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.     

Smart network solutions in an amoeboid organism

We present evidence that the giant amoeboid organism, the true slime mold, constructs a network appropriate for maximizing nutrient uptake. The body of the plasmodium of Physarum polycephalum contains a network of tubular elements by means of which nutrients and chemical signals circulate through the organism. When food pellets were presented at different points on the plasmodium it accumulated at each pellet with a few tubes connecting the plasmodial concentrations. The geometry of the network depended on the positions of the food sources. Statistical analysis showed that the network geometry met the multiple requirements of a smart network: short total length of tubes, close connections among all the branches (a small number of transit food-sites between any two food-sites) and tolerance of accidental disconnection of the tubes. These findings indicate that the plasmodium can achieve a better solution to the problem of network configuration than is provided by the shortest connection of Steiner's minimum tree.     

Traffic optimization in railroad networks using an algorithm mimicking an amoeba-like organism, Physarum plasmodium

Traffic optimization of railroad networks was considered using an algorithm that was biologically inspired by an amoeba-like organism, plasmodium of the true slime mold, Physarum polycephalum. The organism developed a transportation network consisting of a tubular structure to transport protoplasm. It was reported that plasmodium can find the shortest path interconnecting multiple food sites during an adaptation process (Nakagaki et al., 2001. Biophys. Chem. 92, 47-52). By mimicking the adaptation process a path finding algorithm was developed by Tero et al. (2007). In this paper, the algorithm is newly modified for applications of traffic distribution optimization in transportation networks of infrastructure such as railroads under the constraint that the network topology is given. Application of the algorithm to a railroad in metropolitan Tokyo, Japan is demonstrated. The results are evaluated using three performance functions related to cost, traveling efficiency, and network weakness. The traffic distribution suggests that the modified Physarum algorithm balances the performances under a certain parameter range, indicating a biological process.     

A mathematical model for adaptive transport network in path finding by true slime mold

We describe here a mathematical model of the adaptive dynamics of a transport network of the true slime mold Physarum polycephalum, an amoeboid organism that exhibits path-finding behavior in a maze. This organism possesses a network of tubular elements, by means of which nutrients and signals circulate through the plasmodium. When the organism is put in a maze, the network changes its shape to connect two exits by the shortest path. This process of path-finding is attributed to an underlying physiological mechanism: a tube thickens as the flux through it increases. The experimental evidence for this is, however, only qualitative. We constructed a mathematical model of the general form of the tube dynamics. Our model contains a key parameter corresponding to the extent of the feedback regulation between the thickness of a tube and the flux through it. We demonstrate the dependence of the behavior of the model on this parameter.     

Modeling,analysis and simulation of ant-based network routing protocols

Using the metaphor of swarm intelligence, ant-based routing protocols deploy control packets that behave like ants to discover and optimize routes between pairs of nodes. These ant-based routing protocols provide an elegant, scalable solution to the routing problem for both wired and mobile ad hoc networks. The routing problem is highly nonlinear because the control packets alter the local routing tables as they are routed through the network. We mathematically map the local rules by which the routing tables are altered to the dynamics of the entire networks. Using dynamical systems theory, we map local protocol rules to full network performance, which helps us understand the impact of protocol parameters on network performance. In this paper, we systematically derive and analyze global models for simple ant-based routing protocols using both pheromone deposition and evaporation. In particular, we develop a stochastic model by modeling the probability density of ants over the network. The model is validated by comparing equilibrium pheromone levels produced by the global analysis to results obtained from simulation studies. We use both a Matlab simulation with ideal communications and a QualNet simulation with realistic communication models. Using these analytic and computational methods, we map out a complete phase diagram of network behavior over a small multipath network. We show the existence of both stable and unstable (inaccessible) routing solutions having varying properties of efficiency and redundancy depending upon the routing parameters. Finally, we apply these techniques to a larger 50-node network and show that the design principles acquired from studying the small model network extend to larger networks.     

