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Biochimica Et Biophysica Acta.... Oct 2018We compare the way that relationships for diffusion constants scale with the size of diffusing membrane domains and the geometry of their environments. Then, we review... (Review)
Review
We compare the way that relationships for diffusion constants scale with the size of diffusing membrane domains and the geometry of their environments. Then, we review our experimental work on the dynamics of dissolution/growth of membrane domains in crowding induced mixing, phase separation, and Ostwald ripening in a highly confined environment. Overall, the scaling relationships applied to diffusion constants obtained by fits to our dynamic data indicate that dissolution and growth is influenced by the diffusion of clusters or small domains of lipids, in addition to kinetic processes and geometrical constraints.
Topics: Diffusion; Lipids; Membranes; Models, Biological; Solubility
PubMed: 29501605
DOI: 10.1016/j.bbamem.2018.02.028 -
The Journal of Cell Biology May 2023Single-particle tracking microscopy is a powerful technique to investigate how proteins dynamically interact with their environment in live cells. However, the analysis...
Single-particle tracking microscopy is a powerful technique to investigate how proteins dynamically interact with their environment in live cells. However, the analysis of tracks is confounded by noisy molecule localization, short tracks, and rapid transitions between different motion states, notably between immobile and diffusive states. Here, we propose a probabilistic method termed ExTrack that uses the full spatio-temporal information of tracks to extract global model parameters, to calculate state probabilities at every time point, to reveal distributions of state durations, and to refine the positions of bound molecules. ExTrack works for a wide range of diffusion coefficients and transition rates, even if experimental data deviate from model assumptions. We demonstrate its capacity by applying it to slowly diffusing and rapidly transitioning bacterial envelope proteins. ExTrack greatly increases the regime of computationally analyzable noisy single-particle tracks. The ExTrack package is available in ImageJ and Python.
Topics: Bacterial Proteins; Diffusion; Kinetics; Microscopy
PubMed: 36880553
DOI: 10.1083/jcb.202208059 -
Biophysical Journal Feb 2014Biological systems often have to measure extremely low concentrations of chemicals with high precision. When dealing with such small numbers of molecules, the inevitable...
Biological systems often have to measure extremely low concentrations of chemicals with high precision. When dealing with such small numbers of molecules, the inevitable randomness of physical transport processes and binding reactions will limit the precision with which measurements can be made. An important question is what the lower bound on the noise would be in such measurements. Using the theory of diffusion-influenced reactions, we derive an analytical expression for the precision of concentration estimates that are obtained by monitoring the state of a receptor to which a diffusing ligand can bind. The variance in the estimate consists of two terms, one resulting from the intrinsic binding kinetics and the other from the diffusive arrival of ligand at the receptor. The latter term is identical to the fundamental limit derived by Berg and Purcell (Biophys. J., 1977), but disagrees with a more recent expression by Bialek and Setayeshgar. Comparing the theoretical predictions against results from particle-based simulations confirms the accuracy of the resulting expression and reaffirms the fundamental limit established by Berg and Purcell.
Topics: Diffusion; Kinetics; Ligands; Models, Chemical; Protein Binding; Receptors, Cell Surface
PubMed: 24560000
DOI: 10.1016/j.bpj.2013.12.030 -
PLoS Pathogens Nov 2009How viruses are transmitted across the mucosal epithelia of the respiratory, digestive, or excretory tracts, and how they spread from cell to cell and cause systemic... (Review)
Review
How viruses are transmitted across the mucosal epithelia of the respiratory, digestive, or excretory tracts, and how they spread from cell to cell and cause systemic infections, is incompletely understood. Recent advances from single virus tracking experiments have revealed conserved patterns of virus movements on the plasma membrane, including diffusive motions, drifting motions depending on retrograde flow of actin filaments or actin tail formation by polymerization, and confinement to submicrometer areas. Here, we discuss how viruses take advantage of cellular mechanisms that normally drive the movements of proteins and lipids on the cell surface. A concept emerges where short periods of fast diffusive motions allow viruses to rapidly move over several micrometers. Coupling to actin flow supports directional transport of virus particles during entry and cell-cell transmission, and local confinement coincides with either nonproductive stalling or infectious endocytic uptake. These conserved features of virus-host interactions upstream of infectious entry offer new perspectives for anti-viral interference.
