiometric measurements of free intracellular calcium in simple morphologies ofPhysarumnetworks. The spatiotemporal patterns of the free calcium concentration reveal a nearly anti-correlated relation to the tube radius, suggesting that calcium is indeed a key regulator of the actomyosin activity. We compare the experimentally observed phase relation between the radius and the calcium concentration to the predictions of a theoretical model including calcium as an inhibitor. Numerical simulations of the model suggest that calcium indeed inhibits the contractions inPhysarum, although a quantitative difference to the experimentally measured phase relation remains. Unraveling the mechanism underlying the contraction patterns is a key step in gaining further insight into the principles ofPhysarum's complex behavior.

The technique presented here identifies tethered mould designs, optimised for growing cultured tissue with very highly-aligned cells. It is based on a microscopic biophysical model for polarised cellular hydrogels. There is an unmet need for tools to assist mould and scaffold designs for the growth of cultured tissues with bespoke cell organisations, that can be used in applications such as regenerative medicine, drug screening and cultured meat. High-throughput biophysical calculations were made for a wide variety of computer-generated moulds, with cell-matrix interactions and tissue-scale forces simulated using a contractile network dipole orientation model. Elongated moulds with central broadening and one of the following tethering strategies are found to lead to highly-aligned cells: (1) tethers placed within the bilateral protrusions resulting from an indentation on the short edge, to guide alignment (2) tethers placed within a single vertex to shrink the available space for misalignment. As such, proof-of-concept has been shown for mould and tethered scaffold design based on a recently developed biophysical model. The approach is applicable to a broad range of cell types that align in tissues and is extensible for 3D scaffolds.

The interactions between cells and the extracellular matrix are vital for the self-organisation of tissues. In this paper we present proof-of-concept to use machine learning tools to predict the role of this mechanobiology in the self-organisation of cell-laden hydrogels grown in tethered moulds. We develop a process for the automated generation of mould designs with and without key symmetries. We create a large training set withN = 6400 cases by running detailed biophysical simulations of cell-matrix interactions using the contractile network dipole orientation model for the self-organisation of cellular hydrogels within these moulds. These are used to train an implementation of thepix2pixdeep learning model, with an additional 100 cases that were unseen in the training of the neural network for review and testing of the trained model. Comparison between the predictions of the machine learning technique and the reserved predictions from the biophysical algorithm show that the machine learning algorithm makes excellent predictions. The machine learning algorithm is significantly faster than the biophysical method, opening the possibility of very high throughput rational design of moulds for pharmaceutical testing, regenerative medicine and fundamental studies of biology. Future extensions for scaffolds and 3D bioprinting will open additional applications.

It is now established that endo-lysosomes, also referred to as late endosomes, serve as intracellular calcium store, in addition to the endoplasmic reticulum. While abundant calcium-binding proteins provide the latter compartment with its calcium storage capacity, essentially nothing is known about the mechanism responsible for calcium storage in endo-lysosomes. In this paper, we propose that the structural organization of endo-lysosomal membranes drives the calcium storage capacity of the compartment. Indeed, endo-lysosomes exhibit a characteristic multivesicular ultrastructure, with intralumenal membranes providing a large amount of additional bilayer surface. We used a theoretical approach to investigate the calcium storage capacity of endosomes, using known calcium binding affinities for bilayers and morphological data on endo-lysosome membrane organization. Finally, we tested our predictions experimentally after Sorting Nexin 3 depletion to decrease the intralumenal membrane content. We conclude that the major negatively-charge lipids and proteins of endo-lysosomes serve as calcium-binding molecules in the acidic calcium stores of mammalian cells, while the large surface area of intralumenal membranes provide the necessary storage capacity.

Searching for a target is a task of fundamental importance for many living organisms. Long-distance search guided by olfactory cues is a prototypical example of such a process. The searcher receives signals that are sparse and very noisy, making the task extremely difficult. Information-seeking strategies have thus been proven to be effective for individual olfactory search and their extension to collective search has been the subject of some exploratory studies. Here, we study in detail how sharing information among members of a group affects the search behavior when agents adopt information-seeking strategies as Infotaxis and its recently introduced variant, Space-Aware Infotaxis. Our results show that even in absence of explicit coordination, sharing information leads to an effective partitioning of the search space among agents that results in a significant decrease of mean search times.