Environment-dependent morphology in plasmodium of true slime mold Physarum polycephalum and a network growth model

Branching network growth patterns, depending on environmental conditions, in plasmodium of true slime mold Physarum polycephalum were investigated. Surprisingly, the patterns resemble those in bacterial colonies even though the biological mechanisms differ greatly. Bacterial colonies are collectives of microorganisms in which individual organisms have motility and interact through nutritious and chemical fields. In contrast, the plasmodium is a giant amoeba-like multinucleated unicellular organism that forms a network of tubular structures through which protoplasm streams. The cell motility of the plasmodium is generated by oscillation phenomena observed in the partial bodies, which interact through the tubular structures. First, we analyze characteristics of the morphology quantitatively, then we abstract local rules governing the growing process to construct a simple network growth model. This model is independent of specific systems, in which only two rules are applied. Finally, we discuss the mechanism of commonly observed biological pattern formations through comparison with the system of bacterial colonies.     

A mechanism of translocation based on high proton mobility and K+ counterflux at negatively charged surfaces in sieve elements

Large pH gradients between the sources and the sinks involved in translocation of metabolites arise owing to photosynthesis and nitrate reduction in the leaves and respiration in the sinks. pH equalization between the sinks and the sources is proposed to be brought about by a rapid movement of H⁺ from sinks to sources along the negatively charged surfaces lining the translocation pathways and the ray symplast. This movement is made possible by a charge-compensating movement of K⁺ in the electrical double layer. In the sieve tubes and specially at the sieve plate pores the movement of K⁺ in the diffused layer is suggested as the driving force for translocation of metabolites. In the transport network of plants K⁺ moves in loops, acting like a conveyor belt in the phloem. The proposed mechanism explains all experimental observations related to translocation and also solves the problem of pH-stating in the source and sink cells. Its implications for shoot-root cooperation have been also indicated.     

The calcium content of the cellular slime mold, Dictyostelium discoideum, during development and differentiation

A high calcium concentration is known to induce stalk differentiation of the cellular slime mold D. discoideum. Therefore, the change in the calcium content of this organism during differentiation was studied and found to vary during development, more calcium being found in the anterior prestalk cells of the pseudoplasmodium (slug) than in the posterior prespore cells. It is concluded from the results that calcium is of importance in the cell differentiation of this organism and particularly in stalk formation.     

What the papers say: Cellular dedifferentiation and spore germination in Dictyostelium may utilize similar regulatory pathways

Cellular dedifferentiation is an important developmental response to perturbations in morphogenesis. In the cellular slime mold Dictyostelium discoideum this process gives cells the flexibility, when multicellular development is disrupted, to respond to nutrients and reinitiate vegetative growth. Recent studies in D. discoideum described by Soll and colleagues⁽¹⁾ show that genes previously thought to be expressed only during spore germination are also expressed during induced dedifferentiation, suggesting that similar molecular mechanisms are involved in these two developmental processes. It should now be possible to determine whether the developmental programs that control dedifferentiation during spore germination also control conversion of cell types in the multicellular organism.     

AIB-OR: Improving Onion Routing Circuit Construction Using Anonymous Identity-Based Cryptosystems

The rapid growth of Internet applications has made communication anonymity an increasingly important or even indispensable security requirement. Onion routing has been employed as an infrastructure for anonymous communication over a public network, which provides anonymous connections that are strongly resistant to both eavesdropping and traffic analysis. However, existing onion routing protocols usually exhibit poor performance due to repeated encryption operations. In this paper, we first present an improved anonymous multi-receiver identity-based encryption (AMRIBE) scheme, and an improved identity-based one-way anonymous key agreement (IBOWAKE) protocol. We then propose an efficient onion routing protocol named AIB-OR that provides provable security and strong anonymity. Our main approach is to use our improved AMRIBE scheme and improved IBOWAKE protocol in onion routing circuit construction. Compared with other onion routing protocols, AIB-OR provides high efficiency, scalability, strong anonymity and fault tolerance. Performance measurements from a prototype implementation show that our proposed AIB-OR can achieve high bandwidths and low latencies when deployed over the Internet.     

