Seeing around corners: Cells solve mazes and respond at a distance using attractant breakdown

Self-extinguishing relay waves enable homeostatic control of human neutrophil swarming

Neutrophils collectively migrate to sites of injury and infection. How these swarms are coordinated to ensure the proper level of recruitment is unknown. Using an ex vivo model of infection, we show that human neutrophil swarming is organized by multiple pulsatile chemoattractant waves. These waves propagate through active relay in which stimulated neutrophils trigger their neighbors to release additional swarming cues. Unlike canonical active relays, we find these waves to be self-terminating, limiting the spatial range of cell recruitment. We identify an NADPH-oxidase-based negative feedback loop that is needed for this self-terminating behavior. We observe near-constant levels of neutrophil recruitment over a wide range of starting conditions, revealing surprising robustness in the swarming process. This homeostatic control is achieved by larger and more numerous swarming waves at lower cell densities. We link defective wave termination to a broken recruitment homeostat in the context of human chronic granulomatous disease.

Impacts of permeability and effective diffusivity of porous scaffolds on bone ingrowth: In silico and in vivo analyses

The permeability and the effective diffusivity of a porous scaffold are critical in the bone-ingrowth process. However, design guidelines for porous structures are still lacking due to inadequate understanding of the complex physiological processes involved. In this study, a model integrating the fundamental biological processes of bone regeneration was constructed to investigate the roles of permeability and effective diffusivity in regulating bone deposition in scaffolds. The in silico analysis results were confirmed in vivo by examining bone depositions in three diamond lattice scaffolds manufactured using selective laser melting. The findings show that the scaffolds with better permeability and effective diffusivity had deeper bone ingrowth and greater bone volume. Compared to permeability, effective diffusivity exhibited greater sensitivity to the orientation of porous structures, and bone ingrowth was deeper in the directions with higher effective diffusivity in spite of identical pore size. A 4.8-fold increase in permeability and a 1.6-fold increase in effective diffusivity by changing the porous structure led to a 1.5-fold increase in newly formed bone. The effective diffusivity of the porous scaffold affects the distribution of osteogenic growth factor, which in turn impacts cell migration and bone deposition through chemotaxis effects. Therefore, effective diffusivity may be a more suitable indicator for porous scaffolds because our study shows changes in this parameter determine changes in bone distribution and bone volume.

Quorum Sensing in Emulsion Droplet Swarms Driven by a Surfactant Competition System

Quorum sensing enables unicellular organisms to probe their population density and perform behavior that exclusively occurs above a critical density. Quorum sensing is established in emulsion droplet swarms that float at a water surface and cluster above a critical density. The design involves competition between 1) a surface tension gradient that is generated upon release of a surfactant from the oil droplets, and thereby drives their mutual repulsion, and 2) the release of a surfactant precursor from the droplets, that forms a strong imine surfactant which suppresses the surface tension gradient and thereby causes droplet clustering upon capillary (Cheerios) attraction. The production of the imine-surfactant depends on the population density of the droplets releasing the precursor so that the clustering only occurs above a critical population density. The pH-dependence of the imine-surfactant formation is exploited to trigger quorum sensing upon a base stimulus: dynamic droplet swarms are generated that cluster and spread upon spatiotemporally varying acid and base conditions. Next, the clustering of two droplet subpopulations is coupled to a chemical reaction that generates a fluorescent signal. It is foreseen that quorum sensing enables control mechanisms in droplet-based systems that display collective responses in contexts of, e.g., sensing, optics, or dynamically controlled droplet-reactors.

Cancer cell sedimentation in 3D cultures reveals active migration regulated by self-generated gradients and adhesion sites

Cell sedimentation in 3D hydrogel cultures refers to the vertical migration of cells towards the bottom of the space. Understanding this poorly examined phenomenon may allow us to design better protocols to prevent it, as well as provide insights into the mechanobiology of cancer development. We conducted a multiscale experimental and mathematical examination of 3D cancer growth in triple negative breast cancer cells. Migration was examined in the presence and absence of Paclitaxel, in high and low adhesion environments and in the presence of fibroblasts. The observed behaviour was modeled by hypothesizing active migration due to self-generated chemotactic gradients. Our results did not reject this hypothesis, whereby migration was likely to be regulated by the MAPK and TGF-β pathways. The mathematical model enabled us to describe the experimental data in absence (normalized error<40%) and presence of Paclitaxel (normalized error<10%), suggesting inhibition of random motion and advection in the latter case. Inhibition of sedimentation in low adhesion and co-culture experiments further supported the conclusion that cells actively migrated downwards due to the presence of signals produced by cells already attached to the adhesive glass surface.

Deposited footprints let cells switch between confined, oscillatory, and exploratory migration

For eukaryotic cells to heal wounds, respond to immune signals, or metastasize, they must migrate, often by adhering to extracellular matrix (ECM). Cells may also deposit ECM components, leaving behind a footprint that influences their crawling. Recent experiments showed that some epithelial cell lines on micropatterned adhesive stripes move persistently in regions they have previously crawled over, where footprints have been formed, but barely advance into unexplored regions, creating an oscillatory migration of increasing amplitude. Here, we explore through mathematical modeling how footprint deposition and cell responses to footprint combine to allow cells to develop oscillation and other complex migratory motions. We simulate cell crawling with a phase field model coupled to a biochemical model of cell polarity, assuming local contact with the deposited footprint activates Rac1, a protein that establishes the cell's front. Depending on footprint deposition rate and response to the footprint, cells on micropatterned lines can display many types of motility, including confined, oscillatory, and persistent motion. On two-dimensional (2D) substrates, we predict a transition between cells undergoing circular motion and cells developing an exploratory phenotype. Small quantitative changes in a cell's interaction with its footprint can completely alter exploration, allowing cells to tightly regulate their motion, leading to different motility phenotypes (confined vs. exploratory) in different cells when deposition or sensing is variable from cell to cell. Consistent with our computational predictions, we find in earlier experimental data evidence of cells undergoing both circular and exploratory motion.

