Phylogeny of Physarida (Amoebozoa, Myxogastria) Based on the Small-Subunit Ribosomal RNA Gene, Redefinition of Physarum pusillum s. str. and Reinstatement of P. gravidum Morgan.

Myxomycetes (also called Myxogastria or colloquially, slime molds) are worldwide occurring soil amoeboflagellates. Among Amoebozoa, they have the notable characteristic to form, during their life cycle, macroscopic fruiting bodies, that will ultimately release spores. Some 1,000 species have been described, based on the macroscopic and microscopic characteristics of their fruiting bodies. We were interested in Physarum pusillum (Berk. & M.A. Curtis) G. Lister, a very common species described with two variants, each bearing such morphological differences that they could represent two distinct species. In order to test this, we observed key characters in a large selection of specimens attributed to P.  pusillum, to its synonyms (in particular Physarum gravidum), and to related species. In addition, the small-subunit ribosomal RNA gene was obtained from seven of these specimens. Based on these data, we provide a comprehensive phylogeny of the order Physarida (Eukaryota: Amoebozoa: Conosa: Macromycetozoa: Fuscisporidia). Morphology and phylogeny together support the reinstatement of P. gravidum Morgan 1896 with a neotype here designated, distinct from P. pusillum, here redefined.

The life cycles of two species of Myxomycetes in Physarales, Physarum rigidum and Didymium squamulosum.

Myxomycetes are eukaryotic microorganisms containing characteristics akin to both fungi and amoebae. They can complete their whole life cycles while being cultured on agar media, and under-laboratory conditions, which favors taxonomic, phylogenetic, and cytological researches. Here, we describe the life cycles of two such species: Didymium squamulosum collected from the field and Physarum rigidum cultured from moist chamber both belonging to the Order Physarales. Three per cent oat-agar media (OAM) was used to culture the plasmodia until they aggregated and were almost starved. Natural light was then applied to the plasmodia to induce fructification. Their life cycles share the same common stages, namely: spore, myxamoebae, swarm cell, plasmodia, and sporulation. In this study, we describe the morphogenesis from spore to spore of two species by differential interference contrast (DIC) and stereoscopic microscopies, as well as discuss the differences between the development of both species and interspecies. We found that the spore germination method of both species was the same. However, there were differences noted in time taken and fruiting body formation. Unlike P. rigidum, the species D. squamulosum did not require natural light stimulation. Moreover, the maturation process of both species had similar color transitions but exhibited distinct morphology in each developmental stage except during the swarm cell stage.

Article for the "Free-living amoebae special issue": Isolation and characterisation of various amoebophagous fungi and evaluation of their prey spectrum.

This article gives an overview on the isolation and characterisation of endoparasitic fungi invading free-living amoebae (FLA), including the ones forming thalli inside their hosts such as Cochlonema euryblastum and also the predatory fungi which capture amoebae by adhesive hyphae. Acaulopage spp. and Stylopage spp. trap, intrude, and exploit amoebal trophozoites. Previous phylogenetic studies proved Cochlonema to be a member of the Zoopagales. The genetic investigation of Acaulopage tetraceros demonstrated its close relationship to Cochlonema. Co-cultivation of A. tetraceros with a number of FLA revealed a great prey spectrum of this amoebophageous fungus. In addition it was shown that solitary amoebal stages of slime moulds such as Dictyostelium sp. and Physarum sp. are also suited as welcome prey amoebae.

A mathematical model for period-memorizing behavior in Physarum plasmodium.

Mathematical models to describe period-memorizing behavior in Physarum plasmodium are reported. In constructing the model, we first examine the basic characteristics required for the class of models, then create a minimal linear model to fulfill these requirements. We also propose two modifications of the minimal model, nonlinearization and noise addition, which improve the reproducibility of experimental evidences. Differences in the mechanisms and in the reproducibility of experiments between our models and the previous models are discussed.

