Physical constraints on microbial behavior How you act if you are very small

Physical constraints limit the way in which an organism as small asEscherichia coli can interact with its surroundings. These constraints are listed, together with references to the relevant literature.     

Chemotaxis of a eukaryotic cell in complex gradients of chemoattractants

We studied the chemotaxis of a eukaryotic cell by constructing a mathematical model that takes into account chemical kinetics as well as the cellular shape. A cell is defined as a single domain on discrete two-dimensional grids. In the cellular domain each grid contains three kinds of molecule, an activator and inhibitor of the actin polymerization, and polymerized actins. The external signal promotes production of both activator and inhibitor and thus changes the amount of polymerized actins. If the amount of polymerized actins in a grid of the cell border (i.e., the cellular membrane) is larger than a certain threshold, then a new grid adjacent to the border is assigned to the cellular grid. Upon this change of the cellular shape, constraints are imposed to preserve the cellular volume and to make the length of the cellular border as small as possible. The cell moves in the grid space driven by this change of the cellular shape. We succeeded in reproducing chemotaxis in a linear gradient. For two more complex gradients, the behavior of our cell is consistent with experimental results.This work was presented, in part, at the 9th International Symposium on Artificial Life and Robotics, Oita, Japan, January 28–30, 2004     

Effectiveness factor for spatial gradient sensing in living cells

We consider the steady-state pattern of messenger molecules produced in the membrane of a cell perceiving and responding to an extracellular gradient of chemoattractant, which directs cell movement towards the chemoattractant source. Specifically, we analyze the undesirable effect of lateral diffusion in blurring the intracellular messenger profile. The concept of an effectiveness factor, akin to the analysis of reactions in porous catalysts, is applied to the spatial gradient sensing problem, with the distinction that slow, not fast, diffusion is required for effective gradient sensing. Analytical effectiveness factor expressions are derived for ideal geometries and then generalized to arbitrary cell shapes. In the case of mouse fibroblasts responding to gradients of platelet-derived growth factor, we conclude that the cell morphology and orientation with respect to the gradient can dictate whether messenger diffusion obliterates gradient sensing or has very little effect. The analysis outlined here allows the effect of intracellular messenger diffusion on spatial gradient sensing to be quantified for individual cells.     

Individual-based modelling of growth and migration of Salmonella enteritidis in hens' eggs

An individual-based model (IbM) was developed to describe the growth and migration of Salmonella enteritidis in hens' eggs. The Bacteria Simulator (BacSim) environment was used to implement the model; the bacteria are represented by spheres that grow by nutrient uptake and divide in two daughter cells upon exceeding a certain threshold volume. Motility of the Salmonella bacteria was described by a run and tumble mechanism. For the sake of simplicity, the bacteria were assumed to grow exponentially, an appropriate assumption for the initial phase of growth relevant for shelf-life predictions. Both albumen and yolk were assumed to be homogeneous. The impact of several model parameters (chemotaxis, growth rate, initial contamination numbers and bacterial swimming speed) was assessed by a sensitivity analysis. The results show that chemotaxis towards the yolk would have a strong effect on the time needed to reach the vitelline membrane, an aspect that future research should focus on. The contamination position had less impact on the time to reach the vitelline membrane. The simulation results illustrate the need for more detailed knowledge on the subject of bacterial migration in hens' eggs. Our model can easily incorporate this knowledge when it becomes available.     

Direct visualization of receptor arrays in frozen-hydrated sections and plunge-frozen specimens of E. coli engineered to overproduce the chemotaxis receptor Tsr

We have recently reported electron tomographic studies of sections obtained from chemically fixed E. coli cells overproducing the 60‐kDa chemotaxis receptor Tsr. Membrane extracts from these cells prepared in the presence of Tween‐80 display hexagonally close‐packed microcrystalline assemblies of Tsr, with a repeating unit large enough to accommodate six Tsr molecules arranged as trimers of receptor dimers. Here, we report the direct visualization of the Tsr receptor clusters in (i) vitrified cell suspensions of cells overproducing Tsr, prepared by rapid plunge‐freezing, and (ii) frozen‐hydrated sections obtained from cells frozen under high pressure. The frozen‐hydrated sections were generated by sectioning at ?150 °C using a diamond knife with a 25° knife angle, with nominal thicknesses ranging from 20 to 60 nm. There is excellent correspondence between the spatial arrangement of receptors in thin frozen‐hydrated sections and the arrangements found in negatively stained membrane extracts and plunge‐frozen cells, highlighting the potential of using frozen‐hydrated sections for the study of macromolecular assemblies within cells under near‐native conditions.     

Characterization of transport in microfluidic gradient generators

We present a two-dimensional model that describes the concentration profile of a class of previously reported microfluidic devices which are of particular interest in cellular taxis research. The devices generate stable concentration gradients by mixing and dividing two or more external inputs into a large number of discrete streams. This study focuses specifically on modeling the confluence of the discrete streams in a long chamber. We derive a closed-form solution for gradient generators with any arbitrary number of sampling streams. By relating the physical dimensions to the Péclet number, we create a model independent of flow rate and therefore dependent only on the specific nature of the boundary condition provided by the upstream network. As a result, the modeling method we propose may help evaluate the effectiveness of competing gradient generation schemes. Finally, our analytical work introduces a framework for developing simple design rules of interest to experimentalists working with these devices.