Deposited footprints let cells switch between confined, oscillatory, and exploratory migration

For eukaryotic cells to heal wounds, respond to immune signals, or metastasize, they must migrate, often by adhering to extracellular matrix. Cells may also deposit extracellular matrix components, leaving behind a footprint that influences their crawling. Recent experiments showed that some epithelial cells on micropatterned adhesive stripes move persistently in regions they have previously crawled over, where footprints have been formed, but barely advance into unexplored regions, creating an oscillatory migration of increasing amplitude. Here, we explore through mathematical modeling how footprint deposition and cell responses to footprint combine to allow cells to develop oscillation and other complex migratory motions. We simulate cell crawling with a phase field model coupled to a biochemical model of cell polarity, assuming local contact with the deposited footprint activates Rac1, a protein that establishes the cell's front. Depending on footprint deposition rate and response to the footprint, cells on micropatterned lines can display many types of motility, including confined, oscillatory, and persistent motion. On two-dimensional substrates, we predict a transition between cells undergoing circular motion and cells developing an exploratory phenotype. Small quantitative changes in a cell's interaction with its footprint can completely alter exploration, allowing cells to tightly regulate their motion, leading to different motility phenotypes (confined vs exploratory) in different cells when deposition or sensing is variable from cell to cell. Consistent with our computational predictions, we find in earlier experimental data evidence of cells undergoing both circular and exploratory motion.

Immune cell trafficking: a novel perspective on the gut-skin axis

Immune cell trafficking, an essential mechanism for maintaining immunological homeostasis and mounting effective responses to infections, operates under a stringent regulatory framework. Recent advances have shed light on the perturbation of cell migration patterns, highlighting how such disturbances can propagate inflammatory diseases from their origin to distal organs. This review collates and discusses current evidence that demonstrates atypical communication between the gut and skin, which are conventionally viewed as distinct immunological spheres, in the milieu of inflammation. We focus on the aberrant, reciprocal translocation of immune cells along the gut-skin axis as a pivotal factor linking intestinal and dermatological inflammatory conditions. Recognizing that the translation of these findings into clinical practices is nascent, we suggest that therapeutic strategies aimed at modulating the axis may offer substantial benefits in mitigating the widespread impact of inflammatory diseases.

pH-regulated single cell migration

Over the last two decades, extra- and intracellular pH have emerged as fundamental regulators of cell motility. Fundamental physiological and pathological processes relying on appropriate cell migration, such as embryonic development, wound healing, and a proper immune defense on the one hand, and autoimmune diseases, metastatic cancer, and the progression of certain parasitic diseases on the other, depend on surrounding pH. In addition, migrating single cells create their own localized pH nanodomains at their surface and in the cytosol. By this means, the migrating cells locally modulate their adhesion to, and the re-arrangement and digestion of, the extracellular matrix. At the same time, the cytosolic nanodomains tune cytoskeletal dynamics along the direction of movement resulting in concerted lamellipodia protrusion and rear end retraction. Extracellular pH gradients as found in wounds, inflamed tissues, or the periphery of tumors stimulate directed cell migration, and long-term exposure to acidic conditions can engender a more migratory and invasive phenotype persisting for hours up to several generations of cells after they have left the acidic milieu. In the present review, the different variants of pH-dependent single cell migration are described. The underlying pH-dependent molecular mechanisms such as conformational changes of adhesion molecules, matrix protease activity, actin (de-)polymerization, and signaling events are explained, and molecular pH sensors stimulated by H+ signaling are presented.

Size-dependent self-avoidance enables superdiffusive migration in macroscopic unicellulars

Many cells face search problems, such as finding food, mates, or shelter, where their success depends on their search strategy. In contrast to other unicellular organisms, the slime mold Physarum polycephalum forms a giant network-shaped plasmodium while foraging for food. What is the advantage of the giant cell on the verge of multicellularity? We experimentally study and quantify the migration behavior of P. polycephalum plasmodia on the time scale of days in the absence and presence of food. We develop a model which successfully describes its migration in terms of ten data-derived parameters. Using the mechanistic insights provided by our data-driven model, we find that regardless of the absence or presence of food, P. polycephalum achieves superdiffusive migration by performing a self-avoiding run-and-tumble movement. In the presence of food, the run duration statistics change, only controlling the short-term migration dynamics. However, varying organism size, we find that the long-term superdiffusion arises from self-avoidance determined by cell size, highlighting the potential evolutionary advantage that this macroscopically large cell may have.

Frequency Propagation: Multimechanism Learning in Nonlinear Physical Networks

We introduce frequency propagation, a learning algorithm for nonlinear physical networks. In a resistive electrical circuit with variable resistors, an activation current is applied at a set of input nodes at one frequency and an error current is applied at a set of output nodes at another frequency. The voltage response of the circuit to these boundary currents is the superposition of an activation signal and an error signal whose coefficients can be read in different frequencies of the frequency domain. Each conductance is updated proportionally to the product of the two coefficients. The learning rule is local and proved to perform gradient descent on a loss function. We argue that frequency propagation is an instance of a multimechanism learning strategy for physical networks, be it resistive, elastic, or flow networks. Multimechanism learning strategies incorporate at least two physical quantities, potentially governed by independent physical mechanisms, to act as activation and error signals in the training process. Locally available information about these two signals is then used to update the trainable parameters to perform gradient descent. We demonstrate how earlier work implementing learning via chemical signaling in flow networks (Anisetti, Scellier, et al., 2023) also falls under the rubric of multimechanism learning.

Cell motility: Bioelectrical control of behavior without neurons

Single cells are capable of remarkably sophisticated, sometimes animal-like, behaviors. New work demonstrates bioelectric control of motility through the differential regulation of appendage movements in a unicellular organism that walks across surfaces using leg-like bundles of cilia.

