Ensemble heterogeneity mimics ageing for endosomal dynamics within eukaryotic cells.

Transport processes of many structures inside living cells display anomalous diffusion, such as endosomes in eukaryotic cells. They are also heterogeneous in space and time. Large ensembles of single particle trajectories allow the heterogeneities to be quantified in detail and provide insights for mathematical modelling. The development of accurate mathematical models for heterogeneous dynamics has the potential to enable the design and optimization of various technological applications, for example, the design of effective drug delivery systems. Central questions in the analysis of anomalous dynamics are ergodicity and statistical ageing which allow for selecting the proper model for the description. It is believed that non-ergodicity and ageing occur concurrently. However, we found that the anomalous dynamics of endosomes is paradoxical since it is ergodic but shows ageing. We show that this behaviour is caused by ensemble heterogeneity that, in addition to space-time heterogeneity within a single trajectory, is an inherent property of endosomal motion. Our work introduces novel approaches for the analysis and modelling of heterogeneous dynamics.

Intertwined and Finely Balanced: Endoplasmic Reticulum Morphology, Dynamics, Function, and Diseases.

The endoplasmic reticulum (ER) is an organelle that is responsible for many essential subcellular processes. Interconnected narrow tubules at the periphery and thicker sheet-like regions in the perinuclear region are linked to the nuclear envelope. It is becoming apparent that the complex morphology and dynamics of the ER are linked to its function. Mutations in the proteins involved in regulating ER structure and movement are implicated in many diseases including neurodegenerative diseases such as Alzheimer's, Parkinson's, and amyotrophic lateral sclerosis (ALS). The ER is also hijacked by pathogens to promote their replication. Bacteria such as Legionella pneumophila and Chlamydia trachomatis, as well as the Zika virus, bind to ER morphology and dynamics-regulating proteins to exploit the functions of the ER to their advantage. This review covers our understanding of ER morphology, including the functional subdomains and membrane contact sites that the organelle forms. We also focus on ER dynamics and the current efforts to quantify ER motion and discuss the diseases related to ER morphology and dynamics.

Local Analysis of Heterogeneous Intracellular Transport: Slow and Fast Moving Endosomes.

Trajectories 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 Szwabinski and Aleksander Weron.

Non-Markovian intracellular transport with sub-diffusion and run-length dependent detachment rate.

Intracellular transport of organelles is fundamental to cell function and health. The mounting evidence suggests that this transport is in fact anomalous. However, the reasons for the anomaly is still under debate. We examined experimental trajectories of organelles inside a living cell and propose a mathematical model that describes the previously reported transition from sub-diffusive to super-diffusive motion. In order to explain super-diffusive behaviour at long times, we introduce non-Markovian detachment kinetics of the cargo: the rate of detachment is inversely proportional to the time since the last attachment. Recently, we observed the non-Markovian detachment rate experimentally in eukaryotic cells. Here we further discuss different scenarios of how this effective non-Markovian detachment rate could arise. The non-Markovian model is successful in simultaneously describing the time averaged variance (the time averaged mean squared displacement corrected for directed motion), the mean first passage time of trajectories and the multiple peaks observed in the distributions of cargo velocities. We argue that non-Markovian kinetics could be biologically beneficial compared to the Markovian kinetics commonly used for modelling, by increasing the average distance the cargoes travel when a microtubule is blocked by other filaments. In turn, sub-diffusion allows cargoes to reach neighbouring filaments with higher probability, which promotes active motion along the microtubules.

Reduction of coherent artefacts in super-resolution fluorescence localisation microscopy.

Super-resolution localisation microscopy techniques depend on uniform illumination across the field of view, otherwise the resolution is degraded, resulting in imaging artefacts such as fringes. Lasers are currently the light source of choice for switching fluorophores in PALM/STORM methods due to their high power and narrow bandwidth. However, the high coherence of these sources often creates interference phenomena in the microscopes, with associated fringes/speckle artefacts in the images. We quantitatively demonstrate the use of a polymer membrane speckle scrambler to reduce the effect of the coherence phenomena. The effects of speckle in the illumination plane, at the camera and after software localisation of the fluorophores, were characterised. Speckle phenomena degrade the resolution of the microscope at large length scales in reconstructed images, effects that were suppressed by the speckle scrambler, but the small length scale resolution is unchanged at ∼30 nm.

How and why does the endoplasmic reticulum move?

The ER (endoplasmic reticulum) is a fascinating organelle that is highly dynamic, undergoing constant movement and reorganization. It has many key roles, including protein synthesis, folding and trafficking, calcium homoeostasis and lipid synthesis. It can expand in size when needed, and the balance between tubular and lamellar regions can be altered. The distribution and organization of the ER depends on both motile and static interactions with microtubules and the actin cytoskeleton. In the present paper, we review how the ER moves, and consider why this movement may be important for ER and cellular function.

Molecular motors and the Golgi complex: staying put and moving through.

The Golgi apparatus is a highly dynamic organelle through which nascent proteins released from the endoplasmic reticulum (ER) are trafficked. Proteins are post-translationally modified within the Golgi and subsequently packaged into carriers for transport to a variety of cellular destinations. This transit of proteins, as well as the maintenance of Golgi structure and position, is highly dependent upon the actin and microtubule cytoskeletons and their associated molecular motors. Here we review how motors contribute to the correct functioning of the Golgi in higher eukaryotes and discuss the secretory pathway as a model system for studying cooperation between motor proteins.

Microtubule motors: moving forward on many fronts.

Microtubule motors drive the movement of many different cargoes in eukaryotic cells. A combination of in vitro and in vivo approaches has led to a better understanding of their mechanism of action and function and are also revealing that the microtubule track itself may have an important role to play in directing cargo movement within the cell.

N-terminal kinesins: many and various.

Molecular motors are a fascinating group of proteins that have vital roles in a huge variety of cellular processes. They all share the ability to produce force through the hydrolysis of adenosine triphosphate, and fall into classes groups: the kinesins, myosins and the dyneins. The kinesin superfamily itself can be split into three major groups depending on the position of the motor domain, which is localized N-terminally, C-terminally, or internally. This review focuses on the N-terminal kinesins, providing a brief overview of their roles within the cell, and illustrating recent key developments in our understanding of how these proteins function.

Intermediate filaments: vimentin moves in.

Vimentin intermediate filaments move bi-directionally along microtubules in the cell. Recent work has identified the microtubule motor cytoplasmic dynein as the missing inward-directed motor that drives this movement.