[Cytomechanics of oscillatory contractions. Modeling the longitudinal dynamics of Physarum polycephalum protoplasmic strands].

A mathematical model of the longitudinal dynamics of an isolated strand of the Physarum polycephalum plasmodium has been constructed. Its contractile system is considered as a continual viscoelastic medium with passive and active components. The mathematical description of the longitudinal dynamics of the plasmodial strand is reduced to a system of three first-order differential equations, whose variables are its active stress, deformation, and the intracellular concentration of calcium ions. The model is based on the hypothesis that there exists a feedback loop, which appears because of the influence of strand stretching on the rate of the release of calcium ions, which in turn controls the active contraction and deformation of the strand. Nonlinear interactions between the variables evoke a loss of the stationary state stability and a self-excitation of mechanochemical autooscillations when the external load exceeds some critical value. The results of numerical solutions of the model with the empirically determined viscoelastic parameters are in good agreement with the available experimental data and testify to the adequacy of the description of strand dynamics by the mathematical model in which the contractile apparatus is a part of the cellular control system. In particular, this model well simulates the form and duration of transient mechanochemical processes observed under isotonic and isometric conditions immediately after strand isolation, as well as the subsequent excitation of autooscillations of the contractile activity and their activation by strand stretching.

[Involvement of extracellular cAMP-specific phosphodiesterase in control of motile activity of Physarum polycephalum plasmodium].

Possible involvement of extracellular cAMP-specific phosphodiesterase in the control of cell motile behavior has been investigated in Physarum polycephalum plasmodium, a multinuclear amoeboid cell with the autooscillatory mode of motility. It was found that the rate of the hydrolysis of 10 mM cAMP by a partially purified preparation of cAMP-specific phosphodiesterase secreted by the plasmodium in the course of migration decreases 20-30 times under the action of 1 mM dithiothreitol. In the presence of 1-5 mM of this strong reducing agent, the onset of the plasmodium spreading and the transition to the stage of migration were delayed in a concentration-dependent manner. In accordance with the morphological pattern of motile behavior, the duration of the maintenance of high frequency autooscillations, which normally precede the increase in the rate of the spreading and appear also in response to the application of attractants at spatially uniform concentrations, strongly increased by the action of dithiothreitol. The results obtained suggest that the autocrine production of cAMP and extracellular cAMP-specific phosphodiesterase is an important constituent of the mechanism controlling the motile behavior of the Physarum polycephalum plasmodium.

Rheological properties of living cytoplasm: endoplasm of Physarum plasmodium.

Magnetic sphere viscoelastometry, video microscopy, and the Kamiya double chamber method (Kamiya, N., 1940, Science [Wash. DC], 92:462-463.) have been combined in an optical and rheological investigation of the living endoplasm of Physarum polycephalum. The rheological properties examined were yield stress, viscosity (as a function of shear), and elasticity. These parameters were evaluated in directions perpendicular; (X) and parallel (Y) to the plasmodial vein. Known magnetic forces were used for measurements in the X direction, while the falling ball technique was used in the Y direction (Cygan, D.A., and B. Caswell, 1971, Trans. Soc. Rheol. 15:663-683; MacLean-Fletcher, S.D., and T.D. Pollard, 1980, J. Cell Biol., 85:414-428). Approximate yield stresses were calculated in the X and Y directions of 0.58 and 1.05 dyn/cm2, respectively. Apparent viscosities measured in the two directions (eta x and eta y) were found to fluctuate with time. The fluctuations in eta x and eta y were shown, statistically, to occur independently of each other. Frequency correlation with dynamoplasmograms indicated that these fluctuations probably occur independently of the streaming cycle. Viscosity was found to be a complex function of shear, indicating that the endoplasm is non-Newtonian. Plots of shear stress vs. rate of shear both parallel and perpendicular to the vein, showed that endoplasm is not a shear thinning material. These experiments have shown that living endoplasm of Physarum is an anisotropic viscoelastic fluid with a yield stress. The endoplasm appears not to be a homogeneous material, but to be composed of heterogeneous domains.