Perspectives on Principles of Cellular Behavior from the Biophysics of Protists

Cells are the fundamental unit of biological organization. Although it may be easy to think of them as little more than the simple building blocks of complex organisms such as animals, single cells are capable of behaviors of remarkable apparent sophistication. This is abundantly clear when considering the diversity of form and function among the microbial eukaryotes, the protists. How might we navigate this diversity in the search for general principles of cellular behavior? Here, we review cases in which the intensive study of protists from the perspective of cellular biophysics has driven insight into broad biological questions of morphogenesis, navigation and motility, and decision making. We argue that applying such approaches to questions of evolutionary cell biology presents rich, emerging opportunities. Integrating and expanding biophysical studies across protist diversity, exploiting the unique characteristics of each organism, will enrich our understanding of general underlying principles.

Collective signalling drives rapid jumping between cell states

Development can proceed in 'fits and starts', with rapid transitions between cell states involving concerted transcriptome-wide changes in gene expression. However, it is not clear how these transitions are regulated in complex cell populations, in which cells receive multiple inputs. We address this issue using Dictyostelium cells undergoing development in their physiological niche. A continuous single cell transcriptomics time series identifies a sharp 'jump' in global gene expression marking functionally different cell states. By simultaneously imaging the physiological dynamics of transcription and signalling, we show the jump coincides with the onset of collective oscillations of cAMP. Optogenetic control of cAMP pulses shows that different jump genes respond to distinct dynamic features of signalling. Late jump gene expression changes are almost completely dependent on cAMP, whereas transcript changes at the onset of the jump require additional input. The coupling of collective signalling with gene expression is a potentially powerful strategy to drive robust cell state transitions in heterogeneous signalling environments. Based on the context of the jump, we also conclude that sharp gene expression transitions may not be sufficient for commitment.

Environmental memory boosts group formation of clueless individuals

The formation of groups of interacting individuals improves performance and fitness in many decentralised systems, from micro-organisms to social insects, from robotic swarms to artificial intelligence algorithms. Often, group formation and high-level coordination in these systems emerge from individuals with limited information-processing capabilities implementing low-level rules of communication to signal to each other. Here, we show that, even in a community of clueless individuals incapable of processing information and communicating, a dynamic environment can coordinate group formation by transiently storing memory of the earlier passage of individuals. Our results identify a new mechanism of indirect coordination via shared memory that is primarily promoted and reinforced by dynamic environmental factors, thus overshadowing the need for any form of explicit signalling between individuals. We expect this pathway to group formation to be relevant for understanding and controlling self-organisation and collective decision making in both living and artificial active matter in real-life environments.

Active oscillations in microscale navigation

Living organisms routinely navigate their surroundings in search of better conditions, more food, or to avoid predators. Typically, animals do so by integrating sensory cues from the environment with their locomotor apparatuses. For single cells or small organisms that possess motility, fundamental physical constraints imposed by their small size have led to alternative navigation strategies that are specific to the microscopic world. Intriguingly, underlying these myriad exploratory behaviours or sensory functions is the onset of periodic activity at multiple scales, such as the undulations of cilia and flagella, the vibrations of hair cells, or the oscillatory shape modes of migrating neutrophils. Here, I explore oscillatory dynamics in basal microeukaryotes and hypothesize that these active oscillations play a critical role in enhancing the fidelity of adaptive sensorimotor integration.

Tumour follower cells: A novel driver of leader cells in collective invasion (Review)

Collective cellular invasion in malignant tumours is typically characterized by the cooperative migration of multiple cells in close proximity to each other. Follower cells are led away from the tumour by specialized leader cells, and both cell populations play a crucial role in collective invasion. Follower cells form the main body of the migration system and depend on intercellular contact for migration, whereas leader cells indicate the direction for the entire cell population. Although collective invasion can occur in epithelial and non‑epithelial malignant neoplasms, such as medulloblastoma and rhabdomyosarcoma, the present review mainly provided an extensive analysis of epithelial tumours. In the present review, the cooperative mechanisms of contact inhibition locomotion between follower and leader cells, where follower cells coordinate and direct collective movement through physical (mechanical) and chemical (signalling) interactions, is summarised. In addition, the molecular mechanisms of follower cell invasion and metastasis during remodelling and degradation of the extracellular matrix and how chemotaxis and lateral inhibition mediate follower cell behaviour were analysed. It was also demonstrated that follower cells exhibit genetic and metabolic heterogeneity during invasion, unlike leader cells.

CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration

Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein-coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.

Sinking while you swim: A dual role for CCR7 in leukocyte migration

The CCR7 receptor allows dendritic cells to sense the chemokine CCL19. It also depletes CCL19 from the environment by endocytosis, leading to local gradients that can steer cells accurately and robustly through tissues, even over long distances (see related Research Article by Alanko et al.).

Future medicine: from molecular pathways to the collective intelligence of the body

The remarkable anatomical homeostasis exhibited by complex living organisms suggests that they are inherently reprogrammable information-processing systems that offer numerous interfaces to their physiological and anatomical problem-solving capacities. We briefly review data suggesting that the multiscale competency of living forms affords a new path for biomedicine that exploits the innate collective intelligence of tissues and organs. The concept of tissue-level allostatic goal-directedness is already bearing fruit in clinical practice. We sketch a roadmap towards 'somatic psychiatry' by using advances in bioelectricity and behavioral neuroscience to design methods that induce self-repair of structure and function. Relaxing the assumption that cellular control mechanisms are static, exploiting powerful concepts from cybernetics, behavioral science, and developmental biology may spark definitive solutions to current biomedical challenges.

Anomalous diffusion of E. coli under microfluidic confinement and chemical gradient

We report a two-layer microfluidic device to study the combined effect of confinement and chemical gradient on the motility of wild-type E. coli. We track individual E. coli in 50 μm and 10 μm wide microchannels, with a channel height of 2 μm, to generate quasi-2D conditions. We find that contrary to expectations, bacterial trajectories are superdiffusive even in the absence of a chemical (glucose) gradient. The superdiffusive behaviour becomes more pronounced upon introducing a chemical gradient or strengthening the lateral confinement. Run length distributions for weak lateral confinement in the absence of chemical gradients follow an exponential distribution. Both confinement and chemoattraction induce deviations from this behaviour, with the run length distributions approaching a power-law form under these conditions. Both confinement and chemoattraction suppress large-angle tumbles as well. Our results suggest that wild-type E. coli modulates both its runs and tumbles in a similar manner under physical confinement and chemical gradient. Our findings have implications for understanding how bacteria modulate their motility behaviour in natural habitats.