Topics: Cell Membrane; Diffusion; Movement; Virus Diseases; Virus Internalization; Virus Physiological Phenomena; Viruses
PubMed: 19956678
DOI: 10.1371/journal.ppat.1000621 -
Proceedings of the National Academy of... Sep 2022Understanding the physical principle that governs the stimuli-induced swelling and shrinking kinetics of hydrogels is indispensable for their applications. Here, we show...
Understanding the physical principle that governs the stimuli-induced swelling and shrinking kinetics of hydrogels is indispensable for their applications. Here, we show that the shrinking and swelling kinetics of self-healing hydrogels could be intrinsically asymmetric. The structure frustration, formed by the large difference in the heat and solvent diffusions, remarkably slows down the shrinking kinetics. The plateau modulus of viscoelastic gels is found to be a key parameter governing the formation of structure frustration and, in turn, the asymmetric swelling and shrinking kinetics. This work provides fundamental understandings on the temperature-triggered transient structure formation in self-healing hydrogels. Our findings will find broad use in diverse applications of self-healing hydrogels, where cooperative diffusion of water and gel network is involved. Our findings should also give insight into the molecular diffusion in biological systems that possess macromolecular crowding environments similar to self-healing hydrogels.
Topics: Diffusion; Hydrogels; Kinetics; Temperature; Water
PubMed: 36037384
DOI: 10.1073/pnas.2207422119 -
Journal of Biomechanical Engineering Nov 2022Due to lack of full vascularization, the meniscus relies on diffusion through the extracellular matrix to deliver small (e.g., nutrients) and large (e.g., proteins) to...
Due to lack of full vascularization, the meniscus relies on diffusion through the extracellular matrix to deliver small (e.g., nutrients) and large (e.g., proteins) to resident cells. Under normal physiological conditions, the meniscus undergoes up to 20% compressive strains. While previous studies characterized solute diffusivity in the uncompressed meniscus, to date, little is known about the diffusive transport under physiological strain levels. This information is crucial to fully understand the pathophysiology of the meniscus. The objective of this study was to investigate strain-dependent diffusive properties of the meniscus fibrocartilage. Tissue samples were harvested from the central portion of porcine medial menisci and tested via fluorescence recovery after photobleaching to measure diffusivity of fluorescein (332 Da) and 40 K Da dextran (D40K) under 0%, 10%, and 20% compressive strain. Specifically, average diffusion coefficient and anisotropic ratio, defined as the ratio of the diffusion coefficient in the direction of the tissue collagen fibers to that orthogonal, were determined. For all the experimental conditions investigated, fluorescein diffusivity was statistically faster than that of D40K. Also, for both molecules, diffusion coefficients significantly decreased, up to ∼45%, as the strain increased. In contrast, the anisotropic ratios of both molecules were similar and not affected by the strain applied to the tissue. This suggests that compressive strains used in this study did not alter the diffusive pathways in the meniscus. Our findings provide new knowledge on the transport properties of the meniscus fibrocartilage that can be leveraged to further understand tissue pathophysiology and approaches to tissue restoration.
Topics: Animals; Anisotropy; Diffusion; Fibrocartilage; Fluoresceins; Meniscus; Swine
PubMed: 35789377
DOI: 10.1115/1.4054931 -
ELife Sep 2022Single-particle tracking (SPT) directly measures the dynamics of proteins in living cells and is a powerful tool to dissect molecular mechanisms of cellular regulation....
Single-particle tracking (SPT) directly measures the dynamics of proteins in living cells and is a powerful tool to dissect molecular mechanisms of cellular regulation. Interpretation of SPT with fast-diffusing proteins in mammalian cells, however, is complicated by technical limitations imposed by fast image acquisition. These limitations include short trajectory length due to photobleaching and shallow depth of field, high localization error due to the low photon budget imposed by short integration times, and cell-to-cell variability. To address these issues, we investigated methods inspired by Bayesian nonparametrics to infer distributions of state parameters from SPT data with short trajectories, variable localization precision, and absence of prior knowledge about the number of underlying states. We discuss the advantages and disadvantages of these approaches relative to other frameworks for SPT analysis.