Oscillations of calcium ion concentrations in Physarum polycephalum.

Aequorin is a photoprotein which emits light in response to changes in free calcium concentration. When aequorin was microinjected into plasmodia of Physarum polycephalum, light emission varied in synchrony with the motile oscillations of the organisms. Therefore, movement is correlated which changes in the concentration of free calcium.

The effect of heat shock on the cell cycle regulation of tubulin expression in Physarum polycephalum.

In the myxomycete Physarum polycephalum, tubulin synthesis is subject to mitotic cycle control. Virtually all tubulin synthesis is limited to a 2-h period immediately preceding mitosis, and the peak of tubulin protein synthesis is accompanied by a parallel increase in the level of tubulin mRNA. The mechanism by which the accumulation of tubulin mRNA is turned on and off is not clear. To probe the relationship between tubulin regulation and cell cycle controls, we have used heat shocks to delay mitosis and have followed the pattern of tubulin synthesis during these delays. Two peaks of tubulin synthesis are observed after a heat shock. One occurs at a time when synthesis would have occurred without a heat shock, and a second peak immediately precedes the eventual delayed mitosis. These results are clearly due to altered cell cycle regulation. No mitotic activity is detected in delayed plasmodia at the time of the control mitosis, and tubulin behavior is shown to be clearly distinct from that of heat shock proteins. We believe that the tubulin family of proteins is subject to regulation by a thermolabile mitotic control mechanism but that once the cell has been committed to a round of tubulin synthesis the "tubulin clock" runs independently of the heat sensitive system. In delayed plasmodia, the second peak of synthesis may be turned on by a repeat of the commitment event.

Transcription of alpha-tubulin and histone H4 genes begins at the same point in the Physarum cell cycle.

In naturally synchronous plasmodia of Physarum polycephalum, both tubulin and histone gene transcription define periodic cell cycle-regulated events. Using a slot-blot hybridization assay and Northern blot analysis, we have demonstrated that a major peak of accumulation of both alpha-tubulin and histone H4 transcripts occurs in late G2 phase. Nuclear transcription assays indicate that both genes are transcriptionally activated at the same point in the cell cycle: mid G2 phase. While the rate of tubulin gene transcription drops sharply at the M/S-phase boundary, the rate of histone gene transcription remains high through most of S phase. We conclude that the cell cycle regulation of tubulin expression occurs primarily at the level of transcription, while histone regulation involves both transcriptional and posttranscriptional controls. It is possible that the periodic expression of both histone and tubulin genes is triggered by a common cell cycle regulatory mechanism.

Acetylated alpha-tubulin in Physarum: immunological characterization of the isotype and its usage in particular microtubular organelles.

We have used monoclonal antibodies specific for acetylated and unacetylated alpha-tubulin to characterize the acetylated alpha-tubulin isotype of Physarum polycephalum, its expression in the life cycle, and its localization in particular microtubular organelles. We have used the monoclonal antibody 6-11B-1 (Piperno, G., and M. T. Fuller, 1985, J. Cell Biol., 101:2085-2094) as the probe for acetylated alpha-tubulin and have provided a biochemical characterization of the monoclonal antibody KMP-1 as a probe for unacetylated tubulin in Physarum. Concomitant use of these two probes has allowed us to characterize the acetylated alpha-tubulin of Physarum as the alpha 3 isotype. We have detected this acetylated alpha 3 tubulin isotype in both the flagellate and in the myxameba, but not in the plasmodium. In the flagellate, acetylated tubulin is present in both the flagellar axonemes and in an extensive array of cytoplasmic microtubules. The extensive arrangement of acetylated cytoplasmic microtubules and the flagellar axonemes are elaborated during the myxameba-flagellate transformation. In the myxameba, acetylated tubulin is not present in the cytoplasmic microtubules nor in the mitotic spindle microtubules, but is associated with the two centrioles of this cell. These findings, taken together with the apparent absence of acetylated alpha-tubulin in the ephemeral microtubules of the plasmodium suggest a natural correspondence between the presence of acetylated alpha-tubulin and microtubule organelles that are intrinsically stable or cross-linked.