Contemporary approaches to instance segmentation in cell science use 2D or 3D convolutional networks depending on the experiment and data structures. However, limitations in microscopy systems or efforts to prevent phototoxicity commonly require recording sub-optimally sampled data that greatly reduces the utility of such 3D data, especially in crowded sample space with significant axial overlap between objects. In such regimes, 2D segmentations are both more reliable for cell morphology and easier to annotate. In this work, we propose the projection enhancement network (PEN), a novel convolutional module which processes the sub-sampled 3D data and produces a 2D RGB semantic compression, and is trained in conjunction with an instance segmentation network of choice to produce 2D segmentations. Our approach combines augmentation to increase cell density using a low-density cell image dataset to train PEN, and curated datasets to evaluate PEN. We show that with PEN, the learned semantic representation in CellPose encodes depth and greatly improves segmentation performance in comparison to maximum intensity projection images as input, but does not similarly aid segmentation in region-based networks like Mask-RCNN. Finally, we dissect the segmentation strength against cell density of PEN with CellPose on disseminated cells from side-by-side spheroids. We present PEN as a data-driven solution to form compressed representations of 3D data that improve 2D segmentations from instance segmentation networks.

Cells communicate with each other to jointly regulate cellular processes during cellular differentiation and tissue morphogenesis. This multiscale coordination arises through the spatiotemporal activity of morphogens to pattern cell signaling and transcriptional factor activity. This coded information controls cell mechanics, proliferation, and differentiation to shape the growth and morphogenesis of organs. While many of the molecular components and physical interactions have been identified in key model developmental systems, there are still many unresolved questions related to the dynamics involved due to challenges in precisely perturbing and quantitatively measuring signaling dynamics. Recently, a broad range of synthetic optogenetic tools have been developed and employed to quantitatively define relationships between signal transduction and downstream cellular responses. These optogenetic tools can control intracellular activities at the single cell or whole tissue scale to direct subsequent biological processes. In this brief review, we highlight a selected set of studies that develop and implement optogenetic tools to unravel quantitative biophysical mechanisms for tissue growth and morphogenesis across a broad range of biological systems through the manipulation of morphogens, signal transduction cascades, and cell mechanics. More generally, we discuss how optogenetic tools have emerged as a powerful platform for probing and controlling multicellular development.

Understanding the collective physical processes that drive robust morphological transitions in animal development necessitates the characterization of the relevant fields involved in morphogenesis. Calcium (Ca²⁺) is recognized as one such field. In this study, we demonstrate that the spatial fluctuations of Ca²⁺duringHydraregeneration exhibit universal characteristics. To investigate this phenomenon, we employ two distinct controls, an external electric field andheptanol, a gap junction-blocking drug. Both lead to the modulation of the Ca²⁺activity and a reversible halting of the regeneration process. The application of an electric field enhances Ca²⁺activity in theHydra's tissue and increases its spatial correlations, while the administration ofheptanolinhibits its activity and diminishes the spatial correlations. Remarkably, the statistical characteristics of Ca²⁺spatial fluctuations, including the coefficient of variation and skewness, manifest universal shape distributions across tissue samples and conditions. We introduce a field-theoretic model, describing fluctuations in a tilted double-well potential, which successfully captures these universal properties. Moreover, our analysis reveals that the Ca²⁺activity is spatially localized, and theHydra's tissue operates near the onset of bistability, where the local Ca²⁺activity fluctuates between low and high excited states in distinct regions. These findings highlight the prominent role of the Ca²⁺field inHydramorphogenesis and provide insights into the underlying mechanisms governing robust morphological transitions.

Epithelial-mesenchymal transition (EMT) is a key cellular transformation for many physiological and pathological processes ranging from cancer over wound healing to embryogenesis. Changes in cell migration, cell morphology and cellular contractility were identified as hallmarks of EMT. These cellular properties are known to be tightly regulated by the actin cytoskeleton. EMT-induced changes of actin-cytoskeletal regulation were demonstrated by previous reports of changes of actin cortex mechanics in conjunction with modifications of cortex-associated f-actin and myosin. However, at the current state, the changes of upstream actomyosin signaling that lead to corresponding mechanical and compositional changes of the cortex are not well understood. In this work, we show in breast epithelial cancer cells MCF-7 that EMT results in characteristic changes of the cortical association of Rho-GTPases Rac1, RhoA and RhoC and downstream actin regulators cofilin, mDia1 and Arp2/3. In the light of our findings, we propose that EMT-induced changes in cortical mechanics rely on two hitherto unappreciated signaling paths-i) an interaction between Rac1 and RhoC and ii) an inhibitory effect of Arp2/3 activity on cortical association of myosin II.