Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ATP-Dependent Diffusion Entropy and Homogeneity in Living Cells

ABSTRACT: Intracellular dynamics is highly complex, and includes diffusion of poly-dispersed objects in a non-homogeneous, out-of-equilibrium medium. Assuming non-equilibrium steady-state, we developed a framework that relates non-equilibrium fluctuations to diffusion, and generalized entropy in cells. We employed imaging of live Jurkat T cells, and showed that active cells have higher diffusion parameters (K? and ?) and entropy relative to the same cells after ATP depletion. K? and ? were related in ATP-depleted cells while this relation was not apparent in untreated cells, probably due to non-equilibrium applied work. Next we evaluated the effect of intracellular diffusion and entropy on the cell content homogeneity, which was displayed by the extent of its liquid–liquid phase separation (LLPS). Correlations between intracellular diffusion parameters, entropy and cell homogeneity could be demonstrated only in active cells while these correlations disappeared after ATP depletion. We conclude that non-equilibrium contributions to diffusivity and entropy by ATP-dependent mechanical work allow cells to control their content homogeneity and LLPS state. Such understanding may enable better intervention in extreme LLPS conditions associated with various cell malignancies and degenerative diseases.

SUBMITTER: Wohl I

PROVIDER: S-EPMC7514293 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

ATP-dependent mechanics of red blood cells.

Project description:Red blood cells are amazingly deformable structures able to recover their initial shape even after large deformations as when passing through tight blood capillaries. The reason for this exceptional property is found in the composition of the membrane and the membrane-cytoskeleton interaction. We investigate the mechanics and the dynamics of RBCs by a unique noninvasive technique, using weak optical tweezers to measure membrane fluctuation amplitudes with mus temporal and sub nm spatial resolution. This enhanced edge detection method allows to span over >4 orders of magnitude in frequency. Hence, we can simultaneously measure red blood cell membrane mechanical properties such as bending modulus kappa = 2.8 +/- 0.3 x 10(-19)J = 67.6 +/- 7.2 k(B)T, tension sigma = 6.5 +/- 2.1 x 10(-7)N/m, and an effective viscosity eta(eff) = 81 +/- 3.7 x 10(-3) Pa s that suggests unknown dissipative processes. We furthermore show that cell mechanics highly depends on the membrane-spectrin interaction mediated by the phosphorylation of the interconnection protein 4.1R. Inhibition and activation of this phosphorylation significantly affects tension and effective viscosity. Our results show that on short time scales (slower than 100 ms) the membrane fluctuates as in thermodynamic equilibrium. At time scales longer than 100 ms, the equilibrium description breaks down and fluctuation amplitudes are higher by 40% than predicted by the membrane equilibrium theory. Possible explanations for this discrepancy are influences of the spectrin that is not included in the membrane theory or nonequilibrium fluctuations that can be accounted for by defining a nonthermal effective energy of up to E(eff) = 1.4 +/- 0.1 k(B)T, that corresponds to an actively increased effective temperature.

| S-EPMC2741249 | biostudies-literature

Reduced local diffusion homogeneity as a biomarker for temporal lobe epilepsy.

Project description:In the present study, we adopted a novel method-local diffusion homogeneity (LDH)-to characterize the structure feature in mesial temporal lobe epilepsy (MTLE). Diffusion-weighted images were acquired from 11 left MTLE patients, 16 right MTLE patients, and 20 healthy controls from May 2014 to January 2015. Local diffusion homogeneity was compared among patient groups and controls by 2 sample t test. The discriminative value of LDH abnormalities was examined by receiver operating characteristic (ROC) curve analysis. Correlations with disease duration and onset age in both patient groups were assessed using Pearson's coefficient. Both patient groups exhibited lower LDH in the anterior corpus callosum (P < 0.05, corrected), and this regional anomaly exhibited excellent classification performance in left MTLE patients (sensitivity = 82%, specificity = 100%), right MTLE patients (sensitivity = 81%, specificity = 90%), and the entire patient cohort (sensitivity = 82%, specificity = 95%). In summary, left and right MTLE patients show common pathological changes in the anterior corpus callosum. This regional LDH abnormality is a potential quantitative biomarker for MTLE.

| S-EPMC5265813 | biostudies-literature

Revealing Compartmentalized Diffusion in Living Cells with Interferometric Scattering Microscopy.

Project description:The spatiotemporal organization and dynamics of the plasma membrane and its constituents are central to cellular function. Fluorescence-based single-particle tracking has emerged as a powerful approach for studying the single molecule behavior of plasma-membrane-associated events because of its excellent background suppression, at the expense of imaging speed and observation time. Here, we show that interferometric scattering microscopy combined with 40 nm gold nanoparticle labeling can be used to follow the motion of membrane proteins in the plasma membrane of live cultured mammalian cell lines and hippocampal neurons with up to 3 nm precision and 25 ?s temporal resolution. The achievable spatiotemporal precision enabled us to reveal signatures of compartmentalization in neurons likely caused by the actin cytoskeleton.

| S-EPMC6026387 | biostudies-literature

Local Diffusion Homogeneity Provides Supplementary Information in T2DM-Related WM Microstructural Abnormality Detection.

