Plasmodium Of Physarum Polycephalum Research Articles

Bio-Imitation of Mexican Migration Routes to the USA with Slime Mould on 3D Terrains

Plasmodium of Physarum polycephalum (P. polycephalum) is a large single cell visible by an unaided eye. It shows sophisticated behavioural traits in foraging for nutrients and developing an optimal transport network of protoplasmic tubes spanning sources of nutrients. When placed in an environment with distributed sources of nutrients the cell ‘computes’ an optimal graph spanning the nutrients by growing a network of protoplasmic tubes. P. polycephalum imitates development of man-made transport networks of a country when configuration of nutrients represents major urban areas. We employed this feature of the slime mould to imitate mexican migration to USA. The Mexican migration to USA is the World's largest migration system. We bio-physically imitated the migration using slime mould P. polycephalum. In laboratory experiments with 3D Nylon terrains of USA we imitated development of migratory routes from Mexico-USA border to ten urban areas with high concentration of Mexican migrants. From results of laboratory experiments we extracted topologies of migratory routes, and highlighted a role of elevations in shaping the human movement networks.

Amoeba-based computing for traveling salesman problem: Long-term correlations between spatially separated individual cells of Physarum polycephalum

A single-celled, multi-nucleated amoeboid organism, a plasmodium of the true slime mold Physarum polycephalum, can perform sophisticated computing by exhibiting complex spatiotemporal oscillatory dynamics while deforming its amorphous body. We previously devised an “amoeba-based computer (ABC)” to quantitatively evaluate the optimization capability of the amoeboid organism in searching for a solution to the traveling salesman problem (TSP) under optical feedback control. In ABC, the organism changes its shape to find a high quality solution (a relatively shorter TSP route) by alternately expanding and contracting its pseudopod-like branches that exhibit local photoavoidance behavior. The quality of the solution serves as a measure of the optimality of which the organism maximizes its global body area (nutrient absorption) while minimizing the risk of being illuminated (exposure to aversive stimuli). ABC found a high quality solution for the 8-city TSP with a high probability. However, it remains unclear whether intracellular communication among the branches of the organism is essential for computing. In this study, we conducted a series of control experiments using two individual cells (two single-celled organisms) to perform parallel searches in the absence of intercellular communication. We found that ABC drastically lost its ability to find a solution when it used two independent individuals. However, interestingly, when two individuals were prepared by dividing one individual, they found a solution for a few tens of minutes. That is, the two divided individuals remained correlated even though they were spatially separated. These results suggest the presence of a long-term memory in the intrinsic dynamics of this organism and its significance in performing sophisticated computing.

Functional organization of the vascular network of Physarum polycephalum

The plasmodium of the slime mould Physarum polycephalum forms a transportation network of veins, in which protoplasm is transported due to peristaltic pumping. This network forms a planar, weighted, undirected graph that, for the first time, can be extracted automatically from photographs or movies. Thus, data from real transportation networks have now become available for the investigation of network properties. We determine the local drag of the vein segments and use these data to calculate the transport efficiency. We unravel which veins form the backbone of the transportation network by using a centrality measure from graph theory. The principal vein segments lie on relatively ample cycles of veins, and the most important segments are those that belong simultaneously to two of these principal cycles. Each principal cycle contains a series of smaller cycles of veins of lower transport efficiency, thus reflecting the hierarchical and self-similar structure of the transportation network. Finally, we calculate accessibility maps that show how easily different nodes of the network may be reached from a given reference node.

J025024 真性粘菌変形体の運動を観察するためのDark Field Macroscopy 法の開発([J025-02]生体・生物における流れと熱・物質移動(2))

The Plasmodium of Physarum polycephalum is a unicellular and multinuclear giant amoeba. The cell body of the Plasmodium roughly consists of two parts, namely, sheet-like locomotive front and tubular rear part. The tubular structure of the Plasmodium is a kind of transportation network, and some studies have already been done on the structure and function of the plasmodial network. However, there are some difficulties in observing the minute structure of the plasmodial network. We thus developed a new method for the observation of the plasmodium that is a macroscopic implementation of dark-field microscopy.

