116 research outputs found
Precise Particle Tracking Against a Complicated Background: Polynomial Fitting with Gaussian Weight
We present a new particle tracking software algorithm designed to accurately
track the motion of low-contrast particles against a background with large
variations in light levels. The method is based on a polynomial fit of the
intensity around each feature point, weighted by a Gaussian function of the
distance from the centre, and is especially suitable for tracking endogeneous
particles in the cell, imaged with bright field, phase contrast or fluorescence
optical microscopy. Furthermore, the method can simultaneously track particles
of all different sizes, and allows significant freedom in their shape. The
algorithm is evaluated using the quantitative measures of accuracy and
precision of previous authors, using simulated images at variable
signal-to-noise ratios. To these we add a new test of the error due to a
non-uniform background. Finally the tracking of particles in real cell images
is demonstrated. The method is made freely available for non-commencial use as
a software package with a graphical user-inferface, which can be run within the
Matlab programming environment
Direct conversion of rheological compliance measurements into storage and loss moduli
We remove the need for Laplace/inverse-Laplace transformations of
experimental data, by presenting a direct and straightforward mathematical
procedure for obtaining frequency-dependent storage and loss moduli
( and respectively), from time-dependent experimental
measurements. The procedure is applicable to ordinary rheological creep
(stress-step) measurements, as well as all microrheological techniques, whether
they access a Brownian mean-square displacement, or a forced compliance. Data
can be substituted directly into our simple formula, thus eliminating
traditional fitting and smoothing procedures that disguise relevant
experimental noise.Comment: 4 page
Extreme heterogeneity in the microrheology of lamellar surfactant gels analyzed with neural networks
The heterogeneity of the viscoelasticity of a lamellar gel network based on
cetyl-trimethylammonium chloride (CTAC) and ceto-stearyl alcohol was studied
using particle tracking microrheology. A recurrent neural network (RNN)
architecture was used for estimating the Hurst exponent, , on small sections
of tracks of probe spheres moving with fractional Brownian motion. Thus dynamic
segmentation of tracks via neural networks was used in microrheology for the
first time and it is significantly more accurate than using mean square
displacements. An ensemble of 414 particles produces a mean squared
displacement (MSD) that is subdiffusive in time, , with a power law of the
form , indicating power law viscoelasticity. RNN analysis of
the probability distributions of , combined with detailed analysis of the
time-averaged MSDs of individual tracks, revealed diverse diffusion processes
belied by the simple scaling of the ensemble MSD, such as caging phenomena,
which give rise to the complex viscoelasticity of lamellar gels.Comment: 15 pages without references (17 with references), 13 figure
Memory effects and L\'evy walk dynamics in intracellular transport of cargoes
We demonstrate the phenomenon of cumulative inertia in intracellular
transport involving multiple motor proteins in human epithelial cells by
measuring the empirical survival probability of cargoes on the microtubule and
their detachment rates. We found the longer a cargo moves along a microtubule,
the less likely it detaches from it. As a result, the movement of cargoes is
non-Markovian and involves a memory. We observe memory effects on the scale of
up to 2 seconds. We provide a theoretical link between the measured detachment
rate and the super-diffusive Levy walk-like cargo movement.Comment: 9 pages, 6 figure
Network organisation and the dynamics of tubules in the endoplasmic reticulum
From Springer Nature via Jisc Publications RouterHistory: received 2021-04-26, accepted 2021-06-27, registration 2021-07-19, pub-electronic 2021-08-10, online 2021-08-10, collection 2021-12Publication status: PublishedFunder: Biotechnology and Biological Sciences Research Council; doi: http://dx.doi.org/10.13039/501100000268; Grant(s): BB/H017828/1Funder: Wellcome Trust; doi: http://dx.doi.org/10.13039/100010269; Grant(s): 215189/Z/19/ZFunder: Engineering and Physical Sciences Research Council; doi: http://dx.doi.org/10.13039/501100000266Abstract: The endoplasmic reticulum (ER) is a eukaryotic subcellular organelle composed of tubules and sheet-like areas of membrane connected at junctions. The tubule network is highly dynamic and undergoes rapid and continual rearrangement. There are currently few tools to evaluate network organisation and dynamics. We quantified ER network organisation in Vero and MRC5 cells, and developed an analysis workflow for dynamics of established tubules in live cells. The persistence length, tubule length, junction coordination number and angles of the network were quantified. Hallmarks of imbalances in ER tension, indications of interactions with microtubules and other subcellular organelles, and active dynamics were observed. Clear differences in dynamic behaviour were observed for established tubules at different positions within the cell using itemset mining. We found that tubules with activity-driven fluctuations were more likely to be located away from the cell periphery and a population of peripheral tubules with no signs of active motion was found
Intracellular microrheology of motile Amoeba proteus
The motility of motile Amoeba proteus was examined using the technique of
passive particle tracking microrheology, with the aid of newly-developed
particle tracking software, a fast digital camera and an optical microscope. We
tracked large numbers of endogeneous particles in the amoebae, which displayed
subdiffusive motion at short time scales, corresponding to thermal motion in a
viscoelastic medium, and superdiffusive motion at long time scales due to the
convection of the cytoplasm. Subdiffusive motion was characterised by a
rheological scaling exponent of 3/4 in the cortex, indicative of the
semiflexible dynamics of the actin fibres. We observed shear-thinning in the
flowing endoplasm, where exponents increased with increasing flow rate; i.e.
