Single-particle tracking uncovers dynamics of glutamate-induced retrograde transport of NF-κB p65 in living neurons

Retrograde transport of NF-κB from the synapse to the nucleus in neurons is mediated by the dynein/dynactin motor complex and can be triggered by synaptic activation. The calibre of axons is highly variable ranging down to 100 nm, aggravating the investigation of transport processes in neurites of living neurons using conventional light microscopy. In this study we quantified for the first time the transport of the NF-κB subunit p65 using high-density single-particle tracking in combination with photoactivatable fluorescent proteins in living mouse hippocampal neurons. We detected an increase of the mean diffusion coefficient (Dmean) in neurites from 0.12 ± 0.05 µm2/s to 0.61 ± 0.03 µm2/s after stimulation with glutamate. We further observed that the relative amount of retrogradely transported p65 molecules is increased after stimulation. Glutamate treatment resulted in an increase of the mean retrograde velocity from 10.9 ± 1.9 to 15 ± 4.9 µm/s, whereas a velocity increase from 9 ± 1.3 to 14 ± 3 µm/s was observed for anterogradely transported p65. This study demonstrates for the first time that glutamate stimulation leads to an increased mobility of single NF-κB p65 molecules in neurites of living hippocampal neurons.

Simulations of Ground-Water Flow, Transport, Age, and Particle Tracking near York, Nebraska, for a Study of Transport of Anthropogenic and Natural Contaminants (TANC) to Public-Supply Wells

The U.S. Geological Survey (USGS) is committed to providing the Nation with credible scientific information that helps to enhance and protect the overall quality of life and that facilitates effective management of water, biological, energy, and mineral resources (http://www.usgs.gov/). Information on the Nation’s water resources is critical to ensuring long-term availability of water that is safe for drinking and recreation and is suitable for industry, irrigation, and fish and wildlife. Population growth and increasing demands for water make the availability of that water, now measured in terms of quantity and quality, even more essential to the long-term sustainability of our communities and ecosystems. The USGS implemented the National Water-Quality Assessment (NAWQA) Program in 1991 to support national, regional, State, and local information needs and decisions related to water-quality management and policy (http://water.usgs.gov/nawqa). The NAWQA Program is designed to answer: What is the condition of our Nation’s streams and ground water? How are conditions changing over time? How do natural features and human activities affect the quality of streams and ground water, and where are those effects most pronounced? By combining information on water chemistry, physical characteristics, stream habitat, and aquatic life, the NAWQA Program aims to provide science-based insights for current and emerging water issues and priorities. From 1991-2001, the NAWQA Program completed interdisciplinary assessments and established a baseline understanding of water-quality conditions in 51 of the Nation’s river basins and aquifers, referred to as Study Units (http://water.usgs.gov/nawqa/studyu.html).

Anomalous diffusion evidenced by particle tracking at high frame rates.

Diffusion is a common phenomenon in nature and generally is associated with a system trying to reach a local or a global equilibrium state, as a result of highly irregular individual particle motion. Therefore it is of fundamental importance in physics, chemistry and biology. Particle tracking in complex fluids can reveal important characteristics of its properties. In living cells, we coat the microbead with a peptide (RGD) that binds to integrin receptors at the plasma membrane, which connects to the CSK. This procedure is based on the hypothesis that the microsphere can move only if the structure where it is attached move as well. Then, the observed trajectory of microbeads is a probe of the cytoskeleton (CSK), which is governed by several factors, including thermal diffusion, pressure gradients, and molecular motors. The possibility of separating the trajectories into passive and active diffusion may give information about the viscoelasticity of the cell structure and molecular motors activity. And also we could analyze the motion via generalized Stokes-Einstein relation, avoiding the use of any active techniques. Usually a 12 to 16 Frames Per Second (FPS) system is used to track the microbeads in cell for about 5 minutes. Several factors make this FPS limitation: camera computer communication, light, computer speed for online analysis among others. Here we used a high quality camera and our own software, developed in C++ and Linux, to reach high FPS. Measurements were conducted with samples for 10£ and 20£ objectives. We performed sequentially images with different intervals, all with 2 ¹s exposure. The sequences of intervals are in milliseconds: 4 5 ms (maximum speed) 14, 25, 50 and 100 FPS. Our preliminary results highlight the difference between passive and active diffusion, since the passive diffusion is represented by a Gaussian in the distribution of displacements of the center of mass of individual beads between consecutive frames. However, the active process, or anomalous diffusion, shows as long tails in the distribution of displacements.

