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.     

Emergence of morphological order in the network formation of Physarum polycephalum

Emergence in a system appears through the interaction of its components, giving rise to higher order or complexity in the system. We tested for the presence of emergent properties in a biological system using the simplest biological entity of a unicellular organism; the plasmodium of Physarum polycephalum, a giant unicellular amoeboid organism that forms a network-like tubular structure connecting its food sources. We let two plasmodium networks within a single cell interact with each other, and observed how the intracellular interaction affected the morphologenesis of the plasmodium networks. We found that the two networks developed homologous morphology. We further discuss the presence of autonomous and emergent properties in homologous network formation.     

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.     

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.     

Flow-network adaptation in Physarum amoebae

Understanding how biological systems solve problems could aid the design of novel computational methods. Information processing in unicellular eukaryotes is of particular interest, as these organisms have survived for more than a billion years using a simple system. The large amoeboid plasmodium of Physarum is able to solve a maze and to connect multiple food locations via a smart network. This study examined how Physarum amoebae compute these solutions. The mechanism involves the adaptation of the tubular body, which appears to be similar to a network, based on cell dynamics. Our model describes how the network of tubes expands and contracts depending on the flux of protoplasmic streaming, and reproduces experimental observations of the behavior of the organism. The proposed algorithm based on Physarum is simple and powerful.     

Controlling the geometry and the coupling strength of the oscillator system in plasmodium ofPhysarum polycephalum by microfabricated structure

Summary The plasmodium of the true slime moldPhysarum polycephalum, which shows various oscillatory phenomena, can be regarded as a collective of nonlinear oscillators. Partial bodies in the plasmodium, which are assumed to be nonlinear oscillators, are mutually connected by microscale tubes named plasmodial strand. The interactions among the oscillators can be strongly affected by the geometry and the dimension of the tube network. Investigation of the collective behavior under the condition that the configuration of the network can be manipulated gives significant information on the characteristics of the plasmodium from the viewpoint of nonlinear dynamics. In this study, we have developed a new method to control the geometry and the tube dimension of the plasmodium with a microfabricated structure. It is shown that the geometry of the plasmodium can be manipulated with a microstructure which is fabricated of ultrathick photoresist resin by photolithographic processes. In order to confirm that not only the geometry but also the dimension of the tubes can be controlled with the microstructure, we observed the cross section of the patterned plasmodium with a three-dimensional internal-structure microscope. By observing the oscillatory behavior of the partial bodies of the patterned plasmodium, it was confirmed that the coupling strength between two oscillators, which corresponds to the dimension of the plasmodial strand, can be controlled by the microstructure. It is concluded that the present method is suitable for further studies of the network of Physarum plasmodium as a collective nonlinear oscillator system.     

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.     

细弱绒泡菌的生活史

利用燕麦-琼脂培养、基物培养及扫描电镜技术研究了细弱绒泡菌的个体发育过程,在燕麦琼脂培养基上完成了从孢子到孢子的生活史。结果表明,细弱绒泡菌生活史包括单核的黏变形体或游动胞、多核的营养体原质团以及孢子形成阶段。孢子球形,表面具细小疣点。孢子萌发为裂式,释放1黏变形体。黏变形体行变形运动,在有水的条件下,可转变为游动胞。成熟原质团橘黄色。原质团类型为显型,具有扇形网络状菌脉。成熟原质团可形成多个孢囊。琼脂培养基上获得的细弱绒泡菌孢子与野生型相似,并具有可育性。     

Food deprivation is not a prerequisite for the amoebal to plasmodial transition in Physarum polycephalum

The effect of food supply on the onset of asexual and sexual plasmodium formation in Physarum polycephalum was studied. Asexual differentiation occurs readily in amoebae carrying the matAh mating type allele. The density at which these amoebae begin to differentiate is influenced by the ind locus, which controls the production of a diffusible inducer. The alleles ind-1 and ind-2 are known. Strains carring the ind-1 allele begin plasmodium formation at a low amoebal density (rapid differentiation), while strains carring the ind-2 allele differentiate at a higher amoebal density (slow differentiation). The onset of differentiation is characteristic of the strain and did not change with a 20-fold variation in the number of food bacteria available. Sexual differentiation occurs between compatible amoebal strains. For a given pair of amoebal strains the onset of plasmodium formation occurs at a characteristic cell density that is determined by the genetic backgrounds of the strains. The ind locus is one of the genes that influences this cell density. Plasmodia are formed at a lower cell density in crosses involving compatible amoebae carrying the ind-1 allele than they are in crosses with strains carrying the ind-2 allele. As was found for asexual differentiation, an approximate 20-fold variation in the food supply did not affect the initiation of sexual plasmodium formation. These results suggest that in most cases starvation does not trigger the differentiation of amoebae into plasmodia. The time of onset of plasmodium formation is determined largely by genetic factors.     

