Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Inferring transient particle transport dynamics in live cells.

ABSTRACT: Live-cell imaging and particle tracking provide rich information on mechanisms of intracellular transport. However, trajectory analysis procedures to infer complex transport dynamics involving stochastic switching between active transport and diffusive motion are lacking. We applied Bayesian model selection to hidden Markov modeling to infer transient transport states from trajectories of mRNA-protein complexes in live mouse hippocampal neurons and metaphase kinetochores in dividing human cells. The software is available at http://hmm-bayes.org/.

SUBMITTER: Monnier N

PROVIDER: S-EPMC4733533 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Inferring transient particle transport dynamics in live cells.

Monnier Nilah N Barry Zachary Z Park Hye Yoon HY Su Kuan-Chung KC Katz Zachary Z English Brian P BP Dey Arkajit A Pan Keyao K Cheeseman Iain M IM Singer Robert H RH Bathe Mark M

Nature methods 20150720 9

Live-cell imaging and particle tracking provide rich information on mechanisms of intracellular transport. However, trajectory analysis procedures to infer complex transport dynamics involving stochastic switching between active transport and diffusive motion are lacking. We applied Bayesian model selection to hidden Markov modeling to infer transient transport states from trajectories of mRNA-protein complexes in live mouse hippocampal neurons and metaphase kinetochores in dividing human cells. ...[more]

PMID: 26192083

Similar Datasets

Modeling transient particle transport by fast fluid dynamics with the Markov chain method.

Project description:Fast simulation tools for the prediction of transient particle transport are critical in designing the air distribution indoors to reduce the exposure to indoor particles and associated health risks. This investigation proposed a combined fast fluid dynamics (FFD) and Markov chain model for fast predicting transient particle transport indoors. The solver for FFD-Markov-chain model was programmed in OpenFOAM, an open-source CFD toolbox. This study used two cases from the literature to validate the developed model and found well agreement between the transient particle concentrations predicted by the FFD-Markov-chain model and the experimental data. This investigation further compared the FFD-Markov-chain model with the CFD-Eulerian model and CFD-Lagrangian model in terms of accuracy and efficiency. The accuracy of the FFD-Markov-chain model was similar to that of the other two models. For the two studied cases, the FFD-Markovchain model was 4.7 and 6.8 times faster, respectively, than the CFD-Eulerian model, and it was 137.4 and 53.3 times faster than the CFD-Lagrangian model in predicting the steady-state airflow and transient particle transport. Therefore, the FFD-Markov-chain model is able to greatly reduce the computing cost for predicting transient particle transport in indoor environments.

| S-EPMC7090511 | biostudies-literature

GPU-accelerated Red Blood Cells Simulations with Transport Dissipative Particle Dynamics.

Project description:Mesoscopic numerical simulations provide a unique approach for the quantification of the chemical influences on red blood cell functionalities. The transport Dissipative Particles Dynamics (tDPD) method can lead to such effective multiscale simulations due to its ability to simultaneously capture mesoscopic advection, diffusion, and reaction. In this paper, we present a GPU-accelerated red blood cell simulation package based on a tDPD adaptation of our red blood cell model, which can correctly recover the cell membrane viscosity, elasticity, bending stiffness, and cross-membrane chemical transport. The package essentially processes all computational workloads in parallel by GPU, and it incorporates multi-stream scheduling and non-blocking MPI communications to improve inter-node scalability. Our code is validated for accuracy and compared against the CPU counterpart for speed. Strong scaling and weak scaling are also presented to characterizes scalability. We observe a speedup of 10.1 on one GPU over all 16 cores within a single node, and a weak scaling efficiency of 91% across 256 nodes. The program enables quick-turnaround and high-throughput numerical simulations for investigating chemical-driven red blood cell phenomena and disorders.

| S-EPMC5667691 | biostudies-literature

Aquaporin-4 dynamics in orthogonal arrays in live cells visualized by quantum dot single particle tracking.