Chemorepulsion: Moving away from improper attractions

Eukaryotic cells can undergo chemorepulsion, but the molecular mechanisms behind this phenomenon have remained unclear. Using Dictyostelium cells, a new study shows that competition of two ligands for the same receptors results in chemorepulsion, thus revealing a simple rule for eukaryotic cells to achieve negative chemotaxis.

Competition between chemoattractants causes unexpected complexity and can explain negative chemotaxis

Negative chemotaxis, where eukaryotic cells migrate away from repellents, is important throughout biology, for example, in nervous system patterning and resolution of inflammation. However, the mechanisms by which molecules repel migrating cells are unknown. Here, we use predictive modeling and experiments with Dictyostelium cells to show that competition between different ligands that bind to the same receptor leads to effective chemorepulsion. 8-CPT-cAMP, widely described as a simple chemorepellent, is inactive on its own and only repels cells when it acts in combination with the attractant cAMP. If cells degrade either competing ligand, the pattern of migration becomes more complex; cells may be repelled in one part of a gradient but attracted elsewhere, leading to populations moving in different directions in the same assay or converging in an arbitrary place. More counterintuitively still, two chemicals that normally attract cells can become repellent when combined. Computational models of chemotaxis are now accurate enough to predict phenomena that have not been anticipated by experiments. We have used them to identify new mechanisms that drive reverse chemotaxis, which we have confirmed through experiments with real cells. These findings are important whenever multiple ligands compete for the same receptors.

The cell's dilemma: resolving directional decisions

How neutrophils make decisions about polarity and migration path in complex tissue environments in situ remains unclear. Hadjitheodorou et al. describe how an internal mechanical regulator might help cells resolve the dilemma of two competing cell fronts.

Receptors, enzymes and self-attraction as autocrine generators and amplifiers of chemotaxis and cell steering

Cells create their own steering cues, or modify cues from their outside, for a number of reasons. These include generating optimal, legible directional information; probing their environments for information to help decide an optimal route; symmetry breaking; generating new patterns and complexity; and bringing together collectives such as neutrophil swarms. Recent advances include more mechanisms of self-steering, in particular by using cell-generated mechanical cues, and gradients of respired oxygen. An increasing number of cell types are being found to use self-steering, in particular immune cells responding to chemokines and mesodermal cells during gastrulation. Finally, receptor modification has emerged as an important limit on the range of neutrophil swarming, allowing cells to monitor other areas as well as coming together. Self-steering is thus emerging as a dominant feature of cell motility.

ACKR3 promotes CXCL12/CXCR4-mediated cell-to-cell-induced lymphoma migration through LTB4 production

Chemotaxis is an essential physiological process, often harnessed by tumors for metastasis. CXCR4, its ligand CXCL12 and the atypical receptor ACKR3 are overexpressed in many human cancers. Interfering with this axis by ACKR3 deletion impairs lymphoma cell migration towards CXCL12. Here, we propose a model of how ACKR3 controls the migration of the diffused large B-cell lymphoma VAL cells in vitro and in vivo in response to CXCL12. VAL cells expressing full-length ACKR3, but not a truncated version missing the C-terminus, can support the migration of VAL cells lacking ACKR3 (VAL-ko) when allowed to migrate together. This migration of VAL-ko cells is pertussis toxin-sensitive suggesting the involvement of a Gi-protein coupled receptor. RNAseq analysis indicate the expression of chemotaxis-mediating LTB4 receptors in VAL cells. We found that LTB4 acts synergistically with CXCL12 in stimulating the migration of VAL cells. Pharmacologic or genetic inhibition of BLT1R markedly reduces chemotaxis towards CXCL12 suggesting that LTB4 enhances in a contact-independent manner the migration of lymphoma cells. The results unveil a novel mechanism of cell-to-cell-induced migration of lymphoma.

Ariadne’s thread and the extension of cognition: A common but overlooked phenomenon in nature?

Over recent decades, our philosophical and scientific understanding of cognition has changed dramatically. We went from conceiving humans as the sole truly cognitive species on the planet to endowing several organisms with cognitive capacities, from considering brains as the exclusive seat of cognition to extending cognitive faculties to the entire physical body and beyond. That cognition could extend beyond the organism’s body is no doubt one of the most controversial of the recent hypotheses. Extended cognition (ExC) has been discussed not only to explain aspects of the human cognitive process, but also of other species such as spiders and more recently, plants. It has been suggested that ExC could offer insights for the grounding of environmentally extended cognitive traits in evolved ecological functions. Here, we reviewed the ecological literature for possible ExC examples that satisfy the mutual manipulability criterion, which can be used to establish experimentally the boundaries of cognitive systems. Our conclusion is that ExC might be far more common than previously thought, and present in organisms as diverse as plants, fungi, termites, spiders, mammals, and slime moulds. Experimental investigation is needed to clarify this idea which, if proven correct, could illuminate a new path into understanding the origins and evolution of cognition.

The physics of boundary conditions in reaction-diffusion problems

The use of fully or partially absorbing boundary conditions for diffusion-based problems has become paradigmatic in physical chemistry and biochemistry to describe reactions occurring in solutions or in living media. However, as chemical states may indeed disappear, particles cannot, unless such degradation happens physically and should, thus, be accounted for explicitly. Here, we introduce a simple, yet general idea that allows one to derive the appropriate boundary conditions self-consistently from the chemical reaction scheme and the geometry of the physical reaction boundaries. As an illustration, we consider two paradigmatic examples, where the known results are recovered by taking specific physical limits. More generally, we demonstrate that our mathematical analysis delivers physical insight that cannot be accessed through standard treatments.