A systematic approach to the problem of odour source localisation

Although chemical sensing is far simpler than vision or hearing, navigation in a chemical diffusion field is still not well understood. Biological studies have already demonstrated the use of various search methods (e.g., chemotaxis and biased random walk), but robotics research could provide new ways to investigate principles of olfactory-based search skills (Webb, 2000; Grasso, 2001). In previous studies on odour source localisation, we have tested three biologically inspired search strategies: chemotaxis, biased random walk, and a combination of these methods (Kadar and Virk, 1998; Lytridis et al., 2001). The main objective of the present paper is to demonstrate how simulation and robot experiments could be used conjointly to systematically study these search strategies. Specifically, simulation studies are used to calibrate and test our three strategies in concentric diffusion fields with various noise levels. An experiment with a mobile robot was also conducted to assess these strategies in a real diffusion field. The results of this experiment are similar to those of simulation studies showing that chemotaxis is a more efficient but less robust strategy than biased random walk. Overall, the combined strategy seems to be superior to chemotaxis and biased random walk in both simulation and robot experiment. Christodoulos Lytridis received a BEng degree in electronic and computer engineering, MSc degree in mobile robotics and PhD in Olfactory based navigation for mobile robots from the University of Portsmouth. His research interests include odor-based cooperative navigation, biologically inspired navigational methods, and odor sensors for mobile robots. He is an associate member of the Institution of Electrical Engineering. Endre E. Kadar is a senior lecturer in psychology at the University of Portsmouth. He began his academic career as a theoretical mathematician at the Institute of Hydraulic Planning, working in applied modelling on a variety of problems in engineering. Then he moved to the University of Connecticut to work as a teaching and research assistant and received his PhD in experimental psychology in 1996. His PhD research project has dealt with the problem of ecological foundation of perceptual control of locomotion. After moving to Portsmouth in 1996, his theoretical work provided the basis for a productive collaboration with engineers in robotics. Also, these novel field theoretical ideas have resulted in radically new approaches to exploratory learning and visual control of high speed driving. Application of these approaches has been supported by several ESRC grants. Gurvinder S. Virk graduated with first class honours in electrical and electronic engineering (University of Manchester) and received a PhD in control theory (Imperial College, London). He has followed an academic career working at Sheffield City Polytechnic, Universities of Southampton, Sheffield and Bradford, Portsmouth and is now professor of control and robotics at the University of Leeds. His main research interests include robotics, building and energy management systems, and application of advanced model-based control systems. He has held several grants from national and European sources, as well as industry (the total value of ￡11M). He has more then 200 publications, including four books. He coordinated the European thematic network CLAWAR and has been involved in developing robots for exploring volcanic environments, inspection of highway bridges and dams, and biomedical applications. He is chairman of the ISO TC184/SC2 Advisory Group on Standards for mobile service robots. He is Fellow of the Institution of Engineering and Technology, Fellow of the Chartered Institution of Building Services Engineers, Fellow of the Institution of Applied Mathematics and Its Applications. He is Charted Engineer and a Charted Mathematician. He has been awarded the Freedom of the City of London for his work in promoting Information Technology.     

Motility,mixing, and multicellularity

A fundamental issue in evolutionary biology is the transition from unicellular to multicellular organisms, and the cellular differentiation that accompanies the increase in group size. Here we consider recent results on two types of “multicellular” systems, one produced by many unicellular organisms acting collectively, and another that is permanently multicellular. The former system is represented by groups of the bacterium Bacillus subtilis and the latter is represented by members of the colonial volvocalean green algae. In these flagellated organisms, the biology of chemotaxis, metabolism and cell–cell signaling is intimately connected to the physics of buoyancy, motility, diffusion, and mixing. Our results include the discovery in bacterial suspensions of intermittent episodes of disorder and collective coherence characterized by transient, recurring vortex streets and high-speed jets of cooperative swimming. These flow structures markedly enhance transport of passive tracers, and therefore likely have significant implications for intercellular communication. Experiments on the Volvocales reveal that the sterile flagellated somatic cells arrayed on the surface of Volvox colonies are not only important for allowing motion toward light (phototaxis), but also play a crucial role in driving fluid flows that transport dissolved molecular species. These flows, generated by the collective beating of flagella, confer a synergistic advantage with regard to transport of nutrients and chemical messengers. They allow these species to circumvent a nutrient acquisition bottleneck which would exist if transport were purely diffusive, and thereby evolve to larger multicellular individuals. In both cases, a higher level of organization, specialization and complexity counteract the higher costs inherent to larger groups.     

多态细菌趋药性优化

在细菌群趋药性规则与细菌趋药性算法的基础上,提出一种新的函数优化算法——多态细菌趋药性算法。该算法克服了细菌趋药性算法收敛较慢、易陷入局部最优的不足,利用菌群之间的交互信息来修正其觅食过程。对不同函数优化结果表明该算法性能优于遗传算法、粒子群算法、细菌趋药性算法,是一种具有进一步研究价值的集群函数优化方法。