the endoplasm became more fluid-like. The rheology of the cortex is found to be
isotropic, reflecting an isotropic actin gel. A clear difference was seen
between cortical and endoplasmic layers in terms of both viscoelasticity and
flow velocity, where the profile of the latter is close to a Poiseuille flow
for a Newtonian fluid
The First Passage Probability of Intracellular Particle Trafficking
The first passage probability (FPP), of trafficked intracellular particles
reaching a displacement L, in a given time t or inverse velocity S = t/L, can
be calculated robustly from measured particle tracks, and gives a measure of
particle movement in which different types of motion, e.g. diffusion, ballistic
motion, and transient run-rest motion, can readily be distinguished in a single
graph, and compared with mathematical models. The FPP is attractive in that it
offers a means of reducing the data in the measured tracks, without making
assumptions about the mechanism of motion: for example, it does not employ
smoothing, segementation or arbitrary thresholds to discriminate between
different types of motion in a particle track. Taking experimental data from
tracked endocytic vesicles, and calculating the FPP, we see how three molecular
treatments affect the trafficking. We show the FPP can quantify complicated
movement which is neither completely random nor completely deterministic,
making it highly applicable to trafficked particles in cell biology.Comment: Article: 13 pages, 8 figure
Dual self-assembly of supramolecular peptide nanotubes to provide stabilisation in water
Self-assembling peptides have the ability to spontaneously aggregate into large ordered structures. The reversibility of the peptide hydrogen bonded supramolecular assembly make them tunable to a host of different applications, although it leaves them highly dynamic and prone to disassembly at the low concentration needed for biological applications. Here we demonstrate that a secondary hydrophobic interaction, near the peptide core, can stabilise the highly dynamic peptide bonds, without losing the vital solubility of the systems in aqueous conditions. This hierarchical self-assembly process can be used to stabilise a range of different β-sheet hydrogen bonded architectures
Local Analysis of Heterogeneous Intracellular Transport: Slow and Fast Moving Endosomes
From MDPI via Jisc Publications RouterHistory: accepted 2021-07-23, pub-electronic 2021-07-27Publication status: PublishedFunder: Engineering and Physical Sciences Research Council; Grant(s): EP/V008641/1Funder: Wellcome Trust; Grant(s): Grant No. 215189/Z/19/ZFunder: Basque Government; Grant(s): BERC 2018–2021 programsFunder: Spanish Ministry of Economy and Competitiveness MINECO; Grant(s): BCAM Severo Ochoa excellence accreditation SEV-2017-0718Trajectories of endosomes inside living eukaryotic cells are highly heterogeneous in space and time and diffuse anomalously due to a combination of viscoelasticity, caging, aggregation and active transport. Some of the trajectories display switching between persistent and anti-persistent motion, while others jiggle around in one position for the whole measurement time. By splitting the ensemble of endosome trajectories into slow moving subdiffusive and fast moving superdiffusive endosomes, we analyzed them separately. The mean squared displacements and velocity auto-correlation functions confirm the effectiveness of the splitting methods. Applying the local analysis, we show that both ensembles are characterized by a spectrum of local anomalous exponents and local generalized diffusion coefficients. Slow and fast endosomes have exponential distributions of local anomalous exponents and power law distributions of generalized diffusion coefficients. This suggests that heterogeneous fractional Brownian motion is an appropriate model for both fast and slow moving endosomes. This article is part of a Special Issue entitled: “Recent Advances In Single-Particle Tracking: Experiment and Analysis” edited by Janusz Szwabiński and Aleksander Weron
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