Promoting Wired Links in Wireless Mesh Networks: An Efficient Engineering Solution

Wireless Mesh Networks (WMNs) cannot completely guarantee good performance of traffic sources such as video streaming. To improve the network performance, this study proposes an efficient engineering solution named Wireless-to-Ethernet-Mesh-Portal-Passageway (WEMPP) that allows effective use of wired communication in WMNs. WEMPP permits transmitting data through wired and stable paths even when the destination is in the same network as the source (Intra-traffic). Tested with four popular routing protocols (Optimized Link State Routing or OLSR as a proactive protocol, Dynamic MANET On-demand or DYMO as a reactive protocol, DYMO with spanning tree ability and HWMP), WEMPP considerably decreases the end-to-end delay, jitter, contentions and interferences on nodes, even when the network size or density varies. WEMPP is also cost-effective and increases the network throughput. Moreover, in contrast to solutions proposed by previous studies, WEMPP is easily implemented by modifying the firmware of the actual Ethernet hardware without altering the routing protocols and/or the functionality of the IP/MAC/Upper layers. In fact, there is no need for modifying the functionalities of other mesh components in order to work with WEMPPs. The results of this study show that WEMPP significantly increases the performance of all routing protocols, thus leading to better video quality on nodes.     

Predicting the Distribution of Spiral Waves from Cell Properties in a Developmental-Path Model of Dictyostelium Pattern Formation

The slime mold Dictyostelium discoideum is one of the model systems of biological pattern formation. One of the most successful answers to the challenge of establishing a spiral wave pattern in a colony of homogeneously distributed D. discoideum cells has been the suggestion of a developmental path the cells follow (Lauzeral and coworkers). This is a well-defined change in properties each cell undergoes on a longer time scale than the typical dynamics of the cell. Here we show that this concept leads to an inhomogeneous and systematic spatial distribution of spiral waves, which can be predicted from the distribution of cells on the developmental path. We propose specific experiments for checking whether such systematics are also found in data and thus, indirectly, provide evidence of a developmental path.     

Mass Culture of a Slime Mold, Physarum polycephalum

The slime mold, Physarum polycephalum, was cultivated in a soluble natural medium in shake flasks and in 30-liter and 50-gal conventional baffled fermentors. Yields of 6 to 10 g (dry weight) per liter were obtained in the large-scale fermentations. Because of the slow growth of the myxomycete, particular attention had to be paid to aseptic technique. The inability of this organism to withstand the normal degree of agitation employed with most aerobic fermentations made it difficult to obtain adequate aeration. Conditions for growth of the organism on a pilot-plant scale are presented.     

An improved 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) reduction assay for evaluating the viability of Escherichia coli cells

To reduce the interference in MTT reduction assay, we developed an improved protocol for evaluating the viability of Escherichia coli cells by conducting MTT reduction in 1.5-mL centrifuge tubes and formazan dissolution in test tubes. Our study is helpful in developing protocols for measuring the viability of other gram-negative bacteria.     

Turnover of soluble proteins in the wheat sieve tube

Although the enucleate conducting cells of the phloem are incapable of protein synthesis, phloem exudates characteristically contain low concentrations of soluble proteins. The role of these proteins and their movement into and out of the sieve tubes poses important questions for phloem physiology and for cell-to-cell protein movement via plasmodesmata. The occurrence of protein turnover in sieve tubes was investigated by [³⁵S]methionine labeling and by the use of aphid stylets to sample the sieve tube contents at three points along a source-to-sink pathway (flag leaf to grains) in wheat plants (Triticum aestivum L.). Protein concentration and composition were similar at all sampling sites. The kinetics of ³⁵S-labeling of protein suggested a basically source-to-sink pattern of movement for many proteins. However, an appreciable amount of protein synthesis and, presumably, removal also occurred along the path. This movement appeared to be protein specific and not based on passive molecular sieving. The results have important implications for the transport capacities of plasmodesmata between sieve tubes and companion cells. The observations considerably expand the possible basis for ongoing sieve tube-companion cell interactions and, perhaps, interaction between sources and sinks.     

