Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect

Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli) where protein aggregates accumulate at the old pole region of the aging bacterium. Because of the potential of E. coli as a model organism, elucidating aging and protein aggregation in this bacterium may pave the way to significant advances in our global understanding of aging. A first obstacle along this path is to decipher the mechanisms by which protein aggregates are targeted to specific intercellular locations. Here, using an integrated approach based on individual-based modeling, time-lapse fluorescence microscopy and automated image analysis, we show that the movement of aging-related protein aggregates in E. coli is purely diffusive (Brownian). Using single-particle tracking of protein aggregates in live E. coli cells, we estimated the average size and diffusion constant of the aggregates. Our results evidence that the aggregates passively diffuse within the cell, with diffusion constants that depend on their size in agreement with the Stokes-Einstein law. However, the aggregate displacements along the cell long axis are confined to a region that roughly corresponds to the nucleoid-free space in the cell pole, thus confirming the importance of increased macromolecular crowding in the nucleoids. We thus used 3d individual-based modeling to show that these three ingredients (diffusion, aggregation and diffusion hindrance in the nucleoids) are sufficient and necessary to reproduce the available experimental data on aggregate localization in the cells. Taken together, our results strongly support the hypothesis that the localization of aging-related protein aggregates in the poles of E. coli results from the coupling of passive diffusion- aggregation with spatially non-homogeneous macromolecular crowding. They further support the importance of "soft" intracellular structuring (based on macromolecular crowding) in diffusion-based protein localization in E. coli.Comment: PLoS Computational Biology (2013

The Long and Viscous Road: Uncovering Nuclear Diffusion Barriers in Closed Mitosis

During Saccharomyces cerevisiae closed mitosis, parental identity is sustained by the asymmetric segregation of ageing factors. Such asymmetry has been hypothesized to occur via diffusion barriers, constraining protein lateral exchange in cellular membranes. Diffusion barriers have been extensively studied in the plasma membrane, but their identity and organization within the nucleus remain unknown. Here, we propose how sphingolipid domains, protein rings, and morphological changes of the nucleus may coordinate to restrict protein exchange between nuclear lobes. Our spatial stochastic model is based on several lines of experimental evidence and predicts that, while a sphingolipid domain and a protein ring could constitute the barrier during early anaphase; a sphingolipid domain spanning the bridge between lobes during late anaphase would be entirely sufficient. Additionally, we explore the structural organization of plausible diffusion barriers. Our work shows how nuclear diffusion barriers in closed mitosis may be emergent properties of simple nanoscale biophysical interactions.Comment: 21 pages, 6 figures and supplementary material (including 8 additional figures and a Table

Agent-based pedestrian modelling

When the focus of interest in geographical systems is at the very fine scale, at the level of streets and buildings for example, movement becomes central to simulations of how spatial activities are used and develop. Recent advances in computing power and the acquisition of fine scale digital data now mean that we are able to attempt to understand and predict such phenomena with the focus in spatial modelling changing to dynamic simulations of the individual and collective behaviour of individual decision-making at such scales. In this Chapter, we develop ideas about how such phenomena can be modelled showing first how randomness and geometry are all important to local movement and how ordered spatial structures emerge from such actions. We focus on developing these ideas for pedestrians showing how random walks constrained by geometry but aided by what agents can see, determine how individuals respond to locational patterns. We illustrate these ideas with three types of example: first for local scale street scenes where congestion and flocking is all important, second for coarser scale shopping centres such as malls where economic preference interferes much more with local geometry, and finally for semi-organised street festivals where management and control by police and related authorities is integral to the way crowds move

Advances in crowd analysis for urban applications through urban event detection

The recent expansion of pervasive computing technology has contributed with novel means to pursue human activities in urban space. The urban dynamics unveiled by these means generate an enormous amount of data. These data are mainly endowed by portable and radio-frequency devices, transportation systems, video surveillance, satellites, unmanned aerial vehicles, and social networking services. This has opened a new avenue of opportunities, to understand and predict urban dynamics in detail, and plan various real-time services and applications in response to that. Over the last decade, certain aspects of the crowd, e.g., mobility, sentimental, size estimation and behavioral, have been analyzed in detail and the outcomes have been reported. This paper mainly conducted an extensive survey on various data sources used for different urban applications, the state-of-the-art on urban data generation techniques and associated processing methods in order to demonstrate their merits and capabilities. Then, available open-access crowd data sets for urban event detection are provided along with relevant application programming interfaces. In addition, an outlook on a support system for urban application is provided which fuses data from all the available pervasive technology sources and finally, some open challenges and promising research directions are outlined

Continuous measurements of real-life bidirectional pedestrian flows on a wide walkway

Employing partially overlapping overhead \kinectTMS sensors and automatic pedestrian tracking algorithms we recorded the crowd traffic in a rectilinear section of the main walkway of Eindhoven train station on a 24/7 basis. Beside giving access to the train platforms (it passes underneath the railways), the walkway plays an important connection role in the city. Several crowding scenarios occur during the day, including high- and low-density dynamics in uni- and bi-directional regimes. In this paper we discuss our recording technique and we illustrate preliminary data analyses. Via fundamental diagrams-like representations we report pedestrian velocities and fluxes vs. pedestrian density. Considering the density range $0$ - $1.1\,$ped/m$^2$, we find that at densities lower than $0.8\,$ped/m$^2$ pedestrians in unidirectional flows walk faster than in bidirectional regimes. On the opposite, velocities and fluxes for even bidirectional flows are higher above $0.8\,$ped/m$^2$.Comment: 9 pages, 7 figure