Self-generated gradients steer collective migration on viscoelastic collagen networks

Growing evidence suggests that the physical properties of the cellular microenvironment influence cell migration. However, it is not currently understood how active physical remodelling by cells affects migration dynamics. Here we report that cell clusters seeded on deformable collagen-I networks display persistent collective migration despite not showing any apparent intrinsic polarity. Clusters generate transient gradients in collagen density and alignment due to viscoelastic relaxation of the collagen networks. Combining theory and experiments, we show that crosslinking collagen networks or reducing cell cluster size results in reduced network deformation, shorter viscoelastic relaxation time and smaller gradients, leading to lower migration persistence. Traction force and Brillouin microscopy reveal asymmetries in force distributions and collagen stiffness during migration, providing evidence of mechanical cross-talk between cells and their substrate during migration. This physical model provides a mechanism for self-generated directional migration on viscoelastic substrates in the absence of internal biochemical polarity cues.

A self-generated Toddler gradient guides mesodermal cell migration

The sculpting of germ layers during gastrulation relies on the coordinated migration of progenitor cells, yet the cues controlling these long-range directed movements remain largely unknown. While directional migration often relies on a chemokine gradient generated from a localized source, we find that zebrafish ventrolateral mesoderm is guided by a self-generated gradient of the initially uniformly expressed and secreted protein Toddler/ELABELA/Apela. We show that the Apelin receptor, which is specifically expressed in mesodermal cells, has a dual role during gastrulation, acting as a scavenger receptor to generate a Toddler gradient, and as a chemokine receptor to sense this guidance cue. Thus, we uncover a single receptor-based self-generated gradient as the enigmatic guidance cue that can robustly steer the directional migration of mesoderm through the complex and continuously changing environment of the gastrulating embryo.

Inherency and agency in the origin and evolution of biological functions

Although discussed by 20th century philosophers in terms drawn from the sciences of non-living systems, in recent decades biological function has been considered in relationship to organismal capability and purpose. Bringing two phenomena generally neglected in evolutionary theory (i.e. inherency and agency) to bear on questions of function leads to a rejection of the adaptationist ‘selected effects’ notion of biological function. I review work showing that organisms such as the placozoans can thrive with almost no functional embellishments beyond those of their constituent cells and physical properties of their simple tissues. I also discuss work showing that individual tissue cells and their artificial aggregates exhibit agential behaviours that are unprecedented in the histories of their respective lineages. I review findings on the unique metazoan mechanism of developmental gene expression that has recruited, during evolution, inherent ancestral cellular functionalities into specialized cell types and organs of the different animal groups. I conclude that most essential functions in animal species are inherent to the cells from which they evolved, not selected effects, and that many of the others are optional ‘add-ons’, a status inimical to fitness-based models of evolution positing that traits emerge from stringent cycles of selection to meet external challenges.

A unicellular walker controlled by a microtubule-based finite-state machine

Cells are complex biochemical systems whose behaviors emerge from interactions among myriad molecular components. Computation is often invoked as a general framework for navigating this cellular complexity. However, it is unclear how cells might embody computational processes such that the theories of computation, including finite-state machine models, could be productively applied. Here, we demonstrate finite-state-machine-like processing embodied in cells using the walking behavior of Euplotes eurystomus, a ciliate that walks across surfaces using fourteen motile appendages (cirri). We found that cellular walking entails regulated transitions among a discrete set of gait states. The set of observed transitions decomposes into a small group of high-probability, temporally irreversible transitions and a large group of low-probability, time-symmetric transitions, thus revealing stereotypy in the sequential patterns of state transitions. Simulations and experiments suggest that the sequential logic of the gait is functionally important. Taken together, these findings implicate a finite-state-machine-like process. Cirri are connected by microtubule bundles (fibers), and we found that the dynamics of cirri involved in different state transitions are associated with the structure of the fiber system. Perturbative experiments revealed that the fibers mediate gait coordination, suggesting a mechanical basis of gait control.

Interdisciplinary approaches to metastasis

Interdisciplinary research is making a significant contribution to understanding metastasis - one of the grand challenges in cancer research. Examples drawn from apparently unconnected areas of physics, and described at a recent workshop on metastasis, illustrate the value of interdiscplinary thinking.

Microfluidic Lab-on-a-Chip for Studies of Cell Migration under Spatial Confinement

Understanding cell migration is a key step in unraveling many physiological phenomena and predicting several pathologies, such as cancer metastasis. In particular, confinement has been proven to be a key factor in the cellular migration strategy choice. As our insight in the field improves, new tools are needed in order to empower biologists’ analysis capabilities. In this framework, microfluidic devices have been used to engineer the mechanical and spatial stimuli and to investigate cellular migration response in a more controlled way. In this work, we will review the existing technologies employed in the realization of microfluidic cellular migration assays, namely the soft lithography of PDMS and hydrogels and femtosecond laser micromachining. We will give an overview of the state of the art of these devices, focusing on the different geometrical configurations that have been exploited to study specific aspects of cellular migration. Our scope is to highlight the advantages and possibilities given by each approach and to envisage the future developments in in vitro migration studies under spatial confinement in microfluidic devices.

Collective behavior and nongenetic inheritance allow bacterial populations to adapt to changing environments

Collective behaviors require coordination among a group of individuals. As a result, individuals that are too phenotypically different from the rest of the group can be left out, reducing heterogeneity, but increasing coordination. If individuals also reproduce, the offspring can have different phenotypes from their parent(s). This raises the question of how these two opposing processes-loss of diversity by collective behaviors and generation of it through growth and inheritance-dynamically shape the phenotypic composition of an isogenic population. We examine this question theoretically using collective migration of chemotactic bacteria as a model system, where cells of different swimming phenotypes are better suited to navigate in different environments. We find that the differential loss of phenotypes caused by collective migration is environment-dependent. With cell growth, this differential loss enables migrating populations to dynamically adapt their phenotype compositions to the environment, enhancing migration through multiple environments. Which phenotypes are produced upon cell division depends on the level of nongenetic inheritance, and higher inheritance leads to larger composition adaptation and faster migration at steady state. However, this comes at the cost of slower responses to new environments. Due to this trade-off, there is an optimal level of inheritance that maximizes migration speed through changing environments, which enables a diverse population to outperform a nondiverse one. Growing populations might generally leverage the selection-like effects provided by collective behaviors to dynamically shape their own phenotype compositions, without mutations.