Involvement of cyclic adenosine monophosphate in the control of motile behavior of Physarum polycephalum plasmodium

Possible involvement of autocrine factors into the control of motile behavior via a receptor-mediated mechanism was investigated in Physarum polycephalum plasmodium, a multinuclear amoeboid cell with the auto-oscillatory mode of motility. Cyclic adenosine monophosphate (cAMP) and extracellular cAMP-specific phosphodiesterase, its involvement into the control of plasmodium motile behavior was proved by action of its strong inhibitor, were regarded as putative autocrine factors. It was shown that the plasmodium secreted cAMP. When it was introduced into agar support, 0,1-1 mM cAMP induced a delay of the plasmodium spreading and its transition to migration. When locally applied, cAMP at the same concentrations induced typical for attractant action the increase in oscillation frequency and the decrease of ectoplasm elasticity. The ability to exhibit positive chemotaxis in cAMP gradient and the dependence of its realization were shown to depend on the plasmodium state. Chemotaxis test specimens obtained from the migrating plasmodium, unlike those obtained from growing culture, generate alternative fronts which compete effectively with fronts oriented towards the attractant increment. The results obtained support our supposition stated earlier that advance of the Physarum polycephalum plasmodium leading edge is determined by local extracellular cAMP gradients arising from a time delay between secretion and hydrolysis of the nucleotide.

Schlauschleimer in Reichsautobahnen

PurposeThe purpose of this paper is to develop experimental laboratory biological techniques for approximation of principle transport networks, optimizing transport links, and developing optimal solutions to current transport problems. It also aims to study how slime mould of Physarum polycephalum approximate autobahn networks in Germany.Design/methodology/approachThe paper considers the 21 most populous urban areas in Germany. It represents these areas with source of nutrients placed in the positions of slime mould growing substrate corresponding to the areas. At the beginning of each experiment slime mould is inoculated in the Berlin area. Slime mould exhibits foraging behavior and spans sources of nutrients (which represent urban areas) with a network of protoplasmic tubes (which approximate vehicular transport networks). The study analyzes structure of transport networks developed by slime mould and compares it with families of known proximity graphs. It also imitates slime‐mould response to simulated disaster by placing sources of chemo‐repellents in the positions of nuclear power plants.FindingsIt is found that the plasmodium of Physarum polycephalum develops a minimal approximation of a transport network spanning urban areas. Physarum‐developed network matches autobahn network very well. The high degree of similarity is preserved even when we place high‐demand constraints on repeatability of links in the experiments. Physarum approximates almost all major transport links. In response to a sudden disaster, gradually spreading from its epicenter, the Physarum transport networks react by abandoning transport links affected by disaster zone, enhancement of those unaffected directly by the disaster, massive sprouting from the epicenter, and increase of scouting activity in the regions distant to the epicenter of the disaster.Originality/valueExperimental methods and computer analysis techniques presented in the paper lay a foundation of novel biological laboratory approaches to imitation and prognostication of socio‐economical developments.

THE WORLD'S COLONIZATION AND TRADE ROUTES FORMATION AS IMITATED BY SLIME MOULD

The plasmodium of Physarum polycephalum is renowned for spanning sources of nutrients with networks of protoplasmic tubes. The networks transport nutrients and metabolites across the plasmodium's body. To imitate a hypothetical colonization of the world and the formation of major transportation routes we cut continents from agar plates arranged in Petri dishes or on the surface of a three-dimensional globe, represent positions of selected metropolitan areas with oat flakes and inoculate the plasmodium in one of the metropolitan areas. The plasmodium propagates towards the sources of nutrients, spans them with its network of protoplasmic tubes and even crosses bare substrate between the continents. From the laboratory experiments we derive weighted Physarum graphs, analyze their structure, compare them with the basic proximity graphs and generalized graphs derived from the Silk Road and the Asia Highway networks.

Coupling of phospholipase C and PI3K/PTEN signaling pathways in Physarum polycephalum: The action of U73122 on motile and autooscillatory activity of plasmodium

The possibility of tight coupling of phospholipase C with the signal pathway PI3K/ PTEN, a ubiquitous mechanism for the control of chemotaxis and cell shape in free-living amoebae and mammalian tissue cells, has been investigated in Physarum polycephalum plasmodium, a multinuclear amoeboid cell with the autooscillatory mode of motility. It was found that on the maintenance of contractile autooscillations and protoplasmic shuttle streaming, U73122, an inhibitor of the signal transduction to phospholipase C, induces degradation of the plasmodium frontal zone, decreases efficiency of locomotion and suppresses the chemotaxis toward glucose as well as the response of oscillator to this attractant. The identity of the effects of U73122 with those shown for wortmannin and LY294002, widely used PI3K inhibitors (Matveeva et al. 2008. Biophysics. 53, 533–538), suggests a tight coupling of the signal pathways of phospholipase C and PI3K/PTEN. U73122 increases the period of contractile oscillations and abolishes its cyclic changes attributed for the plasmodium migration. The results indicate that motile behavior of the plasmodium is under the receptor-mediated control.