黄柄钙皮菌的生活史

利用基物培养、燕麦-琼脂培养技术及扫描电镜技术研究了黄柄钙皮菌的个体发育过程,在燕麦琼脂培养基上完成了从孢子到孢子的生活史。结果表明,生活史包括单核的黏变形体或游动胞、多核的营养体原质团以及孢子形成阶段。孢子球形,表面具疣突。孢子萌发为裂式,释放1黏变形体。黏变形体行变形运动,在有水的条件下,可转变为游动胞并游动。可观察到1长具极性的鞭毛。合子形成原质团。成熟原质团棕色。原质团类型为显型,具有扇形网络状菌脉。琼脂培养基上获得的黄柄钙皮菌孢子与野生型相似,并具有可育性。     

Fine Structure Observations of Phagotrophic Activity By Plasmodia of Physarum Polycephalum

ABSTRACT. Scanning electron microscopic observations of feeding plasmodia show three characteristic features: 1) extension of multilobed pseudopodia protruding from the leading edge of the plasmodium as it advances onto the surface of a food particle, 2) confluence of the lobes to form a sheath-like pseudopodium attached to the surface of the food particle, and 3) protrusion of small nodules with thin lamellar projections from the leading edge of the plasmodium. Sections through freeze-dried preparations of the feeding plasmodium exhibit a highly convoluted under surface in contact with loosened starch grains that appear to be released by extracellular digestion. the cytoplasm, viewed by transmission electron microscopy, contains branched, internally penetrating canals (ca. 2 μm wide) enclosing engulfed starch grains. Starch grains in the deeper part of the canals are more electron dense and appear to be digested. Micropseudopodia (70-80 nm dia.), projecting from the surface of the canals, protrude toward and into the ingested starch grains. Digestive marker enzyme (acid phosphatase) activity was detected cytochemically in food particles penetrated by micropseu-dopodia indicating a digestive role for these structures not reported previously.     

Rox3 and Rts1 Function in the Global Stress Response Pathway in Baker''s Yeast

Yeast respond to a variety of stresses through a global stress response that is mediated by a number of signal transduction pathways and the cis-acting STRE DNA sequence. The CYC7 gene, encoding iso-2-cytochrome c, has been demonstrated to respond to heat shock, glucose starvation, approach-to-stationary phase, and, as we demonstrate here, to osmotic stress. This response was delayed in a the hog1-Δ1 strain implicating the Hog1 mitogen-activated protein kinase cascade, a known component of the global stress response. Deletion analysis of the CYC7 regulatory region suggested that three STRE elements were each capable of inducing the stress response. Mutations in the ROX3 gene prevented CYC7 RNA accumulation during heat shock and osmotic stress. ROX3 RNA levels were shown to be induced by stress through a novel regulatory element. A selection for high-copy suppressors of a ROX3 temperature-sensitive allele resulted in the isolation of RTS1, encoding a protein with homology to the B' regulatory subunit of protein phosphatase 2A(0). Deletion of RTS1 caused temperature and osmotic sensitivity and increased accumulation of CYC7 RNA under all conditions. Over-expression of this gene caused increased CYC7 RNA accumulation in rox3 mutants but not in wild-type cells.     

Control of interaction strength in a network of the true slime mold by a microfabricated structure

The plasmodium of the true slime mold, Physarum polycephalum, which shows various nonlinear oscillatory phenomena, for example, in its thickness, protoplasmic streaming and concentration of intracellular chemicals, can be regarded as a collective of nonlinear oscillators. The plasmodial oscillators are interconnected by microscale tubes whose dimensions can be closely related to the strength of interaction between the oscillators. Investigation of the collective behavior of the oscillators under the conditions in which the interaction strength can be systematically controlled gives significant information on the characteristics of the system. In this study, we proposed a living model system of a coupled oscillator system in the Physarum plasmodium. We patterned the geometry and dimensions of the microscale tube structure in the plasmodium by a microfabricated structure (microstructure). As the first step, we constructed a two-oscillator system for the plasmodium that has two wells (oscillator part) and a channel (coupling part). We investigated the oscillation behavior by monitoring the thickness oscillation of the plasmodium in the microstructure with various channel widths. It was found that the oscillation behavior of two oscillators dynamically changed depending on the channel width. Based on the results of measurements of the tube dimensions and the velocity of the protoplasmic streaming in the tube, we discuss how the channel width relates to the interaction strength of the coupled oscillator system.     