Relationships Organize Information in Mind and Nature: Empirical Findings of Action–Reaction Relationships (R) in Cognitive and Material Complexity

Diverse phenomena such as feedback, interconnectedness, causality, network dynamics, and complexity are all born from Relationships. They are fundamentally important, as they are transdisciplinary and synonymous with connections, links, edges, and interconnections. The foundation of systems thinking and systems themselves consists of four universals, one of which is action–reaction Relationships. They are also foundational to the consilience of knowledge. This publication gives a formal description of and predictions of action–reaction Relationships (R) or “R-rule”. There are seven original empirical studies presented in this paper. For these seven studies, experiments for the subjects were created on software (unless otherwise noted). The experiments had the subjects complete a task and/or answer a question. The samples are generalizable to a normal distribution of the US population and they vary for each study (ranging from N = 407 to N = 34,398). With high statistical significance the studies support the predictions made by DSRP Theory regarding action–reaction Relationships including its universality as an observable phenomenon in both nature (ontological complexity) and mind (cognitive complexity); mutual dependencies on other universals (i.e., Distinctions, Systems, and Perspectives); role in structural predictions; internal structures and dynamics; efficacy as a metacognitive skill. In conclusion, these data suggest the observable and empirical existence, parallelism (between cognitive and ontological complexity), universality, and efficacy of action–reaction Relationships (R).

Leveraging the model-experiment loop: Examples from cellular slime mold chemotaxis

Interplay between models and experimental data advances discovery and understanding in biology, particularly when models generate predictions that allow well-designed experiments to distinguish between alternative mechanisms. To illustrate how this feedback between models and experiments can lead to key insights into biological mechanisms, we explore three examples from cellular slime mold chemotaxis. These examples include studies that identified chemotaxis as the primary mechanism behind slime mold aggregation, discovered that cells likely measure chemoattractant gradients by sensing concentration differences across cell length, and tested the role of cell-associated chemoattractant degradation in shaping chemotactic fields. Although each study used a different model class appropriate to their hypotheses - qualitative, mathematical, or simulation-based - these examples all highlight the utility of modeling to formalize assumptions and generate testable predictions. A central element of this framework is the iterative use of models and experiments, specifically: matching experimental designs to the models, revising models based on mismatches with experimental data, and validating critical model assumptions and predictions with experiments. We advocate for continued use of this interplay between models and experiments to advance biological discovery.

Vitalism and cognition in a conscious universe

According to the current scientific paradigm, what we call ‘life’, ‘mind’, and ‘consciousness’ are considered epiphenomenal occurrences, or emergent properties or functions of matter and energy. Science does not associate these with an inherent and distinct existence beyond a materialistic/energetic conception. ‘Life’ is a word pointing at cellular and multicellular processes forming organisms capable of specific functions and skills. ‘Mind’ is a cognitive ability emerging from a matrix of complex interactions of neuronal processes, while ‘consciousness’ is an even more elusive concept, deemed a subjective epiphenomenon of brain activity. Historically, however, this has not always been the case, even in the scientific and academic context. Several prominent figures took vitalism seriously, while some schools of Western philosophical idealism and Eastern traditions promoted conceptions in which reality is reducible to mind or consciousness rather than matter. We will argue that current biological sciences did not falsify these alternative paradigms and that some forms of vitalism could be linked to some forms of idealism if we posit life and cognition as two distinct aspects of consciousness preeminent over matter. However, we will not argue in favor of vitalistic and idealistic conceptions. Rather, contrary to a physicalist doctrine, these were and remain coherent worldviews and cannot be ruled out by modern science.

Perspectives Organize Information in Mind and Nature: Empirical Findings of Point-View Perspective (P) in Cognitive and Material Complexity

The importance of perspective-taking crosses disciplines and is foundational to diverse phenomena such as point-of-view, scale, mindset, theory of mind, opinion, belief, empathy, compassion, analysis, and problem solving, etc. This publication gives predictions for and a formal description of point-view Perspectives (P) or the “P-rule”. This makes the P-rule foundational to systems, systems thinking and the consilience of knowledge. It is one of four universals of the organization of information as a whole. This paper presents nine empirical studies in which subjects were asked to complete a task and/or answer a question. The samples vary for each study (ranging from N = 407 to N = 34,398) and are generalizable to a normal distribution of the US population. As was evident in Cabrera, “These studies support—with high statistical significance—the predictions made by DSRP Theory (Distinctions, Systems Relationships, Perspectives) point-view Perspectives including its: universality as an observable phenomenon in both mind (cognitive complexity) and nature (material complexity) (i.e., parallelism); internal structures and dynamics; mutual dependencies on other universals (i.e., Distinctions, Systems, and Relationships); role in structural predictions; and, efficacy as a metacognitive skill”. These data suggest that point-view Perspectives (P) observably and empirically exist, and that universality, efficacy, and parallelism (between cognitive and material complexity) exist as well. The impact of this paper is that it provides empirical evidence for the phenomena of point-view perspective taking (“P-rule”) as a universal pattern/structure of systems thinking, a field in which scholarly debate is often based on invalidated opinioned frameworks; this sets the stage for theory building in the field.

Cellular Sensing Governs the Stability of Chemotactic Fronts

In contexts ranging from embryonic development to bacterial ecology, cell populations migrate chemotactically along self-generated chemical gradients, often forming a propagating front. Here, we theoretically show that the stability of such chemotactic fronts to morphological perturbations is determined by limitations in the ability of individual cells to sense and thereby respond to the chemical gradient. Specifically, cells at bulging parts of a front are exposed to a smaller gradient, which slows them down and promotes stability, but they also respond more strongly to the gradient, which speeds them up and promotes instability. We predict that this competition leads to chemotactic fingering when sensing is limited at too low chemical concentrations. Guided by this finding and by experimental data on E. coli chemotaxis, we suggest that the cells' sensory machinery might have evolved to avoid these limitations and ensure stable front propagation. Finally, as sensing of any stimuli is necessarily limited in living and active matter in general, the principle of sensing-induced stability may operate in other types of directed migration such as durotaxis, electrotaxis, and phototaxis.

Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells

Immune cells are constantly on the move through multicellular organisms to explore and respond to pathogens and other harmful insults. While moving, immune cells efficiently traverse microenvironments composed of tissue cells and extracellular fibers, which together form complex environments of various porosity, stiffness, topography, and chemical composition. In this protocol we describe experimental procedures to investigate immune cell migration through microenvironments of heterogeneous porosity. In particular, we describe micro-channels, micro-pillars, and collagen networks as cell migration paths with alternative pore size choices. Employing micro-channels or micro-pillars that divide at junctions into alternative paths with initially differentially sized pores allows us to precisely (1) measure the cellular translocation time through these porous path junctions, (2) quantify the cellular preference for individual pore sizes, and (3) image cellular components like the nucleus and the cytoskeleton. This reductionistic experimental setup thus can elucidate how immune cells perform decisions in complex microenvironments of various porosity like the interstitium. The setup further allows investigation of the underlying forces of cellular squeezing and the consequences of cellular deformation on the integrity of the cell and its organelles. As a complementary approach that does not require any micro-engineering expertise, we describe the usage of three-dimensional collagen networks with different pore sizes. Whereas we here focus on dendritic cells as a model for motile immune cells, the described protocols are versatile as they are also applicable for other immune cell types like neutrophils and non-immune cell types such as mesenchymal and cancer cells. In summary, we here describe protocols to identify the mechanisms and principles of cellular probing, decision making, and squeezing during cellular movement through microenvironments of heterogeneous porosity. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Immune cell migration in micro-channels and micro-pillars with defined pore sizes Support Protocol 1: Epoxy replica of generated and/or published micro-structures Support Protocol 2: Dendritic cell differentiation Basic Protocol 2: Immune cell migration in 3D collagen networks of variable pore sizes.

Systems Organize Information in Mind and Nature: Empirical Findings of Part-Whole Systems (S) in Cognitive and Material Complexity

Part-whole Systems (S) structure is foundational to a diverse array of phenomena such as belonging and containment, networks, statistics, reductionism, holism, etc. and is extremely similar if not synonymous with sets, sorts, groups, combinations and combinatorics, clusters, etc. In Cabrera (1998), part-whole Systems (S) or “S-rule” is established as one of four universals for the organization of information and thus is foundational to systems and systems thinking as well as the consilience of knowledge. In this paper, seven empirical studies are presented in which (unless otherwise noted) subjects completed a task. Ranging from n = 407 to n = 34,398, the sample sizes vary for each study but are generalizeable to a normal distribution of the US population. With high statistical significance, the results of these studies support the predictions made by DSRP Theory regarding part-whole Systems (a.k.a., “S-rule”) including: the universality of S-rule as an observable phenomenon in both mind (cognitive complexity) and nature (ontological complexity) (i.e., parallelism); the internal structures and dynamics of S-rule; S-rule’s mutual dependencies on other universals of DSRP (Distinctions, Systems, Relationships, and Perspectives (i.e., Distinctions, Relationships, and Perspectives); the role S-rule plays in making structural predictions; and, S-rule’s efficacy as a metacognitive skill. In conclusion, these data suggest the observable and empirical existence, universality, efficacy, and parallelism (between cognitive and ontological complexity) of part-whole Systems (S).

Signalling dynamics, cell decisions, and homeostatic control in health and disease

Cell signalling engenders cells with the capability to receive and process information from the intracellular and extracellular environments, trigger and execute biological responses, and communicate with each other. Ultimately, cell signalling is responsible for maintaining homeostasis at the cellular, tissue and systemic level. For this reason, cell signalling is a topic of intense research efforts aimed to elucidate how cells coordinate transitions between states in developing and adult organisms in physiological and pathological conditions. Here, we review current knowledge of how cell signalling operates at multiple spatial and temporal scales, focusing on how single-cell analytical techniques reveal mechanisms underpinning cell-to-cell variability, signalling plasticity, and collective cellular responses.

Role of extracellular matrix proteoglycans in immune cell recruitment

Leucocyte recruitment is a critical component of the immune response and is central to our ability to fight infection. Paradoxically, leucocyte recruitment is also a central component of inflammatory-based diseases such as rheumatoid arthritis, atherosclerosis and cancer. The role of the extracellular matrix, in particular proteoglycans, in this process has been largely overlooked. Proteoglycans consist of protein cores with glycosaminoglycan sugar side chains attached. Proteoglycans have been shown to bind and regulate the function of a number of proteins, for example chemokines, and also play a key structural role in the local tissue environment/niche. Whilst they have been implicated in leucocyte recruitment and inflammatory disease, their mechanistic function has yet to be fully understood, precluding therapeutic targeting. This review summarizes what is currently known about the role of proteoglycans in the different stages of leucocyte recruitment and proposes a number of areas where more research is needed. A better understanding of the mechanistic role of proteoglycans during inflammatory disease will inform the development of next-generation therapeutics.

Technological Approach to Mind Everywhere: An Experimentally-Grounded Framework for Understanding Diverse Bodies and Minds

Synthetic biology and bioengineering provide the opportunity to create novel embodied cognitive systems (otherwise known as minds) in a very wide variety of chimeric architectures combining evolved and designed material and software. These advances are disrupting familiar concepts in the philosophy of mind, and require new ways of thinking about and comparing truly diverse intelligences, whose composition and origin are not like any of the available natural model species. In this Perspective, I introduce TAME-Technological Approach to Mind Everywhere-a framework for understanding and manipulating cognition in unconventional substrates. TAME formalizes a non-binary (continuous), empirically-based approach to strongly embodied agency. TAME provides a natural way to think about animal sentience as an instance of collective intelligence of cell groups, arising from dynamics that manifest in similar ways in numerous other substrates. When applied to regenerating/developmental systems, TAME suggests a perspective on morphogenesis as an example of basal cognition. The deep symmetry between problem-solving in anatomical, physiological, transcriptional, and 3D (traditional behavioral) spaces drives specific hypotheses by which cognitive capacities can increase during evolution. An important medium exploited by evolution for joining active subunits into greater agents is developmental bioelectricity, implemented by pre-neural use of ion channels and gap junctions to scale up cell-level feedback loops into anatomical homeostasis. This architecture of multi-scale competency of biological systems has important implications for plasticity of bodies and minds, greatly potentiating evolvability. Considering classical and recent data from the perspectives of computational science, evolutionary biology, and basal cognition, reveals a rich research program with many implications for cognitive science, evolutionary biology, regenerative medicine, and artificial intelligence.