Modeling and hardware implementation of an amoeba-like cellular automaton

Over the last few years, an increasing number of publications has shown that living organisms are very effective in finding solutions to complex mathematical problems which usually demand large computation resources. The plasmodium of the slime mould Physarum polycephalum is a successful example that has been used to solve path-finding problems on graphs and combinatorial problems. Cellular automata (CAs) computational model can capture the essential features of systems in which global behavior emerges from the collective effect of simple components, which interact locally (emergent computation). We developed a CA that models exactly the Physarum's behavior and applied it in finding the minimum-length path between two points in a labyrinth, as well as in solving a path-planning problem by guiding the development of adaptive networks, as in the case of the actual rail network of Tokyo. The CA results are in very good agreement with the computation results produced by the living organism experiments in both cases. Moreover, our CA hardware implementation results in faster and more effective computation performance, because of its inherent parallel nature. Consequently, our CA, implemented both in software and hardware, can serve as a powerful and low-cost virtual laboratory that models the slime mould Physarum's computation behavior.

The effects of inhibitors and magnesium ions on the activity of the thermostable extracellular cAMP-Specific phosphodiesterase of Physarum polycephalum plasmodium

Plasmodium of myxomycete Physarum polycephalum produces cyclic nucleotide phosphodiesterase (PDE). The extracellular PDE is cAMP-specific and highly thermostable. This study demonstrates that the extracellular PDE of Ph. polycephalum is weakly inhibited by caffeine, isobutylmethylxantine and theophiline (type I mammalian PDE nonspecific inhibitors), dipyridamole (mammalian PDE5, PDE6, PDE8 and PDE10 inhibitors), and erythro-9-[3-(2-hydroxynonyl)]-adenine (mammalian PDE2 inhibitor). The enzyme does not require Mg2+ for the activity. The results show that the Ph. polycephalum extracellular PDE differs from class I PDEs, represented by mammalian PDE1-PDE11, and, most likely, belongs to a poorly investigated class II PDEs.

Slime Mold Solves Maze in One Pass, Assisted by Gradient of Chemo-Attractants

Plasmodium of Physarum polycephalum is a large cell, visible by unaided eye, which exhibits sophisticated patterns of foraging behaviour. The plasmodium's behaviour is well interpreted in terms of computation, where data are spatially extended configurations of nutrients and obstacles, and results of computation are networks of protoplasmic tubes formed by the plasmodium. In laboratory experiments and numerical simulation we show that if plasmodium of P. polycephalum is inoculated in a maze's peripheral channel and an oat flake (source of attractants) in a the maze's central chamber then the plasmodium grows toward target oat flake and connects the flake with the site of original inoculation with a pronounced protoplasmic tube. The protoplasmic tube represents a path in the maze. The plasmodium solves maze in one pass because it is assisted by a gradient of chemo-attractants propagating from the target oat flake.

Cell Motility Viewed as Softness

In this paper, the authors propose a simple model of cell motility inspired by the plasmodium of Physarum polycephalum. The model focuses on the “softness” of aggregations of protoplasm. The model has only two parameters, yet generates a variety of final states, as well as the morphological changes of Physarum according to the condition of the culture medium.

Multi-scaled adaptability in motility and pattern formation of the Physarum plasmodium

The plasmodium of Physarum polycephalum is a unicellular and multinuclear giant amoeba that has macroscopic size, and by this particular nature the organism is attracting a lot of attention in the research fields such as systems science, nature-inspired bio-computing and swarm behavioural study. In this paper, we investigated how the plasmodium generates new motility and morphology, and found that there are allometric relationships between the cell volume and morphology, and between cell size and cell motility. We further discuss how these relationships are realised, and these relationships are deeply connected to the organism's benefit of being a large-scale unicellular organism.

Allometric Scaling Laws in the Exploratory Behavior of the Physarum Plasmodium

The plasmodium of Physarum polycephalum is a unicellular and multinuclear giant amoeba. In this paper, the authors investigate four allometric laws in the exploratory behavior of the plasmodium, and integrate them into one schema based on the dynamics of cytoplasmic streaming. This study reveals a novel function of the tubular structure of the plasmodium, shedding new light on the adaptive behavior of the organism.