Dynamic aspects of the contractile system in Physarum plasmodium. III. Cyclic contraction-relaxation of the plasmodial fragment in accordance with the generation-degeneration of cytoplasmic actomyosin fibrils.

Plasmodial fragments of Physarum polycephalum, excised from anterior regions of a thin-spread plasmodium, contracted-relaxed cyclicly with a period of 3-5 min. The area of the fragments decreased approximately 10% during contraction. In most cases, there was little endoplasmic streaming which indicates that contractions were synchronized throughout the fragment. By both polarized light and fluorescence microscopy, the organization and distribution of the cytoplasmic actomyosin fibrils in the fragments changed in synchrony with the contraction cycle. The fibrils formed during the contraction phase, and finally became a highly organized framework consisting of a three-dimensional network of numerous fibrils with many converging points (the nodes). During relaxation, the fibrils degenerated and disappeared almost completely, though some very weak fibrils remained near the nodes and the periphery. The results obtained by fluorometry of the fragments, stained with rhodamine-phalloidin, suggested that the G-F transformation of actin is not the main underlying process of the fibrillar formation.

Dynamic organization of ATP and birefringent fibrils during free locomotion and galvanotaxis in the plasmodium of Physarum polycephalum.

Directed migration by a cell is a good phenomenon for studying intracellular coordination. Dynamic organization of both ATP and birefringent fibrils throughout the cell was studied in the multinuclear ameboid cell of the Physarum plasmodium during free locomotion and galvanotaxis. In a directionally migrating plasmodium, waves of ATP as well as thickness oscillations propagated from just inside the advancing front to the rear, and ATP concentration was high at the front on the average. In a DC electric field, locomotion was inhibited more strongly, ATP concentration decreased more, and birefringent fibrils were formed more abundantly at the anodal than at the cathodal side. Inside the cell there were a few undulations in the distributions of ATP and birefringent fibrils. In short, birefringent fibrils become abundant where ATP concentration decreases. The possible mechanism of the coordination in the directed migration and the implications of the scaling law are discussed.

Amphibian oocyte maturation induced by extracts of Physarum polycephalum in mitosis.

The orderly progression of eukaryotic cells from interphase to mitosis requires the close coordination of various nuclear and cytoplasmic events. Studies from our laboratory and others on animal cells indicate that two activities, one present mainly in mitotic cells and the other exclusively in G1-phase cells, play a pivotal role in the regulation of initiation and completion of mitosis, respectively. The purpose of this study was to investigate whether these activities are expressed in the slime mold Physarum polycephalum in which all the nuclei traverse the cell cycle in natural synchrony. Extracts were prepared from plasmodia in various phases of the cell cycle and tested for their ability to induce germinal vesicle breakdown and chromosome condensation after microinjection into Xenopus laevis oocytes. We found that extract of cells at 10-20 min before metaphase consistently induced germinal vesicle breakdown in oocytes. Preliminary characterization, including purification on a DNA-cellulose affinity column, indicated that the mitotic factors from Physarum were functionally very similar to HeLa mitotic factors. We also identified a number of mitosis-specific antigens in extracts from Physarum plasmodia, similar to those of HeLa cells, using the mitosis-specific monoclonal antibodies MPM-2 and MPM-7. Interestingly, we also observed an activity in Physarum at 45 min after metaphase (i.e., in early S phase since it has no G1) that is usually present in HeLa cells only during the G1 phase of the cell cycle. These are the first studies to show that maturation-promoting factor activity is present in Physarum during mitosis and is replaced by the G1 factor (or anti-maturation-promoting factor) activity in a postmitotic stage. A comparative study of these factors in this slime mold and in mammalian cells would be extremely valuable in further understanding their function in the regulation of eukaryotic cell cycle and their evolutionary relationship to one another.