Particle tracking at cryogenic temperatures: the Fast Annihilation Cryogenic Tracking (FACT) detector for the AEgIS antimatter gravity experiment

The AEgIS experiment is an interdisciplinary collaboration between atomic, plasma and particle physicists, with the scientific goal of performing the first precision measurement of the Earth's gravitational acceleration on antimatter. The principle of the experiment is as follows: cold antihydrogen atoms are synthesized in a Penning-Malmberg trap and are Stark accelerated towards a moiré deflectometer, the classical counterpart of an atom interferometer, and annihilate on a position sensitive detector. Crucial to the success of the experiment is an antihydrogen detector that will be used to demonstrate the production of antihydrogen and also to measure the temperature of the anti-atoms and the creation of a beam. The operating requirements for the detector are very challenging: it must operate at close to 4 K inside a 1 T solenoid magnetic field and identify the annihilation of the antihydrogen atoms that are produced during the 1 μs period of antihydrogen production. Our solution—called the FACT detector—is based on a novel multi-layer scintillating fiber tracker with SiPM readout and off the shelf FPGA based readout system. This talk will present the design of the FACT detector and detail the operation of the detector in the context of the AEgIS experiment.

Particle tracking in a salinity gradient: A method for measuring sinking rate of individual phytoplankton in the laboratory

This paper presents a new method to measure the sinking rates of individual phytoplankton “particles” (cells, chains, colonies, and aggregates) in the laboratory. Conventional particle tracking and high resolution video imaging were used to measure particle sinking rates and particle size. The stabilizing force of a very mild linear salinity gradient (1 ppt over 15 cm) prevented the formation of convection currents in the laboratory settling chamber. Whereas bulk settling methods such as SETCOL provide a single value of sinking rate for a population, this method allows the measurement of sinking rate and particle size for a large number of individual particles or phytoplankton within a population. The method has applications where sinking rates vary within a population, or where sinking rate-size relationships are important. Preliminary data from experiments with both laboratory and field samples of marine phytoplankton are presented here to illustrate the use of the technique, its applications, and limitations. Whereas this paper deals only with sinking phytoplankton, the method is equally valid for positively buoyant species, as well as nonbiological particles.

Study on Granular Dynamics in Vertically Vibrated Beds using Tracking Technique

The study of granular material is of great interest to many researchers in both engineering and science communities. The importance of such a study derives from its complex rheological character and also its significant role in a wide range of industrial applications, such as coal, food, plastics, pharmaceutical, powder metallurgy and mineral processing. A number of recent reports have been focused on the physics of non-cohesive granular material submitted to vertical vibration in either experimental or theoretical approaches. Such a kind of system can be used to separate, mix and dry granular materials in industries. It exhibits different instability behaviour on its surface when under vertical vibration, for example, avalanching, surface fluidization and surface wave, and these phenomena have attracted particular interest of many researchers. However, its fundamental understanding of the instability mechanism is not yet well-understood. This paper is therefore to study the dynamics of granular motion in such a kind of system using Positron Emission Particle Tracking (PEPT), which allows the motion of a single tracer particle to be followed in a non-invasive way. Features of the solids motion such as cycle frequency and dispersion index were investigated via means of authors’ specially-written programmes. Regardless of the surface behaviour, particles are found to travel in rotational movement in horizontal plane. Particle cycle frequency is found to increase strongly with increasing vibration amplitude. Particle dispersion also increased strongly with vibration amplitude. Horizontal dispersion is observed to always exceed vertical dispersion.

Tracking individual membrane proteins and their biochemistry: The power of direct observation

The advent of single molecule fluorescence microscopy has allowed experimental molecular biophysics and biochemistry to transcend traditional ensemble measurements, where the behavior of individual proteins could not be precisely sampled. The recent explosion in popularity of new super-resolution and super-localization techniques coupled with technical advances in optical designs and fast highly sensitive cameras with single photon sensitivity and millisecond time resolution have made it possible to track key motions, reactions, and interactions of individual proteins with high temporal resolution and spatial resolution well beyond the diffraction limit. Within the purview of membrane proteins and ligand gated ion channels (LGICs), these outstanding advances in single molecule microscopy allow for the direct observation of discrete biochemical states and their fluctuation dynamics. Such observations are fundamentally important for understanding molecular-level mechanisms governing these systems. Examples reviewed here include the effects of allostery on the stoichiometry of ligand binding in the presence of fluorescent ligands; the observation of subdomain partitioning of membrane proteins due to microenvironment effects; and the use of single particle tracking experiments to elucidate characteristics of membrane protein diffusion and the direct measurement of thermodynamic properties, which govern the free energy landscape of protein dimerization. The review of such characteristic topics represents a snapshot of efforts to push the boundaries of fluorescence microscopy of membrane proteins to the absolute limit.