Dynamic organization of Physarum plasmodium

Birefringent fibrils (BRFs) with a positive sign composed of bundles of F-actin were found throughout the Physarum plasmodium with the mode of existence differing regionally. In the zone behind the leading edge of an advancing plasmodium, where cytoplasmic sol and gel were still not well differentiated, more BRFs came to the foreground when the endoplasm flowed backward (emptying phase), and a substantial portion disappeared when the endoplasm flowed forward (filling phase), except for nodes, from which BRFs were reorganized in the early emptying phase of each cycle. BRFs found in the wall of the streaming channel in the posterior network and the branched vein section ran in parallel to or helically around the channel. They were much more stable and maintained strong birefringence irrespective of the direction of the cytoplasmic flow. When the fan-like expanse ceased moving forward, the BRFs no longer appeared and disappeared cyclically but persisted in the area which had previously been the front. We concluded that the site of the active contraction-relaxation rhythm in an advancing plasmodium with antero-posterior polarity is restricted to its frontal zone and that the rest of the plasmodium is in a state of "tonus" which continuously imparts a certain level of hydrostatic pressure to the interior. The meaning of the tonus and the mechanics of tensile force production in the plasmodium are discussed in terms of a working hypothesis arrived at from the phase relationship between isometric and isotonic contraction waves.     

The role of novelty and fat and sugar concentration in food selection by captive tufted capuchins (Sapajus apella)

Capuchins, like other primates, use feedback from sensory cues and digestion to make decisions about which foods to consume and which to avoid. However, little is known about how capuchins make consumption decisions when simultaneously presented with novel and familiar foods, or how food familiarity and macronutrient concentration together influence food choice, topics with potential implications for developmental and health research. In this study, we evaluated the role of familiarity, as well as fat and sugar concentration, in the food selections of captive tufted capuchins (Sapajus apella). In the first experiment, over 10 sessions, subjects were assigned to either a group that chose between one familiar and one novel food item both high in fat or sugar (high condition), or to a group that chose between one familiar and one novel food item both low in fat or sugar (low condition). In the second experiment, subjects were divided into three groups, familiarized with food over five feeding sessions, and then offered the familiarized food and a novel food that varied in fat or sugar for 10 sessions. When offered foods high in fat, capuchins showed no clear signs of neophobia, forming an initial preference for the novel food, rejecting foods less frequently, and selecting foods faster than when offered foods low in fat. These trends were generally not observed in response to foods with sugar. When presented with options that varied in macronutrient concentration, subjects showed an initial interest in the novel food irrespective of whether it was high in fat or sugar, yet formed a final preference for the higher-concentration item. Findings suggest that the concentration of fat or sugar in novel foods may be an important mediator of exploratory behavior and that capuchins rely on immediate feedback from taste and other sensory cues to make consumption decisions.     

A computational analysis of separating motion signals in transparent random dot kinematograms

When multiple motion directions are presented simultaneously within the same region of the visual field human observers see motion transparency. This perceptual phenomenon requires from the visual system to separate different motion signal distributions, which are characterised by distinct means that correspond to the different dot directions and variances that are determined by the signal and processing noise. Averaging of local motion signals can be employed to reduce noise components, but such pooling could at the same time lead to the averaging of different directional signal components, arising from spatially adjacent dots moving in different directions, which would reduce the visibility of transparent directions. To study the theoretical limitations of encoding transparent motion by a biologically plausible motion detector network, the distributions of motion directions signalled by a motion detector model (2DMD) were analysed here for Random Dot Kinematograms (RDKs). In sparse dot RDKs with two randomly interleaved motion directions, the angular separation that still allows us to separate two directions is limited by the internal noise in the system. Under the present conditions direction differences down to 30 deg could be separated. Correspondingly, in a transparent motion stimulus containing multiple motion directions, more than eight directions could be separated. When this computational analysis is compared to some published psychophysical data, it appears that the experimental results do not reach the predicted limits. Whereas the computer simulations demonstrate that even an unsophisticated motion detector network would be appropriate to represent a considerable number of motion directions simultaneously within the same region, human observers usually are restricted to seeing not more than two or three directions under comparable conditions. This raises the question why human observers do not make full use of information that could be easily extracted from the representation of motion signals at the early stages of the visual system.     

