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The Journal of Physical Chemistry. B Nov 2022Living systems are characterized by their spatially highly inhomogeneous nature which is susceptible to modify fundamentally the behavior of biomolecular species,...
Living systems are characterized by their spatially highly inhomogeneous nature which is susceptible to modify fundamentally the behavior of biomolecular species, including the proteins that underpin biological functionality in cells. Spatial gradients in chemical potential are known to lead to strong transport effects for colloidal particles, but their effect on molecular scale species such as proteins has remained largely unexplored. Here, we improve on existing diffusiophoresis microfluidic technique to measure protein diffusiophoresis in real space. The measurement of proteins is made possible by two ameliorations. First, a label-free microscope is used to suppress label interference. Second, improvements in numerical methods are developed to meet the particular challenges posed by small molecules. We demonstrate that individual proteins can undergo strong diffusiophoretic motion in salt gradients in a manner which is sufficient to overcome diffusion and which leads to dramatic changes in their spatial organization on the scale of a cell. Moreover, we demonstrate that this phenomenon can be used to control the motion of proteins in microfluidic devices. These results open up a path towards a physical understanding of the role of gradients in living systems in the spatial organization of macromolecules and highlight novel routes towards protein sorting applications on device.
Topics: Diffusion; Motion; Macromolecular Substances; Sodium Chloride
PubMed: 36306420
DOI: 10.1021/acs.jpcb.2c04029 -
Philosophical Transactions. Series A,... Dec 2021Skin patterns are the first example of the existence of Turing patterns in living organisms. Extensive research on zebrafish, a model organism with stripes on its skin,... (Review)
Review
Skin patterns are the first example of the existence of Turing patterns in living organisms. Extensive research on zebrafish, a model organism with stripes on its skin, has revealed the principles of pattern formation at the molecular and cellular levels. Surprisingly, although the networks of cell-cell interactions have been observed to satisfy the 'short-range activation and long-range inhibition' prerequisites for Turing pattern formation, numerous individual reactions were not envisioned based on the classical reaction-diffusion model. For example, in real skin, it is not an alteration in concentrations of chemicals, but autonomous migration and proliferation of pigment cells that establish patterns, and cell-cell interactions are mediated via direct contact through cell protrusions. Therefore, the classical reaction-diffusion mechanism cannot be used as it is for modelling skin pattern formation. Various studies are underway to adapt mathematical models to the experimental findings on research into skin patterns, and the purpose of this review is to organize and present them. These novel theoretical methods could be applied to autonomous pattern formation phenomena other than skin patterns. This article is part of the theme issue 'Recent progress and open frontiers in Turing's theory of morphogenesis'.
Topics: Animals; Diffusion; Models, Biological; Morphogenesis; Skin; Zebrafish
PubMed: 34743596
DOI: 10.1098/rsta.2020.0274 -
Current Opinion in Chemical Biology Jun 2022Spatial patterning of cell populations is a ubiquitous phenomenon in nature. Patterns occur at various length and time scales and exhibit immense diversity. In addition... (Review)
Review
Spatial patterning of cell populations is a ubiquitous phenomenon in nature. Patterns occur at various length and time scales and exhibit immense diversity. In addition to offering a deeper understanding of the emergence of patterns in nature, the ability to program synthetic patterns using living cells has the potential for broad applications. To date, however, progress in engineering pattern formation has been hampered by technical challenges. In this Review, we discuss recent advances in programming pattern formation in terms of biological insights, experimental and computational tool development, and potential applications.
Topics: Diffusion; Models, Biological
PubMed: 35472832
DOI: 10.1016/j.cbpa.2022.102147 -
The European Respiratory Journal Jul 2022
Topics: Carbon Monoxide; Diffusion; Humans; Pulmonary Diffusing Capacity
PubMed: 35902101
DOI: 10.1183/13993003.00789-2022 -
Nature Communications May 2023Plasmodium sporozoites actively migrate in the dermis and enter blood vessels to infect the liver. Despite their importance for malaria infection, little is known about...