Deoxyribonucleic Acid Base Composition of Some Cellular Slime Molds*

SYNOPSIS. Deoxyribonucleic acids (DNAs) isolated from 12 representatives of cellular slime molds grown in monoxenic cultures were analyzed by density gradient centrifugation in CsC1. The unique contribution of the DNA of each food organism was subtracted and the DNA base composition of each cellular slime mold determined. The guanine plus cytosine contents range 22–37 moles % within the representatives of the order. Minor bands (satellite bands) of DNA have been observed in preparations from Dictyostelium spp. and from Polysphondylium pallidum.     

A mathematical framework for the study of morphogenetic development in the slime mold

A mathematical continuum model of the slime mold Dictyostelium discoideum in the morphogenetic development stage is presented, which represents the amoebae as a fluid with surface tension, acted upon by a body force due to the presence of a chemical attractant. Assuming that the amoebae at a given time are in quasi-equilibrium, and that the shape of the organism is prescribed, it is possible to calculate from the model plausible concentration and source-sink distributions that are consistent with the given shape. Typical observed shapes are accounted for by the presence of very large concentrations and concentration gradients of the chemical attractant at the top of the structure.     

Mitochondrial tRNA 5′-Editing in Dictyostelium discoideum and Polysphondylium pallidum

Mitochondrial tRNA (mt-tRNA) 5′-editing was first described more than 20 years ago; however, the first candidates for 5′-editing enzymes were only recently identified in a eukaryotic microbe (protist), the slime mold Dictyostelium discoideum. In this organism, eight of 18 mt-tRNAs are predicted to be edited based on the presence of genomically encoded mismatched nucleotides in their aminoacyl-acceptor stem sequences. Here, we demonstrate that mt-tRNA 5′-editing occurs at all predicted sites in D. discoideum as evidenced by changes in the sequences of isolated mt-tRNAs compared with the expected sequences encoded by the mitochondrial genome. We also identify two previously unpredicted editing events in which G-U base pairs are edited in the absence of any other genomically encoded mismatches. A comparison of 5′-editing in D. discoideum with 5′-editing in another slime mold, Polysphondylium pallidum, suggests organism-specific idiosyncrasies in the treatment of U-G/G-U pairs. In vitro activities of putative D. discoideum editing enzymes are consistent with the observed editing reactions and suggest an overall lack of tRNA substrate specificity exhibited by the repair component of the editing enzyme. Although the presence of terminal mismatches in mt-tRNA sequences is highly predictive of the occurrence of mt-tRNA 5′-editing, the variability in treatment of U-G/G-U base pairs observed here indicates that direct experimental evidence of 5′-editing must be obtained to understand the complete spectrum of mt-tRNA editing events in any species.     

Ultrastructural localization of β-galactan in the nuclei of the myxomycete Physarum polycephalum

The acellular slime mold Physarum polycephalum produces an extracellular sulfated and phosphorylated β-D-galactan which was recently isolated from the nuclei of this organism. This polysaccharide has now been localized in the nuclei ofP. polycephalum by electron microscopy using a specific “sandwich” technique: thin sections of P. polycephalum microplasmodia were incubated with the Ricinus communis lectin specific for D-galactose residues. The bound lectin was then localized with gold granules labeled with a galactose-terminated glycoprotein (desialylated ceruloplasmin). The galactin was found in the nuclei mainly associated with chromatin and, also, but to a smaller extent, in the cytoplasma and in some vacuoles. The specificity of the method was assessed by marking under the same condition the galactomannan present in the cell wall of the yeast Schizosaccharomyces pombe.     

The protoplasmic flow in the myxomycete plasmodium as revealed by a volumetric analysis

Summary The manner of the locomotion of the slime mold,Physarum polycephalum, was shown graphically using a double-chamber volumeter developed by the author. It enabled him to represent in undulating curves every detail of the way in which the slime mold moves on little by little by availing itself of the difference in transport-volume of the endoplasm produced at each repetition of the back and forth streaming.The curve showing the locomotion of the organism pointed out that more than 4 mm³ of protoplasm is sometimes shifted in a direction in one streaming duration. No close relationship is found between the streaming duration and the transport-volume of protoplasm. The intensity of the flow, which may be defined as the volume of protoplasm transported per unit time, can be obtained from the transport-volume curve through its graphical differentiation.