Project description:Objectives: We aimed to investigate whether an inter-voxel diffusivity metric (local diffusion homogeneity, LDH), can provide supplementary information to traditional intra-voxel metrics (i.e., fractional anisotropy, FA) in white matter (WM) abnormality detection for type 2 diabetes mellitus (T2DM). Methods: Diffusion tensor imaging was acquired from 34 T2DM patients and 32 healthy controls. Voxel-based group-difference comparisons based on LDH and FA, as well as the association between the diffusion metrics and T2DM risk factors [i.e., body mass index (BMI) and systolic blood pressure (SBP)], were conducted, with age, gender and education level controlled. Results: Compared to the controls, T2DM patients had higher LDH in the pons and left temporal pole, as well as lower FA in the left superior corona radiation (p < 0.05, corrected). In T2DM, there were several overlapping WM areas associated with BMI as revealed by both LDH and FA, including right temporal lobe and left inferior parietal lobe; but the unique areas revealed only by using LDH included left inferior temporal lobe, right supramarginal gyrus, left pre- and post-central gyrus (at the semiovale center), and right superior radiation. Overlapping WM areas that associated with SBP were found with both LDH and FA, including right temporal pole, bilateral orbitofrontal area (rectus gyrus), the media cingulum bundle, and the right cerebellum crus I. However, the unique areas revealed only by LDH included right inferior temporal lobe, right inferior occipital lobe, and splenium of corpus callosum. Conclusion: Inter- and intra-voxel diffusivity metrics may have different sensitivity in the detection of T2DM-related WM abnormality. We suggested that LDH could provide supplementary information and reveal additional underlying brain changes due to diabetes.

| S-EPMC6374310 | biostudies-literature

High rates of calcium-free diffusion in the cytosol of living cells.

Project description:Calcium (Ca2+) is a universal second messenger that participates in the regulation of innumerous physiological processes. The way in which local elevations of the cytosolic Ca2+ concentration spread in space and time is key for the versatility of the signals. Ca2+ diffusion in the cytosol is hindered by its interaction with proteins that act as buffers. Depending on the concentrations and the kinetics of the interactions, there is a large range of values at which Ca2+ diffusion can proceed. Having reliable estimates of this range, particularly of its highest end, which corresponds to the ions free diffusion, is key to understand how the signals propagate. In this work, we present the first experimental results with which the Ca2+-free diffusion coefficient is directly quantified in the cytosol of living cells. By means of fluorescence correlation spectroscopy experiments performed in Xenopus laevis oocytes and in cells of Saccharomyces cerevisiae, we show that the ions can freely diffuse in the cytosol at a higher rate than previously thought.

| S-EPMC8510970 | biostudies-literature

Cationic Europium Complexes for Visualizing Fluctuations in Mitochondrial ATP Levels in Living Cells.

Project description:The ability to study cellular metabolism and enzymatic processes involving adenosine triphosphate (ATP) is impeded by the lack of imaging probes capable of signalling the concentration and distribution of intracellular ATP rapidly, with high sensitivity. We report here the first example of a luminescent lanthanide complex capable of visualizing changes in the concentration of ATP in the mitochondria of living cells. Four cationic europium(III) complexes [Eu.1-4]+ have been synthesized and their binding capabilities towards nucleoside polyphosphate anions examined in aqueous solution at physiological pH. Complexes [Eu.1]+ and [Eu.3]+ bearing hydrogen bond donor groups in the pendant arms showed excellent discrimination between ATP, ADP and monophosphate species. Complex [Eu.3]+ showed relatively strong binding to ATP (logKa =5.8), providing a rapid, long-lived luminescent signal that enabled its detection in a highly competitive aqueous medium containing biologically relevant concentrations of Mg2+ , ADP, GTP, UTP and human serum albumin. This EuIII complex responds linearly to ATP within the physiological concentration range (1-5 mm), and was used to continuously monitor the apyrase-catalyzed hydrolysis of ATP to ADP in vitro. We demonstrate that [Eu.3]+ can permeate mammalian (NIH-3T3) cells efficiently and localize to the mitochondria selectively, permitting real-time visualization of elevated mitochondrial ATP levels following treatment with a broad spectrum kinase inhibitor, staurosporine, as well as depleted ATP levels upon treatment with potassium cyanide under glucose starvation conditions.

| S-EPMC6175470 | biostudies-literature

Demonstration of Non-Gaussian Restricted Diffusion in Tumor Cells Using Diffusion Time-Dependent Diffusion-Weighted Magnetic Resonance Imaging Contrast.