Project description:Freeze-fracture electron microscopy (FFEM) indicates that aquaporin-4 (AQP4) water channels can assemble in cell plasma membranes in orthogonal arrays of particles (OAPs). We investigated the determinants and dynamics of AQP4 assembly in OAPs by tracking single AQP4 molecules labeled with quantum dots at an engineered external epitope. In several transfected cell types, including primary astrocyte cultures, the long N-terminal "M1" form of AQP4 diffused freely, with diffusion coefficient approximately 5 x 10(-10) cm(2)/s, covering approximately 5 microm in 5 min. The short N-terminal "M23" form of AQP4, which by FFEM was found to form OAPs, was relatively immobile, moving only approximately 0.4 microm in 5 min. Actin modulation by latrunculin or jasplakinolide did not affect AQP4-M23 diffusion, but deletion of its C-terminal postsynaptic density 95/disc-large/zona occludens (PDZ) binding domain increased its range by approximately twofold over minutes. Biophysical analysis of short-range AQP4-M23 diffusion within OAPs indicated a spring-like potential, with a restoring force of approximately 6.5 pN/microm. These and additional experiments indicated that 1) AQP4-M1 and AQP4-M23 isoforms do not coassociate in OAPs; 2) OAPs can be imaged directly by total internal reflection fluorescence microscopy; and 3) OAPs are relatively fixed, noninterconvertible assemblies that do not require cytoskeletal or PDZ-mediated interactions for formation. Our measurements are the first to visualize OAPs in live cells.

| S-EPMC2488293 | biostudies-literature

Asymmetric Particle Transport and Light-Cone Dynamics Induced by Anyonic Statistics.

Project description:We study the nonequilibrium dynamics of Abelian anyons in a one-dimensional system. We find that the interplay of anyonic statistics and interactions gives rise to spatially asymmetric particle transport together with a novel dynamical symmetry that depends on the anyonic statistical angle and the sign of interactions. Moreover, we show that anyonic statistics induces asymmetric spreading of quantum information, characterized by asymmetric light cones of out-of-time-ordered correlators. Such asymmetric dynamics is in sharp contrast to the dynamics of conventional fermions or bosons, where both the transport and information dynamics are spatially symmetric. We further discuss experiments with cold atoms where the predicted phenomena can be observed using state-of-the-art technologies. Our results pave the way toward experimentally probing anyonic statistics through nonequilibrium dynamics.

| S-EPMC6990657 | biostudies-literature

Inferring sparse networks for noisy transient processes.

Project description:Inferring causal structures of real world complex networks from measured time series signals remains an open issue. The current approaches are inadequate to discern between direct versus indirect influences (i.e., the presence or absence of a directed arc connecting two nodes) in the presence of noise, sparse interactions, as well as nonlinear and transient dynamics of real world processes. We report a sparse regression (referred to as the l1-min) approach with theoretical bounds on the constraints on the allowable perturbation to recover the network structure that guarantees sparsity and robustness to noise. We also introduce averaging and perturbation procedures to further enhance prediction scores (i.e., reduce inference errors), and the numerical stability of l1-min approach. Extensive investigations have been conducted with multiple benchmark simulated genetic regulatory network and Michaelis-Menten dynamics, as well as real world data sets from DREAM5 challenge. These investigations suggest that our approach can significantly improve, oftentimes by 5 orders of magnitude over the methods reported previously for inferring the structure of dynamic networks, such as Bayesian network, network deconvolution, silencing and modular response analysis methods based on optimizing for sparsity, transients, noise and high dimensionality issues.

| S-EPMC4768174 | biostudies-literature

RNA dynamics in live Escherichia coli cells.

Project description:We describe a method for tracking RNA molecules in Escherichia coli that is sensitive to single copies of mRNA, and, using the method, we find that individual molecules can be followed for many hours in living cells. We observe distinct characteristic dynamics of RNA molecules, all consistent with the known life history of RNA in prokaryotes: localized motion consistent with the Brownian motion of an RNA polymer tethered to its template DNA, free diffusion, and a few examples of polymer chain dynamics that appear to be a combination of chain fluctuation and chain elongation attributable to RNA transcription. We also quantify some of the dynamics, such as width of the displacement distribution, diffusion coefficient, chain elongation rate, and distribution of molecule numbers, and compare them with known biophysical parameters of the E. coli system.

| S-EPMC509199 | biostudies-literature

Correlative live-cell and superresolution microscopy reveals cargo transport dynamics at microtubule intersections.