Topics: Animals; Bayes Theorem; Diffusion; Mammals; Single Molecule Imaging
PubMed: 36066004
DOI: 10.7554/eLife.70169 -
International Journal of Molecular... Oct 2022The mechanisms of transport of substances in the brain parenchyma have been a hot topic in scientific discussion in the past decade. This discussion was triggered by the... (Review)
Review
The mechanisms of transport of substances in the brain parenchyma have been a hot topic in scientific discussion in the past decade. This discussion was triggered by the proposed glymphatic hypothesis, which assumes a directed flow of cerebral fluid within the parenchyma, in contrast to the previous notion that diffusion is the main mechanism. However, when discussing the issue of "diffusion or non-diffusion", much less attention was given to the question that diffusion itself can have a different character. In our opinion, some of the recently published results do not fit into the traditional understanding of diffusion. In this regard, we outline the relevant new theoretical approaches on transport processes in complex random media such as concepts of diffusive diffusivity and time-dependent homogenization, which expands the understanding of the forms of transport of substances based on diffusion.
Topics: Extracellular Space; Brain; Diffusion; Biological Transport; Diffusion Magnetic Resonance Imaging
PubMed: 36293258
DOI: 10.3390/ijms232012401 -
Journal of the Royal Society, Interface Dec 2021Diffusion of water into plant materials is known to decrease their mechanical strength and stiffness but improve formability. Here, we characterize water diffusion...
Diffusion of water into plant materials is known to decrease their mechanical strength and stiffness but improve formability. Here, we characterize water diffusion through areca palm leaf-sheath-a model plant material, with hierarchical structure, used in eco-friendly foodware. The diffusion process is studied using mass gain measurements and imaging of water transport. By treating the areca sheath as homogeneous ensemble, and incorporating effects of material swelling due- to water absorption, a factor typically neglected in prior studies, the diffusion coefficient for water is estimated as (6.5 ± 2.2) × 10 mm s. It is shown that neglecting the swelling results in gross underestimation of . Microstructural effects (e.g. fibre, matrix) on the diffusion are characterized using imaging of the water transport at high resolution. The observations show that the water diffuses an order of magnitude faster in the matrix (8.63 × 10 mm s) than in the fibres (7.19 × 10 mm s). This non-uniformity is also reflected in the swelling-induced strain in the leaf, mapped by image correlation. Lastly, we vary salt concentration by controlled additions of NaCl and note a non-monotonic dependence of the diffusion on concentration. Implications of the results for improving foodware manufacturing processes and product life are discussed.
Topics: Biological Transport; Diffusion; Plant Leaves; Sodium Chloride; Water
PubMed: 34847794
DOI: 10.1098/rsif.2021.0483 -
Journal of Visualized Experiments : JoVE Sep 2018Diffusive convection (DC) occurs when the vertical stratified density is controlled by two opposing scalar gradients that have distinctly different molecular...
Diffusive convection (DC) occurs when the vertical stratified density is controlled by two opposing scalar gradients that have distinctly different molecular diffusivities, and the larger- and smaller- diffusivity scalar gradients have negative and positive contributions for the density distribution, respectively. The DC occurs in many natural processes and engineering applications, for example, oceanography, astrophysics and metallurgy. In oceans, one of the most remarkable features of DC is that the vertical temperature and salinity profiles are staircase-like structure, composed of consecutive steps with thick homogeneous convecting layers and relatively thin and high-gradient interfaces. The DC staircases have been observed in many oceans, especially in the Arctic and Antarctic Oceans, and play an important role on the ocean circulation and climatic change. In the Arctic Ocean, there exist basin-wide and persistent DC staircases in the upper and deep oceans. The DC process has an important effect on diapycnal mixing in the upper ocean and may significantly influence the surface ice-melting. Compared to the limitations of field observations, laboratory experiment shows its unique advantage to effectively examine the dynamic and thermodynamic processes in DC, because the boundary conditions and the controlled parameters can be strictly adjusted. Here, a detailed protocol is described to simulate the evolution process of DC staircase structure, including its generation, development and disappearance, in a rectangular tank filled with stratified saline water. The experimental setup, evolution process, data analysis, and discussion of results are described in detail.
Topics: Antarctic Regions; Arctic Regions; Climate Change; Convection; Diffusion; Ice Cover; Oceans and Seas; Salinity; Seawater; Temperature; Water Movements
PubMed: 30247476
DOI: 10.3791/58316