Numerical issues in Lagrangian tracking and topological evolution of fluid particles in wallbounded turbulent flows

The determination of the local Lagrangian evolution of the flow topology in wall-bounded turbulence, and of the Lagrangian evolution associated with entrainment across the turbulent / non-turbulent interface into a turbulent boundary layer, require accurate tracking of a fluid particle and its local velocity gradients. This paper addresses the implementation of fluid-particle tracking in both a turbulent boundary layer direct numerical simulation and in a fully developed channel flow simulation. Determination of the sub-grid particle velocity is performed using both cubic B-spline, four-point Hermite spline and higher-order Hermite spline interpolation. Both wall-bounded flows show similar oscillations in the Lagrangian tracers of both velocity and velocity gradients, corresponding to the movement of particles across the boundaries of computational cells. While these oscillation in the particle velocity are relatively small and have negligible effect on the particle trajectories for time-steps of the order of CFL = 0.1, they appear to be the cause of significant oscillations in the evolution of the invariants of the velocity gradient tensor.

CFD modelling of the fast pyrolysis of an in-flight cellulosic particle subjected to convective heat transfer

The pyrolysis of a freely moving cellulosic particle inside a 41.7mgs -1 source continuously fed fluid bed reactor subjected to convective heat transfer is modelled. The Lagrangian approach is adopted for the particle tracking inside the reactor, while the flow of the inert gas is treated with the standard Eulerian method for gases. The model incorporates the thermal degradation of cellulose to char with simultaneous evolution of gases and vapours from discrete cellulosic particles. The reaction kinetics is represented according to the Broido–Shafizadeh scheme. The convective heat transfer to the surface of the particle is solved by two means, namely the Ranz–Marshall correlation and the limit case of infinitely fast external heat transfer rates. The results from both approaches are compared and discussed. The effect of the different heat transfer rates on the discrete phase trajectory is also considered.

Single particle motion of polymeric, colloidal, and biological materials

Small particles and their dynamics are of widespread interest due both to their unique properties and their ubiquity. Here, we investigate several classes of small particles: colloids, polymers, and liposomes. All these particles, due to their size on the order of microns, exhibit significant similarity in that they are large enough to be visualized in microscopes, but small enough to be significantly influenced by thermal (or Brownian) motion. Further, similar optical microscopy and experimental techniques are commonly employed to investigate all these particles. In this work, we develop single particle tracking techniques, which allow thorough characterization of individual particle dynamics, observing many behaviors which would be overlooked by methods which time or ensemble average. The various particle systems are also similar in that frequently, the signal-to-noise ratio represented a significant concern. In many cases, development of image analysis and particle tracking methods optimized to low signal-to-noise was critical to performing experimental observations. The simplest particles studied, in terms of their interaction potentials, were chemically homogeneous (though optically anisotropic) hard-sphere colloids. Using these spheres, we explored the comparatively underdeveloped conjunction of translation and rotation and particle hydrodynamics. Developing off this, the dynamics of clusters of spherical colloids were investigated, exploring how shape anisotropy influences the translation and rotation respectively. Transitioning away from uniform hard-sphere potentials, the interactions of amphiphilic colloidal particles were explored, observing the effects of hydrophilic and hydrophobic interactions upon pattern assembly and inter-particle dynamics. Interaction potentials were altered in a different fashion by working with suspensions of liposomes, which, while homogeneous, introduce the possibility of deformation. Even further degrees of freedom were introduced by observing the interaction of particles and then polymers within polymer suspensions or along lipid tubules. Throughout, while examination of the trajectories revealed that while by some measures, the averaged behaviors accorded with expectation, often closer examination made possible by single particle tracking revealed novel and unexpected phenomena.

Particle dynamics and airflow patterns in a ventilated two-zone enclosure

Understanding the transport mechanisms of aerosol particles in enclosures has broad ramifications in the context of cleaning strategies, and health risk assessment (e. g., occupational exposure). This paper addresses airflow pattern and aerosol transport mechanism in a ventilated two-zone enclosure with the outlet (exhaust location) situated at different locations. A numerical approach that combines a Eulerian simulation of turbulent flow with a Lagrangian particle-tracking algorithm is used. Simulations are carried out using solid suspensions with different sizes (1 to 100 micron) and densities (240 and 2300 kg/m3). The effect of location of the outlet (exhaust) on airflow patterns and aerosol dynamics is analyzed and quantified.

Finite element modelling of three-dimensional convection problems in fluid-saturated porous media heated from below

We use the finite element method to model three-dimensional convective pore-fluid flow in fluid-saturated porous media when they are heated from below. In particular, we employ the particle-tracking technique to mimic the trajectories of particles in three-dimensional fluid flow problems. The related numerical results demonstrated that: (1) The progressive asymptotic approach procedure, which was previously developed for the finite element modelling of two-dimensional convective pore-fluid flow problems, is equally applicable to the finite element modelling of three-dimensional convective pore-fluid flow in fluid-saturated porous media heated from below. (2) The perturbation of gravity at different planes has a significant effect on the pattern of three-dimensional convective pore-fluid flow and therefore, may influence the pattern of orebody formation and mineralization in three-dimensional hydrothermal systems. Copyright (C) 2001 John Wiley & Sons, Ltd.