Plasmodium sporozoites actively migrate in the dermis and enter blood vessels to infect the liver. Despite their importance for malaria infection, little is known about these cutaneous processes. We combine intravital imaging in a rodent malaria model and statistical methods to unveil the parasite strategy to reach the bloodstream. We determine that sporozoites display a high-motility mode with a superdiffusive Lévy-like pattern known to optimize the location of scarce targets. When encountering blood vessels, sporozoites frequently switch to a subdiffusive low-motility behavior associated with probing for intravasation hotspots, marked by the presence of pericytes. Hence, sporozoites present anomalous diffusive motility, alternating between superdiffusive tissue exploration and subdiffusive local vessel exploitation, thus optimizing the sequential tasks of seeking blood vessels and pericyte-associated sites of privileged intravasation.
Topics: Animals; Sporozoites; Plasmodium; Diffusion; Liver; Pericytes
PubMed: 37221182
DOI: 10.1038/s41467-023-38706-z -
PLoS Computational Biology Feb 2023Critical phenomena are wildly observed in living systems. If the system is at criticality, it can quickly transfer information and achieve optimal response to external...
Critical phenomena are wildly observed in living systems. If the system is at criticality, it can quickly transfer information and achieve optimal response to external stimuli. Especially, animal collective behavior has numerous critical properties, which are related to other research regions, such as the brain system. Although the critical phenomena influencing collective behavior have been extensively studied, two important aspects require clarification. First, these critical phenomena never occur on a single scale but are instead nested from the micro- to macro-levels (e.g., from a Lévy walk to scale-free correlation). Second, the functional role of group criticality is unclear. To elucidate these aspects, the ambiguous interaction model is constructed in this study; this model has a common framework and is a natural extension of previous representative models (such as the Boids and Vicsek models). We demonstrate that our model can explain the nested criticality of collective behavior across several scales (considering scale-free correlation, super diffusion, Lévy walks, and 1/f fluctuation for relative velocities). Our model can also explain the relationship between scale-free correlation and group turns. To examine this relation, we propose a new method, applying partial information decomposition (PID) to two scale-free induced subgroups. Using PID, we construct information flows between two scale-free induced subgroups and find that coupling of the group morphology (i.e., the velocity distributions) and its fluctuation power (i.e., the fluctuation distributions) likely enable rapid group turning. Thus, the flock morphology may help its internal fluctuation convert to dynamic behavior. Our result sheds new light on the role of group morphology, which is relatively unheeded, retaining the importance of fluctuation dynamics in group criticality.
Topics: Animals; Behavior, Animal; Brain; Mass Behavior; Diffusion
PubMed: 36791061
DOI: 10.1371/journal.pcbi.1010869 -
Proceedings of the National Academy of... Oct 2022Remitted waves are used for sensing and imaging in diverse diffusive media from the Earth's crust to the human brain. Separating the source and detector increases the...
Remitted waves are used for sensing and imaging in diverse diffusive media from the Earth's crust to the human brain. Separating the source and detector increases the penetration depth of light, but the signal strength decreases rapidly, leading to a poor signal-to-noise ratio. Here, we show, experimentally and numerically, that wavefront shaping a laser beam incident on a diffusive sample enables an enhancement of remission by an order of magnitude at depths of up to 10 transport mean free paths. We develop a theoretical model which predicts the maximal remission enhancement. Our analysis reveals a significant improvement in the sensitivity of remitted waves to local changes of absorption deep inside diffusive media. This work illustrates the potential of coherent wavefront control for noninvasive diffuse wave imaging applications, such as diffuse optical tomography and functional near-infrared spectroscopy.