Project description:Intracellular transport plays an essential role in maintaining the organization of polarized cells. Motor proteins tether and move cargos along microtubules during long-range transport to deliver them to their proper location of function. To reach their destination, cargo-bound motors must overcome barriers to their forward motion such as intersection points between microtubules. The ability to visualize how motors navigate these barriers can give important information about the mechanisms that lead to efficient transport. Here, we first develop an all-optical correlative imaging method based on single-particle tracking and superresolution microscopy to map the transport trajectories of cargos to individual microtubules with high spatiotemporal resolution. We then use this method to study the behavior of lysosomes at microtubule-microtubule intersections. Our results show that the intersection poses a significant hindrance that leads to long pauses in transport only when the separation distance of the intersecting microtubules is smaller than ?100 nm. However, the obstructions are typically overcome by the motors with high fidelity by either switching to the intersecting microtubule or eventually passing through the intersection. Interestingly, there is a large tendency to maintain the polarity of motion (anterograde or retrograde) after the intersection, suggesting a high degree of regulation of motor activity to maintain transport in a given direction. These results give insights into the effect of the cytoskeletal geometry on cargo transport and have important implications for the mechanisms that cargo-bound motors use to maneuver through the obstructions set up by the complex cytoskeletal network.

| S-EPMC3587250 | biostudies-literature

Visualization of mycobacterial membrane dynamics in live cells.

Project description:Mycobacteria are endowed with a highly impermeable mycomembrane that confers intrinsic resistance to many antibiotics. Several unique mycomembrane glycolipids have been isolated and structurally characterized, but the underlying organization and dynamics of glycolipids within the cell envelope remain poorly understood. We report here a study of mycomembrane dynamics that was enabled by trehalose-fluorophore conjugates capable of labeling trehalose glycolipids in live actinomycetes. We identified fluorescein-trehalose analogues that are metabolically incorporated into the trehalose mycolates of representative Mycobacterium, Corynebacterium, Nocardia, and Rhodococcus species. Using these probes, we studied the mobilities of labeled glycolipids by time-lapse microscopy and fluorescence recovery after photobleaching experiments and found that mycomembrane fluidity varies widely across species and correlates with mycolic acid structure. Finally, we discovered that treatment of mycobacteria with ethambutol, a front-line tuberculosis (TB) drug, significantly increases mycomembrane fluidity. These findings enhance our understanding of mycobacterial cell envelope structure and dynamics and have implications for development of TB drug cocktails.

| S-EPMC5345120 | biostudies-literature

Compact and blinking-suppressed quantum dots for single-particle tracking in live cells.

Project description:Quantum dots (QDs) offer distinct advantages over organic dyes and fluorescent proteins for biological imaging applications because of their brightness, photostability, and tunability. However, a major limitation is that single QDs emit fluorescent light in an intermittent on-and-off fashion called "blinking". Here we report the development of blinking-suppressed, relatively compact QDs that are able to maintain their favorable optical properties in aqueous solution. Specifically, we show that a linearly graded alloy shell can be grown on a small CdSe core via a precisely controlled layer-by-layer process, and that this graded shell leads to a dramatic suppression of QD blinking in both organic solvents and water. A substantial portion (>25%) of the resulting QDs does not blink (more than 99% of the time in the bright or "on" state). Theoretical modeling studies indicate that this type of linearly graded shell not only can minimize charge carrier access to surface traps but also can reduce lattice defects, both of which are believed to be responsible for carrier trapping and QD blinking. Further, we have evaluated the biological utility of blinking-suppressed QDs coated with polyethylene glycol (PEG)-based ligands and multidentate ligands. The results demonstrate that their optical properties are largely independent of surface coatings and solvating media, and that the blinking-suppressed QDs can provide continuous trajectories in live-cell receptor tracking studies.

| S-EPMC4266335 | biostudies-literature

Transport of Live Cells Under Sterile Conditions Using a Chemotactic Droplet.

Project description:1-Decanol droplets, formed in an aqueous medium containing decanoate at high pH, become chemotactic when a chemical gradient is placed in the external aqueous environment. We investigated if such droplets can be used as transporters for living cells. We developed a partially hydrophobic alginate capsule as a protective unit that can be precisely placed in a droplet and transported along chemical gradients. Once the droplets with cargo reached a defined final destination, the association of the alginate capsule and decanol droplet was disrupted and cargo deposited. Both Escherichia coli and Bacillus subtilis cells survived and proliferated after transport even though transport occurred under harsh and sterile conditions.

| S-EPMC5976712 | 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