华南地区典型生境中红火蚁觅食行为及工蚁召集规律

观察研究了华南地区几种典型生境中红火蚁对不同类型食物的觅食行为和工蚁召集动态规律。研究结果表明红火蚁觅食行为存在搜寻、召集及搬运等主要过程。不同生境中红火蚁对食物的搜寻时间存在一定差异,荔枝园中搜寻时间明显长于其它生境;荔枝园、荒地、路边生境中红火蚁对蜂蜜的搜寻时间明显长于其它几种食物;同一生境中红火蚁对不同重量的同种食物搜寻时间无明显变化。发现食物后召集的工蚁数量随着时间延长呈现不断增加的趋势,对于较大的食物一般30min左右召集的工蚁数量达到最大,之后趋于稳定并逐渐减少,而对于可以直接搬动的食物发现后15min左右群体召集数量达到最大并很快将其搬走。召集工蚁数量与发现后时间的关系符合二次非线性方程,建立了火腿肠、花生油和蜂蜜等食物上红火蚁工蚁召集数量与发现时间的关系模型,分别为Na=4183.91e^-0.0327T-4231.48e^-0.0346T,Na=3253.78e^-0.0233T-3314.59e^-0.0271T,Na=117.97e^-0.0131T-163.93e^-0.0808T。对于不同食物红火蚁发现后召集的最大工蚁数量间有明显差异,其中花生油上最大,平均为176．3头,火腿肠上次之,为90．4头,蜂蜜上最少,为68．0头。对于不同重量的同种食物,工蚁的召集动态规律较为一致,发现食物后25-30min左右工蚁的召集数量均达到最大值,之后缓慢减少,发现食物后时间长度和食物上工蚁数量也符合房室模型函数Na=c1×exp（-c2T）-c3×exp（-c4T）。同种食物不同重量之间同一时间召集的工蚁数量存在较大差异,呈随食物重量增大而增大趋势。不同生境中对相同质量同种食物工蚁召集数量动态总体变化规律相近,但在发现食物后工蚁数量增长的速度和最大召集工蚁的数量存在明显差异,以路边工蚁数量增长最快、工蚁总数最多,苗圃次之,荔枝园、荒地中工蚁增长速度均较低。红火蚁对不同食物种类切割、搬运耗时存在很大差异,搬运完0．5g的火腿肠需要26．23h,而黄粉虫幼虫（重量约为0．1g）仅为15．6min。不同生境中红火蚁对相同重量同一种食物的搬运耗时也不同,荔枝园要长于其它生境。     

Characterization of a novel mammalian SUMO-1/Smt3-specific isopeptidase, a homologue of rat axam, which is an axin-binding protein promoting beta-catenin degradation

A novel SUMO-1/Smt3-specific isopeptidase, SMT3IP2/Axam2 (Smt3-specific isopeptidase 2), was cloned and characterized. The catalytic domains in the carboxyl-terminal region were very much similar to those of other SUMO-1/Smt3-specific proteases, but the amino-terminal part was quite different. The enzyme specifically bound to Smt3a and Smt3b but not to SUMO-1. The SMT3IP2 expressed by Escherichia coli could cleave SUMO-1, Smt3a, or Smt3b from a SUMO-1/RanGAP1, Smt3a/RanGAP1, or Smt3b/RanGAP1 conjugate, respectively, and had the activity of a carboxyl-terminal hydrolase to produce a glycine residue in the carboxyl terminus of these ubiquitin-like proteins. The sequence data indicated that the amino acid sequence of SMT3IP2 was mostly identical to that of rat Axam, which binds to Axin and promotes the degradation of beta-catenin, although its amino-terminal region was much shorter than that of Axam. Therefore, we designated this isopeptidase SMT3IP2/Axam2. When human SW480 cells were transfected with wild-type SMT3IP2/Axam2, the beta-catenin disappeared. When the cells were transfected with the SMT3IP2/Axam2 C500A mutant, which had neither isopeptidase nor carboxyl-terminal hydrolase activity, or with the 1-352 mutant, which lacked the catalytic domain of the enzyme, again the beta-catenin disappeared, indicating that the enzyme activities were not necessary for the instability of beta-catenin in this transfection assay system and that its competition with Dvl for binding to Axin may be important for the instability of beta-catenin as suggested previously for Axam (Kadoya, T., Kishida, S., Fukui, A., Hinoi, T., Michiue, T., Asashima, M., and Kikuchi, A. (2000) J. Biol. Chem. 275, 37030-37037). The involvement of its enzyme activities in the Wnt signaling pathway remains to be elucidated.     

Why do paralogs persist? Molecular evolution of CYCLOIDEA and related floral symmetry genes in Antirrhineae (Veronicaceae)

CYCLOIDEA (CYC) and DICHOTOMA (DICH) are paralogous genes that determine adaxial (dorsal) flower identity in the bilaterally symmetric flowers of Antirrhinum majus (snapdragon). We show here that the duplication leading to the existence of both CYC and DICH in Antirrhinum occurred before the radiation of the Antirrhineae (the tribe to which snapdragon belongs). We find no additional gene duplications within Antirrhineae. Using explicit codon-based models of evolution in a likelihood framework, we show that patterns of molecular evolution after the duplication that gave rise to CYC and DICH are consistent with purifying selection acting at both loci, despite their known functional redundancy in snapdragon. However, for specific gene regions, purifying selection is significantly relaxed across DICH lineages, relative to CYC lineages. In addition, we find evidence for relaxed purifying selection along the lineage leading to snapdragon in one of two putative functional domains of DICH. A model of selection accounting for the persistence of paralogous genes in the absence of diversifying selection is presented. This model takes into account differences in the degree of purifying selection acting at the two loci and is consistent with subfunctionalization models of paralogous gene evolution.