Topics: Brain; Diffusion; Humans; Signal-To-Noise Ratio
PubMed: 36191199
DOI: 10.1073/pnas.2207089119 -
Philosophical Transactions. Series A,... Dec 2021In the nearly seven decades since the publication of Alan Turing's work on morphogenesis, enormous progress has been made in understanding both the mathematical and... (Review)
Review
In the nearly seven decades since the publication of Alan Turing's work on morphogenesis, enormous progress has been made in understanding both the mathematical and biological aspects of his proposed reaction-diffusion theory. Some of these developments were nascent in Turing's paper, and others have been due to new insights from modern mathematical techniques, advances in numerical simulations and extensive biological experiments. Despite such progress, there are still important gaps between theory and experiment, with many examples of biological patterning where the underlying mechanisms are still unclear. Here, we review modern developments in the mathematical theory pioneered by Turing, showing how his approach has been generalized to a range of settings beyond the classical two-species reaction-diffusion framework, including evolving and complex manifolds, systems heterogeneous in space and time, and more general reaction-transport equations. While substantial progress has been made in understanding these more complicated models, there are many remaining challenges that we highlight throughout. We focus on the mathematical theory, and in particular linear stability analysis of 'trivial' base states. We emphasize important open questions in developing this theory further, and discuss obstacles in using these techniques to understand biological reality. This article is part of the theme issue 'Recent progress and open frontiers in Turing's theory of morphogenesis'.
Topics: Diffusion; Mathematics; Models, Biological; Morphogenesis
PubMed: 34743603
DOI: 10.1098/rsta.2020.0268 -
The Journal of Physiology Mar 2021Timely delivery of oxygen (O ) to tissue mitochondria is so essential that elaborate circulatory systems have evolved to minimize diffusion distances within tissue. Yet,... (Review)
Review
Timely delivery of oxygen (O ) to tissue mitochondria is so essential that elaborate circulatory systems have evolved to minimize diffusion distances within tissue. Yet, knowledge is surprisingly limited regarding the diffusion pathway between blood capillaries and tissue mitochondria. An established and growing body of work examines the influence cellular and extracellular structures may have on subcellular oxygen availability. This brief review discusses the physiological and pathophysiological significance of oxygen availability, highlights recent computer modelling studies of transport at the cell-membrane level, and considers alternative diffusion pathways within tissue. Experimental and computer modelling studies suggest that oxygen diffusion may be accelerated by cellular lipids, relative to cytosolic and interstitial fluids. Such acceleration, or 'channelling', would occur due to greatly enhanced oxygen solubility in lipids, especially near the midplane of lipid bilayers. Rapid long-range movement would be promoted by anisotropically enhanced lateral diffusion of oxygen along the midplane and by junctions holding lipid structures in close proximity to one another throughout the tissue. Clarifying the biophysical mechanism of oxygen transport within tissue will shed light on limitations and opportunities in tumour radiotherapy and tissue engineering.
Topics: Capillaries; Cell Membrane Permeability; Diffusion; Mitochondria; Oxygen; Oxygen Consumption
PubMed: 33215707
DOI: 10.1113/JP278815 -
Bulletin of Mathematical Biology Jun 2021Realistic examples of reaction-diffusion phenomena governing spatial and spatiotemporal pattern formation are rarely isolated systems, either chemically or...
Realistic examples of reaction-diffusion phenomena governing spatial and spatiotemporal pattern formation are rarely isolated systems, either chemically or thermodynamically. However, even formulations of 'open' reaction-diffusion systems often neglect the role of domain boundaries. Most idealizations of closed reaction-diffusion systems employ no-flux boundary conditions, and often patterns will form up to, or along, these boundaries. Motivated by boundaries of patterning fields related to the emergence of spatial form in embryonic development, we propose a set of mixed boundary conditions for a two-species reaction-diffusion system which forms inhomogeneous solutions away from the boundary of the domain for a variety of different reaction kinetics, with a prescribed uniform state near the boundary. We show that these boundary conditions can be derived from a larger heterogeneous field, indicating that these conditions can arise naturally if cell signalling or other properties of the medium vary in space. We explain the basic mechanisms behind this pattern localization and demonstrate that it can capture a large range of localized patterning in one, two, and three dimensions and that this framework can be applied to systems involving more than two species. Furthermore, the boundary conditions proposed lead to more symmetrical patterns on the interior of the domain and plausibly capture more realistic boundaries in developmental systems. Finally, we show that these isolated patterns are more robust to fluctuations in initial conditions and that they allow intriguing possibilities of pattern selection via geometry, distinct from known selection mechanisms.
Topics: Diffusion; Embryonic Development; Kinetics; Mathematical Concepts; Models, Biological
PubMed: 34089093
DOI: 10.1007/s11538-021-00913-4