DNA replication in Physarum polycephalum: electron microscopic analysis of patterns of DNA replication in the presence of cycloheximide.

DNA from synchronously replicating nuclei of Physarum polycephalum was studied electron microscopically after 15, 30, 60, and 90 or 120 min of replication in the presence or absence of the protein synthesis inhibitor cycloheximide. The replication-loop size-distribution showed that replication fork progression is severely retarded in the presence of cycloheximide. Analysis of replication-loop frequency showed a similar pattern in control and cyclo-heximide-treated samples, with an increase from 15 to 30 and 60 min. This suggests, surprisingly, that initiations of new replicons either may not be inhibited by cycloheximide or, alternatively, that all initiations have already taken place at the very start of S-phase. The latter conclusion is favored in the light of previous results in our laboratory, discussed here.

Ca++ regulation in caffeine-derived microplasmodia of Physarum polycephalum.

Caffeine-derived microplasmodia possess a Ca++-sequestering system which can initiate motility. The experiments presented here suggest that this system is membranous and nonmitochondrial in nature. Therefore, it is proposed that the shuttle streaming in the plasmodium is controlled by the localized release and uptake of free Ca++ from an intracellular storage system analogous to the sarcoplasmic reticulum.

Control of chemotaxis in Physarum polycephalum.

Plasmodia migrate towards those situations which increase the frequency of their alternations in streaming, and away from those which decrease the frequency. Therefore peristalsis-like waves in Physarum move in the direction opposite from the net movement of the organism. The mechanism is fundamentally related to other known types of chemotaxis.

Active poroelastic two-phase model for the motion of physarum microplasmodia.

The onset of self-organized motion is studied in a poroelastic two-phase model with free boundaries for Physarum microplasmodia (MP). In the model, an active gel phase is assumed to be interpenetrated by a passive fluid phase on small length scales. A feedback loop between calcium kinetics, mechanical deformations, and induced fluid flow gives rise to pattern formation and the establishment of an axis of polarity. Altogether, we find that the calcium kinetics that breaks the conservation of the total calcium concentration in the model and a nonlinear friction between MP and substrate are both necessary ingredients to obtain an oscillatory movement with net motion of the MP. By numerical simulations in one spatial dimension, we find two different types of oscillations with net motion as well as modes with time-periodic or irregular switching of the axis of polarity. The more frequent type of net motion is characterized by mechano-chemical waves traveling from the front towards the rear. The second type is characterized by mechano-chemical waves that appear alternating from the front and the back. While both types exhibit oscillatory forward and backward movement with net motion in each cycle, the trajectory and gel flow pattern of the second type are also similar to recent experimental measurements of peristaltic MP motion. We found moving MPs in extended regions of experimentally accessible parameters, such as length, period and substrate friction strength. Simulations of the model show that the net speed increases with the length, provided that MPs are longer than a critical length of ≈ 120 µm. Both predictions are in line with recent experimental observations.

Liquid brains, solid brains.

Cognitive networks have evolved a broad range of solutions to the problem of gathering, storing and responding to information. Some of these networks are describable as static sets of neurons linked in an adaptive web of connections. These are 'solid' networks, with a well-defined and physically persistent architecture. Other systems are formed by sets of agents that exchange, store and process information but without persistent connections or move relative to each other in physical space. We refer to these networks that lack stable connections and static elements as 'liquid' brains, a category that includes ant and termite colonies, immune systems and some microbiomes and slime moulds. What are the key differences between solid and liquid brains, particularly in their cognitive potential, ability to solve particular problems and environments, and information-processing strategies? To answer this question requires a new, integrative framework. This article is part of the theme issue 'Liquid brains, solid brains: How distributed cognitive architectures process information'.