Distinctions Organize Information in Mind and Nature: Empirical Findings of Identity–Other Distinctions (D) in Cognitive and Material Complexity

The transdisciplinary importance of distinctions is well-established as foundational to such diverse phenomena as recognition, identification, individual and social identity, marginalization, externalities, boundaries, concept formation, etc., and synonymous general ideas, such as thingness, concepts, nodes, objects, etc. Cabrera provides a formal description of and predictions for identity–other distinctions (D) or “D-rule” as one of four universals for the organization of information that is foundational to systems and systems thinking, as well as the consilience of knowledge. This paper presents seven empirical studies in which (unless otherwise noted) software was used to create an experiment for subjects to complete a task and/or answer a question. The samples varied for each study (ranging from N = 407 to N = 34,398) and were generalizable to a normal distribution of the US population. These studies support—with high statistical significance—the predictions made by DSRP theory regarding identity–other distinctions including its: universality as an observable phenomenon in both mind (cognitive complexity) and nature (ontological complexity) (i.e., parallelism); internal structures and dynamics; mutual dependencies on other universals (i.e., relationships, systems, and perspectives); role in structural predictions; and efficacy as a metacognitive skill. In conclusion, these data suggest the observable and empirical existence, universality, efficacy, and parallelism (between cognitive and ontological complexity) of identity–other distinctions (D).

Chemotactic smoothing of collective migration

Collective migration—the directed, coordinated motion of many self-propelled agents—is a fascinating emergent behavior exhibited by active matter with functional implications for biological systems. However, how migration can persist when a population is confronted with perturbations is poorly understood. Here, we address this gap in knowledge through studies of bacteria that migrate via directed motion, or chemotaxis, in response to a self-generated nutrient gradient. We find that bacterial populations autonomously smooth out large-scale perturbations in their overall morphology, enabling the cells to continue to migrate together. This smoothing process arises from spatial variations in the ability of cells to sense and respond to the local nutrient gradient—revealing a population-scale consequence of the manner in which individual cells transduce external signals. Altogether, our work provides insights to predict, and potentially control, the collective migration and morphology of cellular populations and diverse other forms of active matter.

Flocks of birds, schools of fish and herds of animals are all good examples of collective migration, where individuals co-ordinate their behavior to improve survival. This process also happens on a cellular level; for example, when bacteria consume a nutrient in their surroundings, they will collectively move to an area with a higher concentration of food via a process known as chemotaxis.

Several studies have examined how disturbing collective migration can cause populations to fall apart. However, little is known about how groups withstand these interferences. To investigate, Bhattacharjee, Amchin, Alert et al. studied bacteria called Escherichia coli as they moved through a gel towards nutrients.

The E. coli were injected into the gel using a three-dimensional printer, which deposited the bacteria into a wiggly shape that forces the cells apart, making it harder for them to move as a collective group. However, as the bacteria migrated through the gel, they smoothed out the line and gradually made it straighter so they could continue to travel together over longer distances.

Computer simulations revealed that this smoothing process is achieved by differences in how the cells respond to local nutrient levels based on their position. Bacteria towards the front of the group are exposed to more nutrients, causing them to become oversaturated and respond less effectively to the nutrient gradient. As a result, they move more slowly, allowing the cells behind them to eventually catch-up.

These findings reveal a general mechanism in which limitations in how individuals sense and respond to an external signal (in this case local nutrient concentrations) allows them to continue migrating together. This mechanism may apply to other systems that migrate via chemotaxis, as well as groups whose movement is directed by different external factors, such as temperature and light intensity.

The “Fish Tank” Experiments: Metacognitive Awareness of Distinctions, Systems, Relationships, and Perspectives (DSRP) Significantly Increases Cognitive Complexity

In the field of systems thinking, there are far too many opinioned frameworks and far too few empirical studies. This could be described as a “gap” in the research but it is more like a dearth in the research. More theory and empirical validation of theory are needed if the field and the phenomenon of systems thinking holds promise and not just popularity. This validation comes in the form of both basic (existential) and applied (efficacy) research studies. This article presents efficacy data for a set of empirical studies of DSRP Theory. According to Cabrera, Cabrera, and Midgley, DSRP Theory has equal or more empirical evidence supporting it than any existing systems theories (including frameworks, which are not theories). Four separate studies show highly statistically relevant findings for the effect of a short (less than one minute) treatment of D, S, R, and P. Subjects’ cognitive complexity and the systemic nature of their thinking increased in all four studies. These findings indicate that even a short treatment in DSRP is effective in increasing systems thinking skills. Based on these results, a longer, more in-depth treatment—such as a one hour or semester long training, such is the norm—would therefore likely garner transformative results and efficacy.

DSRP Theory: A Primer

DSRP Theory is now over 25 years old with more empirical evidence supporting it than any other systems thinking framework. Yet, it is often misunderstood and described in ways that are inaccurate. DSRP Theory describes four patterns and their underlying elements—identity (i) and other (o) for Distinctions (D), part (p) and whole (w) for Systems (S), action (a) and reaction (r) for Relationships (R), and point (ρ) and view (v) for Perspectives (P)—that are universal in both cognitive complexity (mind) and material complexity (nature). DSRP Theory provides a basis for systems thinking or cognitive complexity as well as material complexity (systems science). This paper, as a relatively short primer on the theory, provides clarity to those wanting to understand DSRP and its implications.