Project description:The diffusion-weighted magnetic resonance imaging (DWI) technique enables quantification of water mobility for probing microstructural properties of biological tissue and has become an effective tool for collecting information about the underlying pathology of cancerous tissue. Measurements using multiple b-values have indicated biexponential signal attenuation, ascribed to "fast" (high ADC) and "slow" (low ADC) diffusion components. In this empirical study, we investigate the properties of the diffusion time (Δ)-dependent components of the diffusion-weighted (DW) signal in a constant b-value experiment. A xenograft gliobastoma mouse was imaged using Δ = 11 ms, 20 ms, 40 ms, 60 ms, and b = 500-4000 s/mm(2) in intervals of 500 s/mm(2). Data were corrected for EPI distortions, and the Δ-dependence on the DW-signal was measured within three regions of interest [intermediate- and high-density tumor regions and normal-appearing brain (NAB) tissue regions]. In this study, we verify the assumption that the slow decaying component of the DW-signal is non-Gaussian and dependent on Δ, consistent with restricted diffusion of the intracellular space. As the DW-signal is a function of Δ and is specific to restricted diffusion, manipulating Δ at constant b-value (cb) provides a complementary and direct approach for separating the restricted from the hindered diffusion component. We found that Δ-dependence is specific to the tumor tissue signal. Based on an extended biexponential model, we verified the interpretation of the diffusion time-dependent contrast and successfully estimated the intracellular restricted ADC, signal volume fraction, and cell size within each ROI.

| S-EPMC4970563 | biostudies-literature

Divergent Deborah number-dependent transition from homogeneity to heterogeneity.

Project description:Heterogeneous structures are ubiquitous in natural organisms. Native heterogeneous structures inspire many artificial structures that are playing important roles in modern society, while it is challenging to identify the relevant factors in forming these structures due to the complexity of living systems. Here, hybrid hydrogels consisting of flexible polymer networks with embedded stiff cellulose nanocrystals (CNCs) are considered an open system to simulate the generalized formation of heterogeneous core-sheath structures. As the result of the modified air drying process of hybrid hydrogels, the formation of heterogeneous core-sheath structure is found to be correlated to the relative evaporation speed. Specifically, the formation of such heterogeneity in xerogel fibers is found to be correlated with the divergence of Deborah number (De). During the transition of De from large to small values with accompanying morphologies, the turning point is around De = 1. The mechanism can be considered a relative humidity-dependent glass transition behavior. These unique heterogeneous structures play a key role in tuning water permeation and water sorption capacity. Insights into these aspects can prospectively contribute to a better understanding of the native heterogeneous structures for bionics design.

| S-EPMC10522598 | biostudies-literature

Spectral Analysis of ATP-Dependent Mechanical Vibrations in T Cells.

Project description:Mechanical vibrations affect multiple cell properties, including its diffusivity, entropy, internal content organization, and thus-function. Here, we used Differential Interference Contrast (DIC), confocal, and Total Internal Reflection Fluorescence (TIRF) microscopies to study mechanical vibrations in live (Jurkat) T cells. Vibrations were measured via the motion of intracellular particles and plasma membrane. These vibrations depend on adenosine triphosphate (ATP) consumption and on Myosin II activity. We then used spectral analysis of these vibrations to distinguish the effects of thermal agitation, ATP-dependent mechanical work and cytoskeletal visco-elasticity. Parameters of spectral analyses could be related to mean square displacement (MSD) analyses with specific advantages in characterizing intracellular mechanical work. We identified two spectral ranges where mechanical work dominated vibrations of intracellular components: 0-3 Hz for intracellular particles and the plasma-membrane, and 100-150 Hz for the plasma-membrane. The 0-3 Hz vibrations of the cell membrane that we measured in an experimental model of immune synapse (IS) are expected to affect the IS formation and function in effector cells. It may also facilitate immunological escape of extensively vibrating malignant cells.

| S-EPMC8222795 | biostudies-literature

Rheological behavior of living cells is timescale-dependent.

Project description:The dynamic mechanical behavior of living cells has been proposed to result from timescale-invariant processes governed by the soft glass rheology theory derived from soft matter physics. But this theory is based on experimental measurements over timescales that are shorter than those most relevant for cell growth and function. Here we report results measured over a wider range of timescales which demonstrate that rheological behaviors of living cells are not timescale-invariant. These findings demonstrate that although soft glass rheology appears to accurately predict certain cell mechanical behaviors, it is not a unified model of cell rheology under biologically relevant conditions and thus, alternative mechanisms need to be considered.

| S-EPMC1989695 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data