Simulating strange attraction of acellular slime mould Physarum polycephaum to herbal tablets

Plasmodium of acellular slime mould Physarum polycephalum exhibits traits of wave-like behaviour. The plasmodium’s behaviour can be finely tuned in laboratory experiments by using herbal tablets. A single tablet acts as a fixed attractor: plasmodium propagates towards the tablet, envelops the tablet with its body and stays around the tablet for several days. Being presented with several tablets the plasmodium executes limit cycle like motions. The plasmodium performs sophisticated routines of movement around tablets: rotation, splitting, and annihilation. We use the two-variable Oregonator model to simulate the plasmodium behaviour in the presence of the herbal tablets. Numerical experiments confirm that using long-distance attracting and short-distance repelling fields we can organise arbitrary movement of plasmodia.

PHYSARUM SPATIAL LOGIC

Plasmodium of Physarum polycephalum is a large single cell capable for distributed sensing, information processing, decentralized decision-making and collective action. In the paper, we interpret basic features of the plasmodium foraging behavior in terms of process calculus and spatial logic and show that this behavior could be regarded as one of the natural implementations of spatial logic without modal operators.

Flow-induced channel formation in the cytoplasm of motile cells

A model is presented to explain the development of flow channels within the cytoplasm of the plasmodium of the giant amoeba Physarum polycephalum. The formation of channels is related to the development of a self-organizing tubular network in large cells. Experiments indicate that the flow of cytoplasm is involved in the development and organization of these networks, and the mathematical model proposed here is motivated by recent experiments involving the observation of development of flow channel in small cells. A model of pressure-driven flow through a polymer network is presented in which the rate of flow increases the rate of depolymerization. Numerical solutions and asymptotic analysis of the model in one spatial dimension show that under very general assumptions this model predicts the formation of channels in response to flow.

On the Internalisation, Intraplasmodial Carriage and Excretion of Metallic Nanoparticles in the Slime Mould, Physarum Polycephalum

The plasmodium of Physarum polycephalum is a large single cell visible with the naked eye. When inoculated on a substrate with attractants and repellents the plasmodium develops optimal networks of protoplasmic tubes which span sites of attractants (i.e. nutrients) yet avoid domains with a high nutrient concentration. It should therefore be possible to program the plasmodium towards deterministic adaptive transformation of internalised nano- and micro-scale materials. In laboratory experiments with magnetite nanoparticles and glass micro-spheres coated with silver metal the authors demonstrate that the plasmodium of P. polycephalum can propagate the nano-scale objects using a number of distinct mechanisms including endocytosis, transcytosis and dragging. The results of the authors’ experiments could be used in the development of novel techniques targeted towards the growth of metallised biological wires and hybrid nano- and micro-circuits.

Approximating Mexican highways with slime mould

Plasmodium of Physarum polycephalum is a single cell visible by unaided eye. During its foraging behavior the cell spans spatially distributed sources of nutrients with a protoplasmic network. The geometrical structure of the protoplasmic networks allows the plasmodium to optimize transport of nutrients between remote parts of its body. Assuming major Mexican cities are sources of nutrients that need to be distributed across Mexico, how much does the structure of the Physarum protoplasmic network correspond to the structure of Mexican Federal highway network? To address the issue we undertook a series of laboratory experiments with living P. polycephalum. We represent geographical locations of major cities (19 locations) by oat flakes, place a piece of plasmodium in the area corresponding to Mexico city, record the plasmodium’s foraging behavior and extract topology of the resulting nutrient transport networks. Results of our experiments show that the protoplasmic network formed by Physarum is isomorphic, subject to limitations imposed, to a network of principal highways. Ideas and results in the paper may contribute towards future developments in bio-inspired road planning.

An associative learning experiment using the plasmodium of Physarum polycephalum

The plasmodium of Physarum polycephalum is a unicellular and multinuclear giant amoeba that shows adaptive behaviors. To test the presence of memory and learning ability in the plasmodium, we performed an associative learning experiment using the unicellular organism. The plasmodium in this experiment seemed to acquire a reversed thermotactic property, a new preference for the lower temperature. The result implied a possibility of unicellular learning, though in a preliminary way. We also discuss a possible mechanism of learning by the organism.